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Conserved domains on  [gi|568961454|ref|XP_006511217|]
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5'-3' exoribonuclease 1 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XRN1 super family cl34882
5'-3' exonuclease [Replication, recombination and repair];
1-735 0e+00

5'-3' exonuclease [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG5049:

Pssm-ID: 227382 [Multi-domain]  Cd Length: 953  Bit Score: 714.39  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454    1 MGVPKFYRWISERYPCLSEVVKEHQIPEFDNLYLDMNGIIHQCSHPNDddVHFRISDDKIFTDIFHYLEVLFRIIKPRKV 80
Cdd:COG5049     1 MGVPSFFRWLSERYPKIIQLIEEKQIPEFDNLYLDMNGILHNCTHPND--GSPPETEEEMYKAVFEYIDHILLKIRPRKL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   81 FFMAVDGVAPRAKMNQQRGRRFRSAKEAEDKIKKAIEKGETLPTEA---------------RFDSNCITPGTEFMARLHE 145
Cdd:COG5049    79 LYMAVDGVAPRAKMNQQRARRFRSAKDASAAALKAEPNGEEIPEEKdeigneidtidvekkKFDSNCITPGTPFMERLAK 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  146 HLKYFVNMKISTDKSWQGVTIYFSGHETPGEGEHKIMEFIRSEKAKPDHDPNTRHCLYGLDADLIMLGLTSHEAHFSLLR 225
Cdd:COG5049   159 VLRYYIHCKLSSDPEWRNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLILR 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  226 EEVRFGGKKTQR---------------VCAPEETTFHLLHLSLMREYIDYEFSalKEKITFKYDIEKIIDDWILMGFLVG 290
Cdd:COG5049   239 EDVFFGSKSRRKrkctkcgrtghsdeeCKVLTHQPFYLLHISLLREYLEREFR--EPTLPFTFDLERILDDWIFLCFFVG 316

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  291 NDFIPHLPHLHINHDALPLLYGTYIAILPELGGYINESGHLNLPRFERYLVKLSDFDREHFSEVFVDLKWFESKVGNKYL 370
Cdd:COG5049   317 NDFLPHLPCLDIREGAIETLTEIWKKSLPHMKGYITCDGVINLARLEVILAILGSFEDDIFKKDHIQEERKNESLERFSL 396

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  371 NEAAGAAAEEAKN-CKEKRKPKGQENS----------------------------------------------LSWAALD 403
Cdd:COG5049   397 RKERKEGLKGMPRvVYEQKKLIGSIKPtlmdqlqekkspdlpdeefidtlalpkdldmknhelflkrfandlgLSISKAI 476

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  404 KSEG-----EGVASRDNFEDETEDD---------------------------DLFETEFRQYKRTYYMTKMGVDVVSDEF 451
Cdd:COG5049   477 KSKGnysleMDIASDSPDEDEEEFEsevdsirkipdkyvniiveeeeeneteKTVNLRFPGWKERYYTSKLHFTTDSEEK 556

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  452 LANQAACYVQAIQWILHYYYHGVQSWSWYYPYHYAPFLSDIRSISTLKIHFELGKPFKPFEQLLAVLPSASKNLLPTCYQ 531
Cdd:COG5049   557 IRDMAKEYVEGLQWVLSYYYRGCPSWDWYYPYHYAPLAADLSKLSDNDIKFELGTPFRPFEQLMAVLPARSKNLVPEGFR 636

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  532 HLMTSEDSPIIEYYPPDFKTDLNGKQQEWEAVVLIPFIDETRLLEAMETCNHSLKKEERKRNQHSECLMCWYDRDTEFty 611
Cdd:COG5049   637 PLMDDEKSPIIDFYPEEFKLDMNGKTASWQAVVLLPFIDERRLLSAVAVKYPTLSEEERKRNLRGLDLLFSSNKKSDL-- 714

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  612 sspwPEKFPAIERCCTRYKMISLDAWRVDINKNKITRVDQKALyfcgFPTLKHIKHKFFLKKSGVQVFQQSSRGENLMLE 691
Cdd:COG5049   715 ----SELFKDLYSKCKQKEYITMCSKESPYGLFGTVKLGAEGL----APNLLSLCPISFLSYPGLMVFLEYSKNQSARLV 786

                         810       820       830       840
                  ....*....|....*....|....*....|....*....|....
gi 568961454  692 ISVNAEpdELRIENIASAVLGKAVFVNWPHLEEARVVAVSDGET 735
Cdd:COG5049   787 IEDPKS--TVTNKSIVLRGFIKPINVLWPYLRESKLVSLTDGSY 828
XRN1_D1 super family cl39678
Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) ...
 658-843 2.38e-34

Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity.


The actual alignment was detected with superfamily member pfam18332:

Pssm-ID: 436418  Cd Length: 192  Bit Score: 131.06  E-value: 2.38e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   658 GFPTLKHIKHKFFLKKSGVQVFQQSSRGENlMLeISVNAEPDELRIENIASAVLGKAVFVNWPHLEEARVVAVSDGETKF 737
Cdd:pfam18332   15 GFPSLKTLPFTAQLGFHGVNVFQQDSRNES-MV-VTIENKEENRTVEEIAKRKLGKRVFVGWPFLQEAKVVAVSDELFDY 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   738 YIEEPPGTqkvylgktapPSKVIQ--LTDKEQSNWTKEIQGISEQYLRRKGIIINETSAVVYAQLLTGRKYQisQNGEvr 815
Cdd:pfam18332   93 ELSEVVDG----------GKKIVSrpHSPREIKQWKKKAERIERNYSKRLGVIIGDVEVLVHVRPLKGLKRT--DDGA-- 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 568961454   816 LEKQWSKQI-LPFVY--QTIVKDIRAFDSRF 843
Cdd:pfam18332  159 LVKEYAEIPeYETDYalQLVVDEVVNEDERF 189
SH3_12 pfam18129
Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the ...
 1101-1171 4.25e-26

Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation. The Sh3-like domain in Xrn1 lacks the canonical SH3 residues normally involved in binding proline-rich peptide motifs and instead engages in non-canonical interactions with the catalytic domain. Additionally it is essential in maintaining the structural integrity of Xrn1, since partial truncation of this domain in yeast Xrn1 yields an inactive protein. There is a long loop projecting from the SH3-like domain that contacts the PAZ/Tudor domain, occluding the functional surface that binds RNA or peptide motifs containing methylated arginines, respectively, in canonical PAZ and Tudor domain.


:

Pssm-ID: 465661  Cd Length: 68  Bit Score: 102.64  E-value: 4.25e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568961454  1101 AEFRLFDRVVNVRESFSVPVGLRGTVIGIKGasreaDVLFEVLFDEEFPGGLTI--RCSPGRGYRLPTSALVN 1171
Cdd:pfam18129    1 QKFRLGDRVVYVRDSGGVPFGLKGTVVGKGE-----DTLLDVLFDEPFMGGTTLggRCSTYRGLTVPPSALLN 68
XRN1_D2_D3 super family cl39680
Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 ...
 853-934 4.21e-04

Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 pfam18332 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment pfam03159.


The actual alignment was detected with superfamily member pfam18334:

Pssm-ID: 436419  Cd Length: 87  Bit Score: 40.91  E-value: 4.21e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   853 FPPRTMVFMLGTPYYGctGEVQDSGDliTEGRIRVV---FSIPCEPNLDALIQNQHKYSIKYNPGYVLAGRLGVSGYLVS 929
Cdd:pfam18334    6 FPEGSRAFFLGEYAYG--RPAQVTGH--SDGKLSVVvskFKSDKEPNFGKKRIVQAERSNRYYPSFAVAKMLGLHPLALS 81


                   ....*
gi 568961454   930 RFTGS 934
Cdd:pfam18334   82 KITSS 86
DSRM_SF super family cl00054
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 1473-1538 4.72e-03

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


The actual alignment was detected with superfamily member cd19872:

Pssm-ID: 444671  Cd Length: 75  Bit Score: 37.66  E-value: 4.72e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568961454 1473 TPVTELSRICSLVGMPQPDFSFLRTTQT----MTVCQV---KLSNGLLVHGPQ--CHSESEAKERAALFALQQLG 1538
Cdd:cd19872     1 NPVQILEEICQKNGWGEPVYQLLSTSSNnevqLFIYKVtipNLPNGRLTFQPDklCRTPEEAKVLAAEFVLAQLG 75
 
Name Accession Description Interval E-value
XRN1 COG5049
5'-3' exonuclease [Replication, recombination and repair];
1-735 0e+00

5'-3' exonuclease [Replication, recombination and repair];


Pssm-ID: 227382 [Multi-domain]  Cd Length: 953  Bit Score: 714.39  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454    1 MGVPKFYRWISERYPCLSEVVKEHQIPEFDNLYLDMNGIIHQCSHPNDddVHFRISDDKIFTDIFHYLEVLFRIIKPRKV 80
Cdd:COG5049     1 MGVPSFFRWLSERYPKIIQLIEEKQIPEFDNLYLDMNGILHNCTHPND--GSPPETEEEMYKAVFEYIDHILLKIRPRKL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   81 FFMAVDGVAPRAKMNQQRGRRFRSAKEAEDKIKKAIEKGETLPTEA---------------RFDSNCITPGTEFMARLHE 145
Cdd:COG5049    79 LYMAVDGVAPRAKMNQQRARRFRSAKDASAAALKAEPNGEEIPEEKdeigneidtidvekkKFDSNCITPGTPFMERLAK 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  146 HLKYFVNMKISTDKSWQGVTIYFSGHETPGEGEHKIMEFIRSEKAKPDHDPNTRHCLYGLDADLIMLGLTSHEAHFSLLR 225
Cdd:COG5049   159 VLRYYIHCKLSSDPEWRNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLILR 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  226 EEVRFGGKKTQR---------------VCAPEETTFHLLHLSLMREYIDYEFSalKEKITFKYDIEKIIDDWILMGFLVG 290
Cdd:COG5049   239 EDVFFGSKSRRKrkctkcgrtghsdeeCKVLTHQPFYLLHISLLREYLEREFR--EPTLPFTFDLERILDDWIFLCFFVG 316

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  291 NDFIPHLPHLHINHDALPLLYGTYIAILPELGGYINESGHLNLPRFERYLVKLSDFDREHFSEVFVDLKWFESKVGNKYL 370
Cdd:COG5049   317 NDFLPHLPCLDIREGAIETLTEIWKKSLPHMKGYITCDGVINLARLEVILAILGSFEDDIFKKDHIQEERKNESLERFSL 396

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  371 NEAAGAAAEEAKN-CKEKRKPKGQENS----------------------------------------------LSWAALD 403
Cdd:COG5049   397 RKERKEGLKGMPRvVYEQKKLIGSIKPtlmdqlqekkspdlpdeefidtlalpkdldmknhelflkrfandlgLSISKAI 476

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  404 KSEG-----EGVASRDNFEDETEDD---------------------------DLFETEFRQYKRTYYMTKMGVDVVSDEF 451
Cdd:COG5049   477 KSKGnysleMDIASDSPDEDEEEFEsevdsirkipdkyvniiveeeeeneteKTVNLRFPGWKERYYTSKLHFTTDSEEK 556

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  452 LANQAACYVQAIQWILHYYYHGVQSWSWYYPYHYAPFLSDIRSISTLKIHFELGKPFKPFEQLLAVLPSASKNLLPTCYQ 531
Cdd:COG5049   557 IRDMAKEYVEGLQWVLSYYYRGCPSWDWYYPYHYAPLAADLSKLSDNDIKFELGTPFRPFEQLMAVLPARSKNLVPEGFR 636

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  532 HLMTSEDSPIIEYYPPDFKTDLNGKQQEWEAVVLIPFIDETRLLEAMETCNHSLKKEERKRNQHSECLMCWYDRDTEFty 611
Cdd:COG5049   637 PLMDDEKSPIIDFYPEEFKLDMNGKTASWQAVVLLPFIDERRLLSAVAVKYPTLSEEERKRNLRGLDLLFSSNKKSDL-- 714

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  612 sspwPEKFPAIERCCTRYKMISLDAWRVDINKNKITRVDQKALyfcgFPTLKHIKHKFFLKKSGVQVFQQSSRGENLMLE 691
Cdd:COG5049   715 ----SELFKDLYSKCKQKEYITMCSKESPYGLFGTVKLGAEGL----APNLLSLCPISFLSYPGLMVFLEYSKNQSARLV 786

                         810       820       830       840
                  ....*....|....*....|....*....|....*....|....
gi 568961454  692 ISVNAEpdELRIENIASAVLGKAVFVNWPHLEEARVVAVSDGET 735
Cdd:COG5049   787 IEDPKS--TVTNKSIVLRGFIKPINVLWPYLRESKLVSLTDGSY 828
XRN_N pfam03159
XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of ...
 2-223 1.03e-138

XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC:3.1.11.-. Thus, the aligned region may be necessary for 5' to 3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalysing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus.


Pssm-ID: 460832 [Multi-domain]  Cd Length: 231  Bit Score: 428.11  E-value: 1.03e-138
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454     2 GVPKFYRWISERYP-CLSEVVKEHQI--PEFDNLYLDMNGIIHQCSHPNDDdvHFRISDDKIFTDIFHYLEVLFRIIKPR 78
Cdd:pfam03159    1 GVPAFFRWLSERYPlIISQVIEESRPngKEFDNLYLDMNGIIHPCSHPEDG--PAPKTEEEMFKNIFAYIDRLFNIVRPR 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454    79 KVFFMAVDGVAPRAKMNQQRGRRFRSAKEAEDKIKKAIE--------KGETLPTEARFDSNCITPGTEFMARLHEHLKYF 150
Cdd:pfam03159   79 KLLYMAVDGVAPRAKMNQQRSRRFRSAKEAEELEEKAEElreelekeGGEEPPEEETFDSNCITPGTEFMEKLSEALRYY 158

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568961454   151 VNMKISTDKSWQGVTIYFSGHETPGEGEHKIMEFIRSEKAKPDHDPNTRHCLYGLDADLIMLGLTSHEAHFSL 223
Cdd:pfam03159  159 IKKKLNTDPAWKNLKVILSDANVPGEGEHKIMDFIRKQRSQPDYDPNTRHCIYGLDADLIMLGLATHEPHFSI 231
PIN_XRN1-2-like cd18673
FEN-like PIN domains of XRN1, XRN2, and related proteins; XRN1 (5'-3' exoribonuclease 1, also ...
 32-258 7.02e-128

FEN-like PIN domains of XRN1, XRN2, and related proteins; XRN1 (5'-3' exoribonuclease 1, also known as SEP1) is a processive 5'-3' exoribonuclease that degrades the body of transcripts in the major pathway of RNA decay; XRN2 (5'-3' exoribonuclease 2) is predominantly localized in the nucleus and recognizes single-stranded RNAs with a 5'-terminal monophosphate to degrade them possessively to mononucleotides. XRN2 has a critical function to process maturation of 5.8S and 25S/28S rRNAs as well as degradation of some spacer fragments that are excised during rRNA maturation. Both XRN1 and XRN2 preferentially cleave 5'-monophosphorylated RNA. XRN2 is also known as Rat1p in yeast. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350240  Cd Length: 240  Bit Score: 398.88  E-value: 7.02e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   32 LYLDMNGIIHQCSHPNDDDvhFRISDDKIFTDIFHYLEVLFRIIKPRKVFFMAVDGVAPRAKMNQQRGRRFRSAKEAEDK 111
Cdd:cd18673     1 LYLDMNGIIHPCTHPEDRP--APKSEEEMFQNIFKYIDRLFNIVRPRKLLYIAVDGVAPRAKMNQQRSRRFRSAKEAEEK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  112 IKKA------IEKGETLPTEARFDSNCITPGTEFMARLHEHLKYFVNMKISTDKSWQGVTIYFSGHETPGEGEHKIMEFI 185
Cdd:cd18673    79 EAKEeeleseGKELGEEEEKERFDSNCITPGTEFMERLSKALRYYIAKKLNTDPGWKNLKVILSDSNVPGEGEHKIMDFI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  186 RSEKAKPDHDPNTRHCLYGLDADLIMLGLTSHEAHFSLLREEVRFGGKKTQRVCAPEETT---------FHLLHLSLMRE 256
Cdd:cd18673   159 RSQRAQPGYDPNTRHCIYGLDADLIMLGLATHEPNFSILREEVFFGKPKPKKLCCGEKSEkktrakekkFQFLHISVLRE 238


                  ..
gi 568961454  257 YI 258
Cdd:cd18673   239 YL 240
XRN1_D1 pfam18332
Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) ...
 658-843 2.38e-34

Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity.


Pssm-ID: 436418  Cd Length: 192  Bit Score: 131.06  E-value: 2.38e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   658 GFPTLKHIKHKFFLKKSGVQVFQQSSRGENlMLeISVNAEPDELRIENIASAVLGKAVFVNWPHLEEARVVAVSDGETKF 737
Cdd:pfam18332   15 GFPSLKTLPFTAQLGFHGVNVFQQDSRNES-MV-VTIENKEENRTVEEIAKRKLGKRVFVGWPFLQEAKVVAVSDELFDY 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   738 YIEEPPGTqkvylgktapPSKVIQ--LTDKEQSNWTKEIQGISEQYLRRKGIIINETSAVVYAQLLTGRKYQisQNGEvr 815
Cdd:pfam18332   93 ELSEVVDG----------GKKIVSrpHSPREIKQWKKKAERIERNYSKRLGVIIGDVEVLVHVRPLKGLKRT--DDGA-- 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 568961454   816 LEKQWSKQI-LPFVY--QTIVKDIRAFDSRF 843
Cdd:pfam18332  159 LVKEYAEIPeYETDYalQLVVDEVVNEDERF 189
SH3_12 pfam18129
Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the ...
 1101-1171 4.25e-26

Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation. The Sh3-like domain in Xrn1 lacks the canonical SH3 residues normally involved in binding proline-rich peptide motifs and instead engages in non-canonical interactions with the catalytic domain. Additionally it is essential in maintaining the structural integrity of Xrn1, since partial truncation of this domain in yeast Xrn1 yields an inactive protein. There is a long loop projecting from the SH3-like domain that contacts the PAZ/Tudor domain, occluding the functional surface that binds RNA or peptide motifs containing methylated arginines, respectively, in canonical PAZ and Tudor domain.


Pssm-ID: 465661  Cd Length: 68  Bit Score: 102.64  E-value: 4.25e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568961454  1101 AEFRLFDRVVNVRESFSVPVGLRGTVIGIKGasreaDVLFEVLFDEEFPGGLTI--RCSPGRGYRLPTSALVN 1171
Cdd:pfam18129    1 QKFRLGDRVVYVRDSGGVPFGLKGTVVGKGE-----DTLLDVLFDEPFMGGTTLggRCSTYRGLTVPPSALLN 68
XRN1_D2_D3 pfam18334
Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 ...
 853-934 4.21e-04

Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 pfam18332 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment pfam03159.


Pssm-ID: 436419  Cd Length: 87  Bit Score: 40.91  E-value: 4.21e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   853 FPPRTMVFMLGTPYYGctGEVQDSGDliTEGRIRVV---FSIPCEPNLDALIQNQHKYSIKYNPGYVLAGRLGVSGYLVS 929
Cdd:pfam18334    6 FPEGSRAFFLGEYAYG--RPAQVTGH--SDGKLSVVvskFKSDKEPNFGKKRIVQAERSNRYYPSFAVAKMLGLHPLALS 81


                   ....*
gi 568961454   930 RFTGS 934
Cdd:pfam18334   82 KITSS 86
DSRM_A1CF-like cd19872
double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding ...
 1473-1538 4.72e-03

double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding protein 46 (RBM46) and similar proteins; The family includes two dsRNA-binding motif-containing proteins, A1CF and RBM46. A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. RBM46 (also called cancer/testis antigen 68 (CT68), or RNA-binding motif protein 46) plays a novel role in the regulation of embryonic stem cell (ESC) differentiation by regulating the degradation of beta-catenin mRNA. It also regulates trophectoderm specification by stabilizing Cdx2 mRNA in early mouse embryos. Members of this family contain three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380701  Cd Length: 75  Bit Score: 37.66  E-value: 4.72e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568961454 1473 TPVTELSRICSLVGMPQPDFSFLRTTQT----MTVCQV---KLSNGLLVHGPQ--CHSESEAKERAALFALQQLG 1538
Cdd:cd19872     1 NPVQILEEICQKNGWGEPVYQLLSTSSNnevqLFIYKVtipNLPNGRLTFQPDklCRTPEEAKVLAAEFVLAQLG 75
 
Name Accession Description Interval E-value
XRN1 COG5049
5'-3' exonuclease [Replication, recombination and repair];
1-735 0e+00

5'-3' exonuclease [Replication, recombination and repair];


Pssm-ID: 227382 [Multi-domain]  Cd Length: 953  Bit Score: 714.39  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454    1 MGVPKFYRWISERYPCLSEVVKEHQIPEFDNLYLDMNGIIHQCSHPNDddVHFRISDDKIFTDIFHYLEVLFRIIKPRKV 80
Cdd:COG5049     1 MGVPSFFRWLSERYPKIIQLIEEKQIPEFDNLYLDMNGILHNCTHPND--GSPPETEEEMYKAVFEYIDHILLKIRPRKL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   81 FFMAVDGVAPRAKMNQQRGRRFRSAKEAEDKIKKAIEKGETLPTEA---------------RFDSNCITPGTEFMARLHE 145
Cdd:COG5049    79 LYMAVDGVAPRAKMNQQRARRFRSAKDASAAALKAEPNGEEIPEEKdeigneidtidvekkKFDSNCITPGTPFMERLAK 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  146 HLKYFVNMKISTDKSWQGVTIYFSGHETPGEGEHKIMEFIRSEKAKPDHDPNTRHCLYGLDADLIMLGLTSHEAHFSLLR 225
Cdd:COG5049   159 VLRYYIHCKLSSDPEWRNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLILR 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  226 EEVRFGGKKTQR---------------VCAPEETTFHLLHLSLMREYIDYEFSalKEKITFKYDIEKIIDDWILMGFLVG 290
Cdd:COG5049   239 EDVFFGSKSRRKrkctkcgrtghsdeeCKVLTHQPFYLLHISLLREYLEREFR--EPTLPFTFDLERILDDWIFLCFFVG 316

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  291 NDFIPHLPHLHINHDALPLLYGTYIAILPELGGYINESGHLNLPRFERYLVKLSDFDREHFSEVFVDLKWFESKVGNKYL 370
Cdd:COG5049   317 NDFLPHLPCLDIREGAIETLTEIWKKSLPHMKGYITCDGVINLARLEVILAILGSFEDDIFKKDHIQEERKNESLERFSL 396

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  371 NEAAGAAAEEAKN-CKEKRKPKGQENS----------------------------------------------LSWAALD 403
Cdd:COG5049   397 RKERKEGLKGMPRvVYEQKKLIGSIKPtlmdqlqekkspdlpdeefidtlalpkdldmknhelflkrfandlgLSISKAI 476

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  404 KSEG-----EGVASRDNFEDETEDD---------------------------DLFETEFRQYKRTYYMTKMGVDVVSDEF 451
Cdd:COG5049   477 KSKGnysleMDIASDSPDEDEEEFEsevdsirkipdkyvniiveeeeeneteKTVNLRFPGWKERYYTSKLHFTTDSEEK 556

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  452 LANQAACYVQAIQWILHYYYHGVQSWSWYYPYHYAPFLSDIRSISTLKIHFELGKPFKPFEQLLAVLPSASKNLLPTCYQ 531
Cdd:COG5049   557 IRDMAKEYVEGLQWVLSYYYRGCPSWDWYYPYHYAPLAADLSKLSDNDIKFELGTPFRPFEQLMAVLPARSKNLVPEGFR 636

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  532 HLMTSEDSPIIEYYPPDFKTDLNGKQQEWEAVVLIPFIDETRLLEAMETCNHSLKKEERKRNQHSECLMCWYDRDTEFty 611
Cdd:COG5049   637 PLMDDEKSPIIDFYPEEFKLDMNGKTASWQAVVLLPFIDERRLLSAVAVKYPTLSEEERKRNLRGLDLLFSSNKKSDL-- 714

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  612 sspwPEKFPAIERCCTRYKMISLDAWRVDINKNKITRVDQKALyfcgFPTLKHIKHKFFLKKSGVQVFQQSSRGENLMLE 691
Cdd:COG5049   715 ----SELFKDLYSKCKQKEYITMCSKESPYGLFGTVKLGAEGL----APNLLSLCPISFLSYPGLMVFLEYSKNQSARLV 786

                         810       820       830       840
                  ....*....|....*....|....*....|....*....|....
gi 568961454  692 ISVNAEpdELRIENIASAVLGKAVFVNWPHLEEARVVAVSDGET 735
Cdd:COG5049   787 IEDPKS--TVTNKSIVLRGFIKPINVLWPYLRESKLVSLTDGSY 828
XRN_N pfam03159
XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of ...
 2-223 1.03e-138

XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC:3.1.11.-. Thus, the aligned region may be necessary for 5' to 3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalysing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus.


Pssm-ID: 460832 [Multi-domain]  Cd Length: 231  Bit Score: 428.11  E-value: 1.03e-138
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454     2 GVPKFYRWISERYP-CLSEVVKEHQI--PEFDNLYLDMNGIIHQCSHPNDDdvHFRISDDKIFTDIFHYLEVLFRIIKPR 78
Cdd:pfam03159    1 GVPAFFRWLSERYPlIISQVIEESRPngKEFDNLYLDMNGIIHPCSHPEDG--PAPKTEEEMFKNIFAYIDRLFNIVRPR 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454    79 KVFFMAVDGVAPRAKMNQQRGRRFRSAKEAEDKIKKAIE--------KGETLPTEARFDSNCITPGTEFMARLHEHLKYF 150
Cdd:pfam03159   79 KLLYMAVDGVAPRAKMNQQRSRRFRSAKEAEELEEKAEElreelekeGGEEPPEEETFDSNCITPGTEFMEKLSEALRYY 158

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568961454   151 VNMKISTDKSWQGVTIYFSGHETPGEGEHKIMEFIRSEKAKPDHDPNTRHCLYGLDADLIMLGLTSHEAHFSL 223
Cdd:pfam03159  159 IKKKLNTDPAWKNLKVILSDANVPGEGEHKIMDFIRKQRSQPDYDPNTRHCIYGLDADLIMLGLATHEPHFSI 231
PIN_XRN1-2-like cd18673
FEN-like PIN domains of XRN1, XRN2, and related proteins; XRN1 (5'-3' exoribonuclease 1, also ...
 32-258 7.02e-128

FEN-like PIN domains of XRN1, XRN2, and related proteins; XRN1 (5'-3' exoribonuclease 1, also known as SEP1) is a processive 5'-3' exoribonuclease that degrades the body of transcripts in the major pathway of RNA decay; XRN2 (5'-3' exoribonuclease 2) is predominantly localized in the nucleus and recognizes single-stranded RNAs with a 5'-terminal monophosphate to degrade them possessively to mononucleotides. XRN2 has a critical function to process maturation of 5.8S and 25S/28S rRNAs as well as degradation of some spacer fragments that are excised during rRNA maturation. Both XRN1 and XRN2 preferentially cleave 5'-monophosphorylated RNA. XRN2 is also known as Rat1p in yeast. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350240  Cd Length: 240  Bit Score: 398.88  E-value: 7.02e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   32 LYLDMNGIIHQCSHPNDDDvhFRISDDKIFTDIFHYLEVLFRIIKPRKVFFMAVDGVAPRAKMNQQRGRRFRSAKEAEDK 111
Cdd:cd18673     1 LYLDMNGIIHPCTHPEDRP--APKSEEEMFQNIFKYIDRLFNIVRPRKLLYIAVDGVAPRAKMNQQRSRRFRSAKEAEEK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  112 IKKA------IEKGETLPTEARFDSNCITPGTEFMARLHEHLKYFVNMKISTDKSWQGVTIYFSGHETPGEGEHKIMEFI 185
Cdd:cd18673    79 EAKEeeleseGKELGEEEEKERFDSNCITPGTEFMERLSKALRYYIAKKLNTDPGWKNLKVILSDSNVPGEGEHKIMDFI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  186 RSEKAKPDHDPNTRHCLYGLDADLIMLGLTSHEAHFSLLREEVRFGGKKTQRVCAPEETT---------FHLLHLSLMRE 256
Cdd:cd18673   159 RSQRAQPGYDPNTRHCIYGLDADLIMLGLATHEPNFSILREEVFFGKPKPKKLCCGEKSEkktrakekkFQFLHISVLRE 238


                  ..
gi 568961454  257 YI 258
Cdd:cd18673   239 YL 240
XRN_M pfam17846
Xrn1 helical domain; This helical domain is part of the Xrn1 catalytic core. Xrn1 is a ...
 272-593 6.54e-99

Xrn1 helical domain; This helical domain is part of the Xrn1 catalytic core. Xrn1 is a cytoplasmic 5'-3' exonuclease that degrades decapped mRNAs.


Pssm-ID: 375377  Cd Length: 442  Bit Score: 326.29  E-value: 6.54e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   272 KYDIEKIIDDWILMGFLVGNDFIPHLPHLHINHDALPLLYGTYIAILPELGGYINESGHLNLPRFERYLVKLSDFDREHF 351
Cdd:pfam17846    1 QFDFERIIDDFVFMCFFVGNDFLPHLPSLEIREGAIDLLMTVYKKEFYKTGGYLTDNGYVNLDRVELFVSLVGTYEEKIF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   352 S---------EVFVDLKWFESKVGNKYLNEAAGAAAEEAKNCKEKRKPKGQENS----LSWAALDKSEGEGVASRDNFED 418
Cdd:pfam17846   81 RkrqrredrkRRRLARREEASKEDDTNLEAANATNPSVGSHKAGSANATPSNESeasaEAKATSELREKNGKELDDSESD 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   419 ETEDDD--LFETefrQYKRTYYMTKMgvDVVSDEFLA----NQAACYVQAIQWILHYYYHGVQSWSWYYPYHYAPFLSDI 492
Cdd:pfam17846  161 GDGVDKvrLGEP---GWKERYYKEKF--SVKSTEDIEfrreDVVQKYVEGLCWVLRYYYQGCCSWTWFYPYHYAPFASDL 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   493 RSISTLKIHFELGKPFKPFEQLLAVLPSASKNLLPTCYQHLMTSEDSPIIEYYPPDFKTDLNGKQQEWEAVVLIPFIDET 572
Cdd:pfam17846  236 KNLAQLKIKFEKGQPFKPFEQLMGVFPAASKHALPKPYQALMTDPDSPIIDFYPEDFEIDLNGKRYAWQGVALLPFIDEK 315

                          330       340
                   ....*....|....*....|.
gi 568961454   573 RLLEAMETCNHSLKKEERKRN 593
Cdd:pfam17846  316 RLLEALRKLENELTEEEVKRN 336
XRN1_D1 pfam18332
Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) ...
 658-843 2.38e-34

Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity.


Pssm-ID: 436418  Cd Length: 192  Bit Score: 131.06  E-value: 2.38e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   658 GFPTLKHIKHKFFLKKSGVQVFQQSSRGENlMLeISVNAEPDELRIENIASAVLGKAVFVNWPHLEEARVVAVSDGETKF 737
Cdd:pfam18332   15 GFPSLKTLPFTAQLGFHGVNVFQQDSRNES-MV-VTIENKEENRTVEEIAKRKLGKRVFVGWPFLQEAKVVAVSDELFDY 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   738 YIEEPPGTqkvylgktapPSKVIQ--LTDKEQSNWTKEIQGISEQYLRRKGIIINETSAVVYAQLLTGRKYQisQNGEvr 815
Cdd:pfam18332   93 ELSEVVDG----------GKKIVSrpHSPREIKQWKKKAERIERNYSKRLGVIIGDVEVLVHVRPLKGLKRT--DDGA-- 158

                          170       180       190
                   ....*....|....*....|....*....|.
gi 568961454   816 LEKQWSKQI-LPFVY--QTIVKDIRAFDSRF 843
Cdd:pfam18332  159 LVKEYAEIPeYETDYalQLVVDEVVNEDERF 189
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 33-251 3.69e-31

FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Structure-specific 5' nucleases are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner. The family includes the PIN (PilT N terminus) domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the PIN domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4- and T5-5' nucleases, and other homologs. Canonical members of this FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350204 [Multi-domain]  Cd Length: 174  Bit Score: 121.05  E-value: 3.69e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   33 YLDMNGIIHQCSHPNDDDVHfriSDDKIFTDIFHYLEVLFRIIKPRKVFFMAVDGVAPRAKMNQQRGRRFRSAKEAEdki 112
Cdd:cd09853     1 VIDGMNIAFNFAHPVRNLKE---EEGSDFQGYFSAVDDLVKKLKPGIKPILLFDGGKPKAKKGNRDKRRERRAREED--- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454  113 kkaiEKGETLPTEARFDSNCITPGTEFMARLHEHLKYFVNMKISTDkswqgvtiyfsghetPGEGEHKIMEFIRSEKAKp 192
Cdd:cd09853    75 ----RKKGQLKEHKEFDKRLIELGPEYLIRLFELLKHFMGIPVMDA---------------PGEAEDEIAYLVKKHKHL- 134

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568961454  193 dhdpNTRHCLYGLDADLIMLGLtsheAHFSLLREEVRFggkktqrvcapEETTFHLLHL 251
Cdd:cd09853   135 ----GTVHLIISTDGDFLLLGT----DHPYIPRNLLTV-----------KEETFQEFHL 174
SH3_12 pfam18129
Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the ...
 1101-1171 4.25e-26

Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation. The Sh3-like domain in Xrn1 lacks the canonical SH3 residues normally involved in binding proline-rich peptide motifs and instead engages in non-canonical interactions with the catalytic domain. Additionally it is essential in maintaining the structural integrity of Xrn1, since partial truncation of this domain in yeast Xrn1 yields an inactive protein. There is a long loop projecting from the SH3-like domain that contacts the PAZ/Tudor domain, occluding the functional surface that binds RNA or peptide motifs containing methylated arginines, respectively, in canonical PAZ and Tudor domain.


Pssm-ID: 465661  Cd Length: 68  Bit Score: 102.64  E-value: 4.25e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568961454  1101 AEFRLFDRVVNVRESFSVPVGLRGTVIGIKGasreaDVLFEVLFDEEFPGGLTI--RCSPGRGYRLPTSALVN 1171
Cdd:pfam18129    1 QKFRLGDRVVYVRDSGGVPFGLKGTVVGKGE-----DTLLDVLFDEPFMGGTTLggRCSTYRGLTVPPSALLN 68
XRN1_D2_D3 pfam18334
Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 ...
 853-934 4.21e-04

Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 pfam18332 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment pfam03159.


Pssm-ID: 436419  Cd Length: 87  Bit Score: 40.91  E-value: 4.21e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568961454   853 FPPRTMVFMLGTPYYGctGEVQDSGDliTEGRIRVV---FSIPCEPNLDALIQNQHKYSIKYNPGYVLAGRLGVSGYLVS 929
Cdd:pfam18334    6 FPEGSRAFFLGEYAYG--RPAQVTGH--SDGKLSVVvskFKSDKEPNFGKKRIVQAERSNRYYPSFAVAKMLGLHPLALS 81


                   ....*
gi 568961454   930 RFTGS 934
Cdd:pfam18334   82 KITSS 86
DSRM_A1CF-like cd19872
double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding ...
 1473-1538 4.72e-03

double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding protein 46 (RBM46) and similar proteins; The family includes two dsRNA-binding motif-containing proteins, A1CF and RBM46. A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. RBM46 (also called cancer/testis antigen 68 (CT68), or RNA-binding motif protein 46) plays a novel role in the regulation of embryonic stem cell (ESC) differentiation by regulating the degradation of beta-catenin mRNA. It also regulates trophectoderm specification by stabilizing Cdx2 mRNA in early mouse embryos. Members of this family contain three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380701  Cd Length: 75  Bit Score: 37.66  E-value: 4.72e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568961454 1473 TPVTELSRICSLVGMPQPDFSFLRTTQT----MTVCQV---KLSNGLLVHGPQ--CHSESEAKERAALFALQQLG 1538
Cdd:cd19872     1 NPVQILEEICQKNGWGEPVYQLLSTSSNnevqLFIYKVtipNLPNGRLTFQPDklCRTPEEAKVLAAEFVLAQLG 75
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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