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Conserved domains on  [gi|119617338|gb|EAW96932|]
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ubiquitin specific peptidase 52, isoform CRA_e [Homo sapiens]

Protein Classification

PAN2-PAN3 deadenylation complex catalytic subunit PAN2( domain architecture ID 13237162)

PAN2-PAN3 deadenylation complex catalytic subunit PAN2 is the catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
UCH_1 pfam13423
Ubiquitin carboxyl-terminal hydrolase;
517-897 1.43e-115

Ubiquitin carboxyl-terminal hydrolase;


:

Pssm-ID: 463872 [Multi-domain]  Cd Length: 305  Bit Score: 361.59  E-value: 1.43e-115
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   517 AGLEPHIPNAYCNCMIQVLYFLEPVRCLIQNHL---CQKEFCLACELGFLFHMLDLSRGDPCQGNNFLRAFRTIPEASAL 593
Cdd:pfam13423    1 SGLETHIPNSYTNSLLQLLRFIPPLRNLALSHLateCLKEHCLLCELGFLFDMLEKAKGKNCQASNFLRALSSIPEASAL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   594 GLIlADSDEASGKGNLARLIQRWNRFILTQLHQDMQELEIPQayrgaggsfcSSGDSVIGQLFSCEMENCSLC-RCGSET 672
Cdd:pfam13423   81 GLL-DEDRETNSAISLSSLIQSFNRFLLDQLSSEENSTPPNP----------SPAESPLEQLFGIDAETTIRCsNCGHES 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   673 VRASSTLLFTLSYPDGSKS-DKTGKNYDFAQVLKRSICLDQNTQAWCDTCEKYQPTIQTRNIRHLPDILVINCEVNSSKE 751
Cdd:pfam13423  150 VRESSTHVLDLIYPRKPSSnNKKPPNQTFSSILKSSLERETTTKAWCEKCKRYQPLESRRTVRNLPPVLSLNAALTNEEW 229
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   752 ADFWRmqaevafkmavkkhggeisknkefaladwkelgspegvlvcpsieelKNVWLPFSIRMKMTKNKGLDvcnwtdgd 831
Cdd:pfam13423  230 RQLWK-----------------------------------------------TPGWLPPEIGLTLSDDLQGD-------- 254
                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119617338   832 emqwgparaeeeHGVYVYDLMATVVHILDSRTGGSLVAHIKVGETYHqrkEGVTHQQWYLFNDFLI 897
Cdd:pfam13423  255 ------------NEIVKYELRGVVVHIGDSGTSGHLVSFVKVADSEL---EDPTESQWYLFNDFLV 305
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
974-1147 1.49e-114

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.


:

Pssm-ID: 99846  Cd Length: 174  Bit Score: 353.46  E-value: 1.49e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  974 VGLDAEFVTLNEEEAELRSDGTKSTIKPSQMSVARITCVRGQGPNEGIPFIDDYISTQEQVVDYLTQYSGIKPGDLDAKI 1053
Cdd:cd06143     1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338 1054 SSKHLTTLKSTYLKLRFLIDIGVKFVGHGLQKDFRVINLMVPKDQVLDTVYLFHMPRKRMISLRFLAWYFLDLKIQGETH 1133
Cdd:cd06143    81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSETH 160
                         170
                  ....*....|....
gi 119617338 1134 DSIEDARTALQLYR 1147
Cdd:cd06143   161 DSIEDARTALKLYR 174
WD40 super family cl29593
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
204-357 9.04e-04

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


The actual alignment was detected with superfamily member cd00200:

Pssm-ID: 475233 [Multi-domain]  Cd Length: 289  Bit Score: 42.71  E-value: 9.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  204 QTNRFFFCGHTSGKVSLRDLRTFKVEHEFDAFSGSLSDFDVH--GNLLAACGfssrltglaCDRFLKVYDLRMMRAITPL 281
Cdd:cd00200   145 PDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSpdGEKLLSSS---------SDGTIKLWDLSTGKCLGTL 215
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  282 QVHVDPA-FLRFIPtytSRLAIIS------------QSGQCQFCeptgLANpadifHVNPVGpllmTFDVSASKQALAFG 348
Cdd:cd00200   216 RGHENGVnSVAFSP---DGYLLASgsedgtirvwdlRTGECVQT----LSG-----HTNSVT----SLAWSPDGKRLASG 279

                  ....*....
gi 119617338  349 DSEGCVHLW 357
Cdd:cd00200   280 SADGTIRIW 288
 
Name Accession Description Interval E-value
UCH_1 pfam13423
Ubiquitin carboxyl-terminal hydrolase;
517-897 1.43e-115

Ubiquitin carboxyl-terminal hydrolase;


Pssm-ID: 463872 [Multi-domain]  Cd Length: 305  Bit Score: 361.59  E-value: 1.43e-115
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   517 AGLEPHIPNAYCNCMIQVLYFLEPVRCLIQNHL---CQKEFCLACELGFLFHMLDLSRGDPCQGNNFLRAFRTIPEASAL 593
Cdd:pfam13423    1 SGLETHIPNSYTNSLLQLLRFIPPLRNLALSHLateCLKEHCLLCELGFLFDMLEKAKGKNCQASNFLRALSSIPEASAL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   594 GLIlADSDEASGKGNLARLIQRWNRFILTQLHQDMQELEIPQayrgaggsfcSSGDSVIGQLFSCEMENCSLC-RCGSET 672
Cdd:pfam13423   81 GLL-DEDRETNSAISLSSLIQSFNRFLLDQLSSEENSTPPNP----------SPAESPLEQLFGIDAETTIRCsNCGHES 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   673 VRASSTLLFTLSYPDGSKS-DKTGKNYDFAQVLKRSICLDQNTQAWCDTCEKYQPTIQTRNIRHLPDILVINCEVNSSKE 751
Cdd:pfam13423  150 VRESSTHVLDLIYPRKPSSnNKKPPNQTFSSILKSSLERETTTKAWCEKCKRYQPLESRRTVRNLPPVLSLNAALTNEEW 229
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   752 ADFWRmqaevafkmavkkhggeisknkefaladwkelgspegvlvcpsieelKNVWLPFSIRMKMTKNKGLDvcnwtdgd 831
Cdd:pfam13423  230 RQLWK-----------------------------------------------TPGWLPPEIGLTLSDDLQGD-------- 254
                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119617338   832 emqwgparaeeeHGVYVYDLMATVVHILDSRTGGSLVAHIKVGETYHqrkEGVTHQQWYLFNDFLI 897
Cdd:pfam13423  255 ------------NEIVKYELRGVVVHIGDSGTSGHLVSFVKVADSEL---EDPTESQWYLFNDFLV 305
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
974-1147 1.49e-114

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.


Pssm-ID: 99846  Cd Length: 174  Bit Score: 353.46  E-value: 1.49e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  974 VGLDAEFVTLNEEEAELRSDGTKSTIKPSQMSVARITCVRGQGPNEGIPFIDDYISTQEQVVDYLTQYSGIKPGDLDAKI 1053
Cdd:cd06143     1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338 1054 SSKHLTTLKSTYLKLRFLIDIGVKFVGHGLQKDFRVINLMVPKDQVLDTVYLFHMPRKRMISLRFLAWYFLDLKIQGETH 1133
Cdd:cd06143    81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSETH 160
                         170
                  ....*....|....
gi 119617338 1134 DSIEDARTALQLYR 1147
Cdd:cd06143   161 DSIEDARTALKLYR 174
Peptidase_C19P cd02672
A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are ...
502-920 7.80e-83

A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.


Pssm-ID: 239137 [Multi-domain]  Cd Length: 268  Bit Score: 271.31  E-value: 7.80e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  502 GLEDFDFKHYNKTLFAGLEPHIPNAYCNCMIQVLYFLEPVRC--LIQNHLCQKEFCLACELGFLFhmldlsrgdpcqgnn 579
Cdd:cd02672     1 GTEDFDFEFYNKTNYAGLENHITNSYCNSLLQLLYFIPPFRNftAIILVACPKESCLLCELGYLF--------------- 65
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  580 flrafrtipeasalgliladsdeasgkgnlarliqrwnrfiltqlhqdmqeleipqayrgaggsfcssgdSVIGQLFSCE 659
Cdd:cd02672    66 ----------------------------------------------------------------------STLIQNFTRF 75
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  660 MENCSLCRCG-----SETVRASSTLLFTLSYPDGSKsdKTGKNYDFAQVLKRSICLDQNTQAWCDTCEKYQPTIQTRNIR 734
Cdd:cd02672    76 LLETISQDQLgtpfsCGTSRNSVSLLYTLSLPLGST--KTSKESTFLQLLKRSLDLEKVTKAWCDTCCKYQPLEQTTSIR 153
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  735 HLPDILvincevnsskeadfwrmqaevafkmavkkhggeisknkefaladwkelgspegvlvcpsieelknvWLPFSIRM 814
Cdd:cd02672   154 HLPDIL------------------------------------------------------------------LLVLVINL 167
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  815 KMTKNKGLDV-CNWTDGDEMQWGPARAEEEH----------GVYVYDLMATVVHILDSrtggSLVAHIKVGETYHQRKeg 883
Cdd:cd02672   168 SVTNGEFDDInVVLPSGKVMQNKVSPKAIDHdklvknrgqeSIYKYELVGYVCEINDS----SRGQHNVVFVIKVNEE-- 241
                         410       420       430
                  ....*....|....*....|....*....|....*..
gi 119617338  884 VTHQQWYLFNDFLIEPIDkheavqfdmnwKVPAILYY 920
Cdd:cd02672   242 STHGRWYLFNDFLVTPVS-----------ELAYILLY 267
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
973-1151 3.23e-26

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 106.23  E-value: 3.23e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338    973 LVGLDAEFVTLNEEEAELrsdgtkstikpsqmsvARITCVRGQGPNEGIPFiDDYISTQEQVVDYLTQYSGIKPGDLDAK 1052
Cdd:smart00479    2 LVVIDCETTGLDPGKDEI----------------IEIAAVDVDGGEIIEVF-DTYVKPDRPITDYATEIHGITPEMLDDA 64
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   1053 IsskhltTLKSTYLKLRFLIDIGVKFVGHGLQKDFRVINLMVPK--------DQVLDTVYLFHM--PRKRMISLRFLAWY 1122
Cdd:smart00479   65 P------TFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRlgikqppkLPVIDTLKLARAtnPGLPKYSLKKLAKR 138
                           170       180
                    ....*....|....*....|....*....
gi 119617338   1123 FLdLKIQGETHDSIEDARTALQLYRKYLE 1151
Cdd:smart00479  139 LL-LEVIQRAHRALDDARATAKLFKKLLE 166
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
974-1146 8.55e-19

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 84.71  E-value: 8.55e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   974 VGLDAEFVTLNEEEAELrsdgtkstikpsqMSVARITCVRGQgpNEGIPFIDDYISTQE--QVVDYLTQYSGIKPGDLDA 1051
Cdd:pfam00929    1 VVIDLETTGLDPEKDEI-------------IEIAAVVIDGGE--NEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDN 65
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  1052 KISSKH-LTTLKSTYLKLRFLIDIGVKF-VGHGLQKDFRVINLMVPK-DQVLDTVYLFHMPRKRM--ISLRFLAWYFlDL 1126
Cdd:pfam00929   66 KPSFEEvLEEFLEFLRKGNLLVAHNASFdVGFLRYDDKRFLKKPMPKlNPVIDTLILDKATYKELpgRSLDALAEKL-GL 144
                          170       180
                   ....*....|....*....|
gi 119617338  1127 KIQGETHDSIEDARTALQLY 1146
Cdd:pfam00929  145 EHIGRAHRALDDARATAKLF 164
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
204-357 9.04e-04

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 42.71  E-value: 9.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  204 QTNRFFFCGHTSGKVSLRDLRTFKVEHEFDAFSGSLSDFDVH--GNLLAACGfssrltglaCDRFLKVYDLRMMRAITPL 281
Cdd:cd00200   145 PDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSpdGEKLLSSS---------SDGTIKLWDLSTGKCLGTL 215
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  282 QVHVDPA-FLRFIPtytSRLAIIS------------QSGQCQFCeptgLANpadifHVNPVGpllmTFDVSASKQALAFG 348
Cdd:cd00200   216 RGHENGVnSVAFSP---DGYLLASgsedgtirvwdlRTGECVQT----LSG-----HTNSVT----SLAWSPDGKRLASG 279

                  ....*....
gi 119617338  349 DSEGCVHLW 357
Cdd:cd00200   280 SADGTIRIW 288
PRK07247 PRK07247
3'-5' exonuclease;
1126-1155 9.40e-03

3'-5' exonuclease;


Pssm-ID: 180906 [Multi-domain]  Cd Length: 195  Bit Score: 38.61  E-value: 9.40e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 119617338 1126 LKIQGETHDSIEDARTALQLYRKYLELSKN 1155
Cdd:PRK07247  142 LGIKGRGHNSLEDARMTARVYESFLESDQN 171
 
Name Accession Description Interval E-value
UCH_1 pfam13423
Ubiquitin carboxyl-terminal hydrolase;
517-897 1.43e-115

Ubiquitin carboxyl-terminal hydrolase;


Pssm-ID: 463872 [Multi-domain]  Cd Length: 305  Bit Score: 361.59  E-value: 1.43e-115
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   517 AGLEPHIPNAYCNCMIQVLYFLEPVRCLIQNHL---CQKEFCLACELGFLFHMLDLSRGDPCQGNNFLRAFRTIPEASAL 593
Cdd:pfam13423    1 SGLETHIPNSYTNSLLQLLRFIPPLRNLALSHLateCLKEHCLLCELGFLFDMLEKAKGKNCQASNFLRALSSIPEASAL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   594 GLIlADSDEASGKGNLARLIQRWNRFILTQLHQDMQELEIPQayrgaggsfcSSGDSVIGQLFSCEMENCSLC-RCGSET 672
Cdd:pfam13423   81 GLL-DEDRETNSAISLSSLIQSFNRFLLDQLSSEENSTPPNP----------SPAESPLEQLFGIDAETTIRCsNCGHES 149
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   673 VRASSTLLFTLSYPDGSKS-DKTGKNYDFAQVLKRSICLDQNTQAWCDTCEKYQPTIQTRNIRHLPDILVINCEVNSSKE 751
Cdd:pfam13423  150 VRESSTHVLDLIYPRKPSSnNKKPPNQTFSSILKSSLERETTTKAWCEKCKRYQPLESRRTVRNLPPVLSLNAALTNEEW 229
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   752 ADFWRmqaevafkmavkkhggeisknkefaladwkelgspegvlvcpsieelKNVWLPFSIRMKMTKNKGLDvcnwtdgd 831
Cdd:pfam13423  230 RQLWK-----------------------------------------------TPGWLPPEIGLTLSDDLQGD-------- 254
                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119617338   832 emqwgparaeeeHGVYVYDLMATVVHILDSRTGGSLVAHIKVGETYHqrkEGVTHQQWYLFNDFLI 897
Cdd:pfam13423  255 ------------NEIVKYELRGVVVHIGDSGTSGHLVSFVKVADSEL---EDPTESQWYLFNDFLV 305
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
974-1147 1.49e-114

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.


Pssm-ID: 99846  Cd Length: 174  Bit Score: 353.46  E-value: 1.49e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  974 VGLDAEFVTLNEEEAELRSDGTKSTIKPSQMSVARITCVRGQGPNEGIPFIDDYISTQEQVVDYLTQYSGIKPGDLDAKI 1053
Cdd:cd06143     1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338 1054 SSKHLTTLKSTYLKLRFLIDIGVKFVGHGLQKDFRVINLMVPKDQVLDTVYLFHMPRKRMISLRFLAWYFLDLKIQGETH 1133
Cdd:cd06143    81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSETH 160
                         170
                  ....*....|....
gi 119617338 1134 DSIEDARTALQLYR 1147
Cdd:cd06143   161 DSIEDARTALKLYR 174
Peptidase_C19P cd02672
A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are ...
502-920 7.80e-83

A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.


Pssm-ID: 239137 [Multi-domain]  Cd Length: 268  Bit Score: 271.31  E-value: 7.80e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  502 GLEDFDFKHYNKTLFAGLEPHIPNAYCNCMIQVLYFLEPVRC--LIQNHLCQKEFCLACELGFLFhmldlsrgdpcqgnn 579
Cdd:cd02672     1 GTEDFDFEFYNKTNYAGLENHITNSYCNSLLQLLYFIPPFRNftAIILVACPKESCLLCELGYLF--------------- 65
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  580 flrafrtipeasalgliladsdeasgkgnlarliqrwnrfiltqlhqdmqeleipqayrgaggsfcssgdSVIGQLFSCE 659
Cdd:cd02672    66 ----------------------------------------------------------------------STLIQNFTRF 75
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  660 MENCSLCRCG-----SETVRASSTLLFTLSYPDGSKsdKTGKNYDFAQVLKRSICLDQNTQAWCDTCEKYQPTIQTRNIR 734
Cdd:cd02672    76 LLETISQDQLgtpfsCGTSRNSVSLLYTLSLPLGST--KTSKESTFLQLLKRSLDLEKVTKAWCDTCCKYQPLEQTTSIR 153
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  735 HLPDILvincevnsskeadfwrmqaevafkmavkkhggeisknkefaladwkelgspegvlvcpsieelknvWLPFSIRM 814
Cdd:cd02672   154 HLPDIL------------------------------------------------------------------LLVLVINL 167
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  815 KMTKNKGLDV-CNWTDGDEMQWGPARAEEEH----------GVYVYDLMATVVHILDSrtggSLVAHIKVGETYHQRKeg 883
Cdd:cd02672   168 SVTNGEFDDInVVLPSGKVMQNKVSPKAIDHdklvknrgqeSIYKYELVGYVCEINDS----SRGQHNVVFVIKVNEE-- 241
                         410       420       430
                  ....*....|....*....|....*....|....*..
gi 119617338  884 VTHQQWYLFNDFLIEPIDkheavqfdmnwKVPAILYY 920
Cdd:cd02672   242 STHGRWYLFNDFLVTPVS-----------ELAYILLY 267
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
974-1147 1.72e-45

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins; This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA.


Pssm-ID: 99840  Cd Length: 161  Bit Score: 161.29  E-value: 1.72e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  974 VGLDAEFVTLNEEeaelrsdgtkstikpsQMSVARITCVRGqgpNEGIPFIDDYISTQEQVVDYLTQYSGIKPGDL--DA 1051
Cdd:cd06137     1 VALDCEMVGLADG----------------DSEVVRISAVDV---LTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLeeAA 61
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338 1052 KISSKHLTTLKSTYLKLRFlIDIGVKFVGHGLQKDFRVINLMvpKDQVLDTVYLFHMPRKRM-----ISLRFLAWYFLDL 1126
Cdd:cd06137    62 KAGKTIFGWEAARAALWKF-IDPDTILVGHSLQNDLDALRMI--HTRVVDTAILTREAVKGPlakrqWSLRTLCRDFLGL 138
                         170       180
                  ....*....|....*....|...
gi 119617338 1127 KIQG--ETHDSIEDARTALQLYR 1147
Cdd:cd06137   139 KIQGggEGHDSLEDALAAREVVL 161
Peptidase_C19 cd02257
Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ...
618-921 2.21e-26

Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.


Pssm-ID: 239072 [Multi-domain]  Cd Length: 255  Bit Score: 109.49  E-value: 2.21e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  618 RFILTQLHQDMQELEipqayrgAGGSFCSSGDSVIGQLFSCEMENCSLC-RCGSETVRASSTLLFTLSYPDgsksdKTGK 696
Cdd:cd02257    30 LFLLDKLHEELKKSS-------KRTSDSSSLKSLIHDLFGGKLESTIVClECGHESVSTEPELFLSLPLPV-----KGLP 97
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  697 NYDFAQVLKRSICLDQNTQAWCDTCE--KYQPTIQTRNIRHLPDILVINCEvnsskeadfwRmqaevaFKMAVKKHGGEI 774
Cdd:cd02257    98 QVSLEDCLEKFFKEEILEGDNCYKCEkkKKQEATKRLKIKKLPPVLIIHLK----------R------FSFNEDGTKEKL 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  775 SKNKEFaladwkelgspegvlvcpsieelknvwlPFSIRMKMTKNKGLDVCNwtdgdemqwgparaeEEHGVYVYDLMAT 854
Cdd:cd02257   162 NTKVSF----------------------------PLELDLSPYLSEGEKDSD---------------SDNGSYKYELVAV 198
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 119617338  855 VVHILDSRTGGSLVAHIKVGEtyhqrkegvtHQQWYLFNDFLIEPIDKHEAVQFDMNWKVPAILYYV 921
Cdd:cd02257   199 VVHSGTSADSGHYVAYVKDPS----------DGKWYKFNDDKVTEVSEEEVLEFGSLSSSAYILFYE 255
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
973-1151 3.23e-26

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 106.23  E-value: 3.23e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338    973 LVGLDAEFVTLNEEEAELrsdgtkstikpsqmsvARITCVRGQGPNEGIPFiDDYISTQEQVVDYLTQYSGIKPGDLDAK 1052
Cdd:smart00479    2 LVVIDCETTGLDPGKDEI----------------IEIAAVDVDGGEIIEVF-DTYVKPDRPITDYATEIHGITPEMLDDA 64
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   1053 IsskhltTLKSTYLKLRFLIDIGVKFVGHGLQKDFRVINLMVPK--------DQVLDTVYLFHM--PRKRMISLRFLAWY 1122
Cdd:smart00479   65 P------TFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRlgikqppkLPVIDTLKLARAtnPGLPKYSLKKLAKR 138
                           170       180
                    ....*....|....*....|....*....
gi 119617338   1123 FLdLKIQGETHDSIEDARTALQLYRKYLE 1151
Cdd:smart00479  139 LL-LEVIQRAHRALDDARATAKLFKKLLE 166
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
1004-1145 3.00e-25

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


Pssm-ID: 99848  Cd Length: 150  Bit Score: 102.95  E-value: 3.00e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338 1004 MSVARITCVRGqgpnEGIPFIDDYISTQEQVVDYLTQYSGIKPGDLDAKIsskhlTTLKSTYLKLRFLIDIGVKFVGHGL 1083
Cdd:cd06145    14 LELTRVTVVDE----NGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVT-----TTLEDVQKKLLSLISPDTILVGHSL 84
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 119617338 1084 QKDFRVINLMVPKdqVLDTVYLFHMPRKRM--ISLRFLAWYFLDLKIQGET--HDSIEDARTALQL 1145
Cdd:cd06145    85 ENDLKALKLIHPR--VIDTAILFPHPRGPPykPSLKNLAKKYLGRDIQQGEggHDSVEDARAALEL 148
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
974-1147 6.18e-25

DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.


Pssm-ID: 99847  Cd Length: 152  Bit Score: 101.82  E-value: 6.18e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  974 VGLDAEFVtlneeeaELRSDGTKStikpsqmSVARITCVrgqgpNE-GIPFIDDYISTQEQVVDYLTQYSGIKPGDLDAK 1052
Cdd:cd06144     1 VALDCEMV-------GVGPDGSES-------ALARVSIV-----NEdGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDA 61
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338 1053 ISSKHLTTLKSTYLKLRFLidigvkfVGHGLQKDFRVINLMVPKDQVLDT---VYLFHMPRKRMISLRFLAWYFLDLKIQ 1129
Cdd:cd06144    62 PDFEEVQKKVAELLKGRIL-------VGHALKNDLKVLKLDHPKKLIRDTskyKPLRKTAKGKSPSLKKLAKQLLGLDIQ 134
                         170
                  ....*....|....*...
gi 119617338 1130 GETHDSIEDARTALQLYR 1147
Cdd:cd06144   135 EGEHSSVEDARAAMRLYR 152
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
974-1146 8.55e-19

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 84.71  E-value: 8.55e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   974 VGLDAEFVTLNEEEAELrsdgtkstikpsqMSVARITCVRGQgpNEGIPFIDDYISTQE--QVVDYLTQYSGIKPGDLDA 1051
Cdd:pfam00929    1 VVIDLETTGLDPEKDEI-------------IEIAAVVIDGGE--NEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDN 65
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  1052 KISSKH-LTTLKSTYLKLRFLIDIGVKF-VGHGLQKDFRVINLMVPK-DQVLDTVYLFHMPRKRM--ISLRFLAWYFlDL 1126
Cdd:pfam00929   66 KPSFEEvLEEFLEFLRKGNLLVAHNASFdVGFLRYDDKRFLKKPMPKlNPVIDTLILDKATYKELpgRSLDALAEKL-GL 144
                          170       180
                   ....*....|....*....|
gi 119617338  1127 KIQGETHDSIEDARTALQLY 1146
Cdd:pfam00929  145 EHIGRAHRALDDARATAKLF 164
UCH pfam00443
Ubiquitin carboxyl-terminal hydrolase;
527-920 5.28e-15

Ubiquitin carboxyl-terminal hydrolase;


Pssm-ID: 425685 [Multi-domain]  Cd Length: 310  Bit Score: 77.48  E-value: 5.28e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   527 YCNCMIQVLYFLEPVRCLIQN--HLC-----QKEFCLACELGFLFH-MLDLSRGDPCQGNNFLRAFRTIPEasalglila 598
Cdd:pfam00443   11 YMNSVLQSLFSIPPFRDYLLRisPLSedsryNKDINLLCALRDLFKaLQKNSKSSSVSPKMFKKSLGKLNP--------- 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   599 dsDEASGKGNLArliQRWNRFILTQLHQDMQeleipqayrgagGSFCSSGDSVIGQLFSCEMENCSLCR-CGSETVRASS 677
Cdd:pfam00443   82 --DFSGYKQQDA---QEFLLFLLDGLHEDLN------------GNHSTENESLITDLFRGQLKSRLKCLsCGEVSETFEP 144
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   678 TLLFTLSYPDGSKSDKTGKNYDFAQVLKRSICLDQNTQAWCDTCEKYQPTIQTRNIRHLPDILVINcevnsSKEADFWRM 757
Cdd:pfam00443  145 FSDLSLPIPGDSAELKTASLQICFLQFSKLEELDDEEKYYCDKCGCKQDAIKQLKISRLPPVLIIH-----LKRFSYNRS 219
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   758 qaevafkMAVKkhggeISKNKEFaladwkelgspegvlvcpsieelknvwlPFSIRMKMTKNKGLDvcnwtdgdemqwgp 837
Cdd:pfam00443  220 -------TWEK-----LNTEVEF----------------------------PLELDLSRYLAEELK-------------- 245
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338   838 araEEEHGVYVYDLMATVVHiLDSRTGGSLVAHIKVGEtyhqrkegvtHQQWYLFNDFLIEPIDKHEAVQFDMnwkvPAI 917
Cdd:pfam00443  246 ---PKTNNLQDYRLVAVVVH-SGSLSSGHYIAYIKAYE----------NNRWYKFDDEKVTEVDEETAVLSSS----AYI 307

                   ...
gi 119617338   918 LYY 920
Cdd:pfam00443  308 LFY 310
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
1025-1147 4.72e-14

DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins; Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral response.


Pssm-ID: 99852  Cd Length: 157  Bit Score: 70.93  E-value: 4.72e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338 1025 DDYISTQEQVVDYLTQYSGIKPGDLdakissKHLTTLKSTYLKLRFLIDiGVKFVGHGLQKDFRVINLMVPKDQVLDTVY 1104
Cdd:cd06149    34 DKYIRPEGPVTDYRTRWSGIRRQHL------VNATPFAVAQKEILKILK-GKVVVGHAIHNDFKALKYFHPKHMTRDTST 106
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 119617338 1105 ------LFHMPRKRMISLRFLAWYFLDLKIQG--ETHDSIEDARTALQLYR 1147
Cdd:cd06149   107 ipllnrKAGFPENCRVSLKVLAKRLLHRDIQVgrQGHSSVEDARATMELYK 157
Peptidase_C19L cd02668
A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are ...
831-902 3.75e-04

A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.


Pssm-ID: 239133 [Multi-domain]  Cd Length: 324  Bit Score: 43.95  E-value: 3.75e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119617338  831 DEMQWGPARAEEEHGVYVYDLMATVVHILDSRTGGSLVAHIKVGETyhqrkegvthQQWYLFNDFLIEPIDK 902
Cdd:cd02668   228 EILDMGEYLAESDEGSYVYELSGVLIHQGVSAYSGHYIAHIKDEQT----------GEWYKFNDEDVEEMPG 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
204-357 9.04e-04

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 42.71  E-value: 9.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  204 QTNRFFFCGHTSGKVSLRDLRTFKVEHEFDAFSGSLSDFDVH--GNLLAACGfssrltglaCDRFLKVYDLRMMRAITPL 281
Cdd:cd00200   145 PDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSpdGEKLLSSS---------SDGTIKLWDLSTGKCLGTL 215
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119617338  282 QVHVDPA-FLRFIPtytSRLAIIS------------QSGQCQFCeptgLANpadifHVNPVGpllmTFDVSASKQALAFG 348
Cdd:cd00200   216 RGHENGVnSVAFSP---DGYLLASgsedgtirvwdlRTGECVQT----LSG-----HTNSVT----SLAWSPDGKRLASG 279

                  ....*....
gi 119617338  349 DSEGCVHLW 357
Cdd:cd00200   280 SADGTIRIW 288
PRK07247 PRK07247
3'-5' exonuclease;
1126-1155 9.40e-03

3'-5' exonuclease;


Pssm-ID: 180906 [Multi-domain]  Cd Length: 195  Bit Score: 38.61  E-value: 9.40e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 119617338 1126 LKIQGETHDSIEDARTALQLYRKYLELSKN 1155
Cdd:PRK07247  142 LGIKGRGHNSLEDARMTARVYESFLESDQN 171
 
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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