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Conserved domains on  [gi|528484546|ref|XP_005172268|]
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crossover junction endonuclease MUS81 isoform X1 [Danio rerio]

Protein Classification

crossover junction endonuclease MUS81( domain architecture ID 15338741)

crossover junction endonuclease MUS81 interacts with EME1 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick

EC:  3.1.21.10
Gene Ontology:  GO:0048257|GO:0008821|GO:0003677|GO:0046872|GO:0006308|GO:0006281|GO:0006302
PubMed:  17363897

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XPF_nuclease_Mus81 cd20074
XPF-like nuclease domain of Mus81; Mus81 is a crossover junction endonuclease that interacts ...
 318-479 7.14e-76

XPF-like nuclease domain of Mus81; Mus81 is a crossover junction endonuclease that interacts with Eme1 and Eme2 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. The typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. Mus81 may be required in mitosis for the processing of stalled or collapsed replication forks. Mus81 consists of the active nuclease domain with the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity and two helix-hairpin-helix (HhH2) domains.


:

Pssm-ID: 410850 [Multi-domain]  Cd Length: 150  Bit Score: 238.15  E-value: 7.14e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 318 SYDIVLCVDLCETTGGSSvrKQELVKELQRNSVTFDVRKLNVGDFLWVARERVTPvpgqlrppvGKELVLDYIIERKRMD 397
Cdd:cd20074    1 SYEVVLLVDNREVKGKKD--RDYFQRELEKLGVKVETRSLPVGDFLWVARHKSDT---------GEELVLDYIVERKRLD 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 398 DLCGSIIDGRFREQKFRLKRCGLRKPIYLVEECGSaAAHLSIPESTLQQAIVNTQVVDGFFVKRVQDAKESAAYLTIMTR 477
Cdd:cd20074   70 DLASSIKDGRYHEQKFRLKRSGIKNVIYLVEGDGS-AQSGGLPEEALKTALANTQVVDGFFVKRTKSLDETVRYLARLTR 148


                 ..
gi 528484546 478 YL 479
Cdd:cd20074  149 AL 150
WH_MUS81 cd21036
winged helix domain found in crossover junction endonuclease MUS81 and similar proteins; MUS81 ...
 146-236 1.04e-41

winged helix domain found in crossover junction endonuclease MUS81 and similar proteins; MUS81 is a crossover junction endonuclease that interacts with EME1 (essential meiotic structure-specific endonuclease 1) and EME2, to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. The MUS80-EME1 endonuclease maintains genomic integrity in metazoans by cleaving branched DNA structures that can form during mitosis and fission yeast meiosis, and during processing of damaged replication folks. This model corresponds to the winged helix (WH) domain of MUS81, which is responsible for DNA binding. It comprises four helices and two beta strands.


:

Pssm-ID: 411029  Cd Length: 94  Bit Score: 145.75  E-value: 1.04e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 146 YVPQKRSGGYAVLLTLYRHIQMPGsKGFMFRNELQTEAQPLCEKSFTVPDLGSKYTAWSSVSTLIQKELV-KTHNPARYS 224
Cdd:cd21036    1 YVPKYRSGAYAILLALYKLDKEPG-KGGLTKEELIRRAQPYCDSSFTIPDPGSFYTAWSSMKTLIKKGLVyKEGRPARYS 79

                         90
                 ....*....|..
gi 528484546 225 LTDQGLSLAEKL 236
Cdd:cd21036   80 LTEEGRELAEKL 91
NT_Pol-beta-like super family cl11966
Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This ...
 44-85 3.28e-04

Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. Two of the three catalytic carboxylates are found in Rel-Spo enzymes, with the second carboxylate of the DXD motif missing. Evidence supports a single-cation synthetase mechanism for Rel-Spo enzymes.


The actual alignment was detected with superfamily member cd00141:

Pssm-ID: 472251 [Multi-domain]  Cd Length: 307  Bit Score: 42.95  E-value: 3.28e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 528484546  44 YQKAINSLKKYPLPLKNGKEAKILQNFGDGICKILDE-----RLQKH 85
Cdd:cd00141   27 YRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEiletgKLRKL 73
 
Name Accession Description Interval E-value
XPF_nuclease_Mus81 cd20074
XPF-like nuclease domain of Mus81; Mus81 is a crossover junction endonuclease that interacts ...
 318-479 7.14e-76

XPF-like nuclease domain of Mus81; Mus81 is a crossover junction endonuclease that interacts with Eme1 and Eme2 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. The typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. Mus81 may be required in mitosis for the processing of stalled or collapsed replication forks. Mus81 consists of the active nuclease domain with the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity and two helix-hairpin-helix (HhH2) domains.


Pssm-ID: 410850 [Multi-domain]  Cd Length: 150  Bit Score: 238.15  E-value: 7.14e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 318 SYDIVLCVDLCETTGGSSvrKQELVKELQRNSVTFDVRKLNVGDFLWVARERVTPvpgqlrppvGKELVLDYIIERKRMD 397
Cdd:cd20074    1 SYEVVLLVDNREVKGKKD--RDYFQRELEKLGVKVETRSLPVGDFLWVARHKSDT---------GEELVLDYIVERKRLD 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 398 DLCGSIIDGRFREQKFRLKRCGLRKPIYLVEECGSaAAHLSIPESTLQQAIVNTQVVDGFFVKRVQDAKESAAYLTIMTR 477
Cdd:cd20074   70 DLASSIKDGRYHEQKFRLKRSGIKNVIYLVEGDGS-AQSGGLPEEALKTALANTQVVDGFFVKRTKSLDETVRYLARLTR 148


                 ..
gi 528484546 478 YL 479
Cdd:cd20074  149 AL 150
WH_MUS81 cd21036
winged helix domain found in crossover junction endonuclease MUS81 and similar proteins; MUS81 ...
 146-236 1.04e-41

winged helix domain found in crossover junction endonuclease MUS81 and similar proteins; MUS81 is a crossover junction endonuclease that interacts with EME1 (essential meiotic structure-specific endonuclease 1) and EME2, to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. The MUS80-EME1 endonuclease maintains genomic integrity in metazoans by cleaving branched DNA structures that can form during mitosis and fission yeast meiosis, and during processing of damaged replication folks. This model corresponds to the winged helix (WH) domain of MUS81, which is responsible for DNA binding. It comprises four helices and two beta strands.


Pssm-ID: 411029  Cd Length: 94  Bit Score: 145.75  E-value: 1.04e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 146 YVPQKRSGGYAVLLTLYRHIQMPGsKGFMFRNELQTEAQPLCEKSFTVPDLGSKYTAWSSVSTLIQKELV-KTHNPARYS 224
Cdd:cd21036    1 YVPKYRSGAYAILLALYKLDKEPG-KGGLTKEELIRRAQPYCDSSFTIPDPGSFYTAWSSMKTLIKKGLVyKEGRPARYS 79

                         90
                 ....*....|..
gi 528484546 225 LTDQGLSLAEKL 236
Cdd:cd21036   80 LTEEGRELAEKL 91
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
 325-475 6.40e-33

ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.


Pssm-ID: 426945 [Multi-domain]  Cd Length: 139  Bit Score: 122.92  E-value: 6.40e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546  325 VDLCEttggssVRKQELVKELQRNSVTFDVRKLNVGDFLWVARERVTpvpgqlrppvGKELVLDYIIERKRMDDLCGSII 404
Cdd:pfam02732   1 VDTRE------LRSSIPELLLEELGVEVVVETLPVGDYLWVPREYDL----------ELEVVLDVIVERKSLDDLVSSII 64

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 528484546  405 DGRFREQKFRLKRcGLRKPIYLVEECGSAAAHL-----SIPESTLQQAIVNTQVVDGFFVKRVQDAKESAAYLTIM 475
Cdd:pfam02732  65 DGRLFEQKSRLKR-GYKKPILLVEGLDLFSRKLknkrrDINPNAIEGALASLQVDYGVRIIRTRSAEETAEWLASL 139
ERCC4 smart00891
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, ...
 322-428 2.43e-26

ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.


Pssm-ID: 214888 [Multi-domain]  Cd Length: 98  Bit Score: 103.20  E-value: 2.43e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546   322 VLCVDLCETtggSSVRKQELVKELQ-RNSVTFDVRKLNVGDFLWVARERvtpvpgqlRPPVGKELVLDYIIERKRMDDLC 400
Cdd:smart00891   1 EIIVDSREL---RSALEAPIPRSLRwKRGVKVEYDRLEAGDFVLVARDK--------QSLLPHVNSLNELVERKSLTDLV 69

                           90       100
                   ....*....|....*....|....*...
gi 528484546   401 GSIIDGRFREQKFRLKRCGLRKPIYLVE 428
Cdd:smart00891  70 ASIPDGRLFEQVRRLQQIAYPSPQLLVE 97
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
337-604 1.86e-08

ERCC4-type crossover junction endonuclease [Replication, recombination and repair];


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 55.18  E-value: 1.86e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 337 RKQELVKELQRNSVTFDVRKLNVGDFLwVArERVtpvpgqlrppvgkelvldyIIERKRMDDLCGSIIDGRFREQKFRLK 416
Cdd:COG1948   11 KNSGVPRLLSRLGVEVRVKTLEVGDYV-VS-DRV-------------------AVERKTVRDFVNSLIDGRLFEQASRLA 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 417 RCgLRKPIYLVEECGsAAAHLSIPESTLQQAIVnTQVVD-GFFVKRVQDAKESAAYLTIMTRylqklyqnctlfcrsREL 495
Cdd:COG1948   70 EA-YERPVLIIEGDL-LYEERNIHPNAIRGALA-SLALDfGIPVLPTRDAEDTAELLVTLAR---------------REQ 131

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 496 EGDGeaesekmvanlscslmafTEFNYGAIKnKCQTVREvfaRQLMQISGVSG---DKAAAVLEHYSTVSSLLQAydkcs 572
Cdd:COG1948  132 EEEK------------------REVSLHGKK-KPKTLRE---QQLYVVESLPGigpKLARRLLEHFGSVEAVFNA----- 184

                        250       260       270
                 ....*....|....*....|....*....|..
gi 528484546 573 SETEkeklLSSVKygklkrNLGPALSRTIYQL 604
Cdd:COG1948  185 SEEE----LMKVE------GIGEKTAERIREV 206
PRK13766 PRK13766
Hef nuclease; Provisional
 342-477 1.26e-05

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 48.33  E-value: 1.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 342 VKELQRNSVTFDVRKLNVGDFlwVARERVtpvpgqlrppvgkelvldyIIERKRMDDLCGSIIDGRFREQKFRLKRcGLR 421
Cdd:PRK13766 577 ARHLKRLGAEVELKTLEVGDY--VVSDRV-------------------AVERKTAEDFVDSIIDRRLFEQVKDLKR-AYE 634

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 528484546 422 KPIYLVEecGSAAAHLSIPESTLQQAIVnTQVVD-GFFVKRVQDAKESAAYL-TIMTR 477
Cdd:PRK13766 635 RPVLIIE--GDLYTIRNIHPNAIRGALA-SIAVDfGIPILFTRDEEETADLLkVIAKR 689
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 44-85 3.28e-04

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 42.95  E-value: 3.28e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 528484546  44 YQKAINSLKKYPLPLKNGKEAKILQNFGDGICKILDE-----RLQKH 85
Cdd:cd00141   27 YRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEiletgKLRKL 73
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
 44-80 8.27e-03

DNA polymerase X family; includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases


Pssm-ID: 214688  Cd Length: 334  Bit Score: 38.89  E-value: 8.27e-03
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 528484546    44 YQKAINSLKKYPLPLKNGKEAKILQNFGDGICKILDE 80
Cdd:smart00483  30 FRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEE 66
 
Name Accession Description Interval E-value
XPF_nuclease_Mus81 cd20074
XPF-like nuclease domain of Mus81; Mus81 is a crossover junction endonuclease that interacts ...
 318-479 7.14e-76

XPF-like nuclease domain of Mus81; Mus81 is a crossover junction endonuclease that interacts with Eme1 and Eme2 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. The typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. Mus81 may be required in mitosis for the processing of stalled or collapsed replication forks. Mus81 consists of the active nuclease domain with the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity and two helix-hairpin-helix (HhH2) domains.


Pssm-ID: 410850 [Multi-domain]  Cd Length: 150  Bit Score: 238.15  E-value: 7.14e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 318 SYDIVLCVDLCETTGGSSvrKQELVKELQRNSVTFDVRKLNVGDFLWVARERVTPvpgqlrppvGKELVLDYIIERKRMD 397
Cdd:cd20074    1 SYEVVLLVDNREVKGKKD--RDYFQRELEKLGVKVETRSLPVGDFLWVARHKSDT---------GEELVLDYIVERKRLD 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 398 DLCGSIIDGRFREQKFRLKRCGLRKPIYLVEECGSaAAHLSIPESTLQQAIVNTQVVDGFFVKRVQDAKESAAYLTIMTR 477
Cdd:cd20074   70 DLASSIKDGRYHEQKFRLKRSGIKNVIYLVEGDGS-AQSGGLPEEALKTALANTQVVDGFFVKRTKSLDETVRYLARLTR 148


                 ..
gi 528484546 478 YL 479
Cdd:cd20074  149 AL 150
WH_MUS81 cd21036
winged helix domain found in crossover junction endonuclease MUS81 and similar proteins; MUS81 ...
 146-236 1.04e-41

winged helix domain found in crossover junction endonuclease MUS81 and similar proteins; MUS81 is a crossover junction endonuclease that interacts with EME1 (essential meiotic structure-specific endonuclease 1) and EME2, to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. The MUS80-EME1 endonuclease maintains genomic integrity in metazoans by cleaving branched DNA structures that can form during mitosis and fission yeast meiosis, and during processing of damaged replication folks. This model corresponds to the winged helix (WH) domain of MUS81, which is responsible for DNA binding. It comprises four helices and two beta strands.


Pssm-ID: 411029  Cd Length: 94  Bit Score: 145.75  E-value: 1.04e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 146 YVPQKRSGGYAVLLTLYRHIQMPGsKGFMFRNELQTEAQPLCEKSFTVPDLGSKYTAWSSVSTLIQKELV-KTHNPARYS 224
Cdd:cd21036    1 YVPKYRSGAYAILLALYKLDKEPG-KGGLTKEELIRRAQPYCDSSFTIPDPGSFYTAWSSMKTLIKKGLVyKEGRPARYS 79

                         90
                 ....*....|..
gi 528484546 225 LTDQGLSLAEKL 236
Cdd:cd21036   80 LTEEGRELAEKL 91
XPF_ERCC4_MUS81-like cd22367
XPF family DNA repair endonuclease; (Xeroderma Pigmentosum group F) DNA repair gene homologs ...
 323-475 2.01e-35

XPF family DNA repair endonuclease; (Xeroderma Pigmentosum group F) DNA repair gene homologs are members of the XPF/Rad1/Mus81-dependent nuclease family which specifically cleave branched structures generated during DNA repair, replication, and recombination, and they are essential for maintaining genome stability. They belong to a wider superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411771 [Multi-domain]  Cd Length: 123  Bit Score: 129.30  E-value: 2.01e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 323 LCVDLCEttggssvRKQELVKELQRNSVTFDVRKLNVGDFLWVArervtpvpgqlrppvgkelvlDYIIERKRMDDLCGS 402
Cdd:cd22367    1 IVVDSRE-------RRSGLPELLRKLGVRVEVRTLEVGDYILSA---------------------DIIVERKTVSDLISS 52

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528484546 403 IIDGRFREQKFRLKRCGLRkPIYLVEECGSaAAHLSIPESTLQQAIVNTQVVDGFFVKRVQDAKESAAYLTIM 475
Cdd:cd22367   53 IIDGRLFEQAERLKRSYER-PILLIEGDPD-KARRLVRPAALGAAISSLLVIGGLLVLRTPNFETTALLLSLL 123
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
 325-475 6.40e-33

ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.


Pssm-ID: 426945 [Multi-domain]  Cd Length: 139  Bit Score: 122.92  E-value: 6.40e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546  325 VDLCEttggssVRKQELVKELQRNSVTFDVRKLNVGDFLWVARERVTpvpgqlrppvGKELVLDYIIERKRMDDLCGSII 404
Cdd:pfam02732   1 VDTRE------LRSSIPELLLEELGVEVVVETLPVGDYLWVPREYDL----------ELEVVLDVIVERKSLDDLVSSII 64

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 528484546  405 DGRFREQKFRLKRcGLRKPIYLVEECGSAAAHL-----SIPESTLQQAIVNTQVVDGFFVKRVQDAKESAAYLTIM 475
Cdd:pfam02732  65 DGRLFEQKSRLKR-GYKKPILLVEGLDLFSRKLknkrrDINPNAIEGALASLQVDYGVRIIRTRSAEETAEWLASL 139
ERCC4 smart00891
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, ...
 322-428 2.43e-26

ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.


Pssm-ID: 214888 [Multi-domain]  Cd Length: 98  Bit Score: 103.20  E-value: 2.43e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546   322 VLCVDLCETtggSSVRKQELVKELQ-RNSVTFDVRKLNVGDFLWVARERvtpvpgqlRPPVGKELVLDYIIERKRMDDLC 400
Cdd:smart00891   1 EIIVDSREL---RSALEAPIPRSLRwKRGVKVEYDRLEAGDFVLVARDK--------QSLLPHVNSLNELVERKSLTDLV 69

                           90       100
                   ....*....|....*....|....*...
gi 528484546   401 GSIIDGRFREQKFRLKRCGLRKPIYLVE 428
Cdd:smart00891  70 ASIPDGRLFEQVRRLQQIAYPSPQLLVE 97
XPF_nuclease-like cd19940
nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap ...
 323-477 3.81e-23

nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap endonuclease that act upon 3'-flap structures and involved in DNA repair pathways that are necessary for the removal of UV-light-induced DNA lesions and cross-links between DNA strands. Family members exist either as heterodimers or as homodimers in their functionally competent states which consist of a catalytic and a noncatalytic subunit. The catalytic subunits have a DX(n)RKX(3)D motif. This motif is required for metal-dependent endonuclease activity but not for DNA junction binding. The equivalent regions of the noncatalytic subunits (ERCC1, EME1, and FAAP24) have diverged. The noncatalytic subunits have roles such as binding ssDNA or an ability to target the endonuclease to defined DNA structures or sites of DNA damage.


Pssm-ID: 410849 [Multi-domain]  Cd Length: 126  Bit Score: 95.14  E-value: 3.81e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 323 LCVDLCETTGgssvrkqELVKELQRNSVTFDVRKLNVGDFLWVARervtpvpgqlrppvgkelvldYIIERKRMDDLCGS 402
Cdd:cd19940    2 IVVDPRERRS-------ELLSELQRLGVQVEFEDLAVGDYVLSNR---------------------TCVERKSLSDLVSS 53

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528484546 403 IIDGRFREQKFRLKRCGLRkPIYLVEECGSaAAHLSIPESTLQQAIVNTQVVDGFFVKRVQDAKESAAYLTIMTR 477
Cdd:cd19940   54 INKGRLREQLQRLTRKFER-RVLLVEKDRS-KFRSMVSSVQALSALTKLQLLTGIRLLIVASPKETADLLEELTQ 126
XPF_nuclease_XPF_arch cd20075
nuclease domain of XPF found in archaea; XPF, also called DNA excision repair protein ERCC-4, ...
 337-477 1.09e-11

nuclease domain of XPF found in archaea; XPF, also called DNA excision repair protein ERCC-4, or DNA repair protein complementing XP-F cells, or Xeroderma pigmentosum group F-complementing protein, is a 3'-flap repair endonuclease that cleaves 5' of ds/ssDNA interfaces in 3' flap structures, although it also cuts bubble, Y-DNA structures and mobile and immobile Holliday junctions. XPF cuts preferentially after pyrimidines, may continue to progressively cleave substrate upstream of the initial cleavage, at least in vitro. It may be involved in nucleotide excision repair. The nuclease domains of the catalytic subunits XPF have the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity but not for DNA junction binding. XPF-ERRC1 and its yeast homolog Rad1-Rad10 play key roles in the excision of DNA lesions and are required for certain types of homologous recombination events and for the repair of DNA cross-links.


Pssm-ID: 410851 [Multi-domain]  Cd Length: 127  Bit Score: 62.40  E-value: 1.09e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 337 RKQELVKELQRNSVTFDVRKLNVGDFlwVARERVtpvpgqlrppvgkelvldyIIERKRMDDLCGSIIDGRFREQKFRLK 416
Cdd:cd20075    9 KNSGVVRELKELGVEVEFKQLEVGDY--IVSDRV-------------------AIERKTVDDFVSSIIDGRLFDQAKRLK 67

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 528484546 417 RCGlRKPIYLVEecGS-AAAHLSIPESTLQQAIVnTQVVDG----FFVKrvqDAKESAAYLTIMTR 477
Cdd:cd20075   68 EAY-EKPILIIE--GDlLYLKRRIHPNAIRGALA-SIALDFgipiIFTK---DPEETAELLYSLAK 126
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
337-604 1.86e-08

ERCC4-type crossover junction endonuclease [Replication, recombination and repair];


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 55.18  E-value: 1.86e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 337 RKQELVKELQRNSVTFDVRKLNVGDFLwVArERVtpvpgqlrppvgkelvldyIIERKRMDDLCGSIIDGRFREQKFRLK 416
Cdd:COG1948   11 KNSGVPRLLSRLGVEVRVKTLEVGDYV-VS-DRV-------------------AVERKTVRDFVNSLIDGRLFEQASRLA 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 417 RCgLRKPIYLVEECGsAAAHLSIPESTLQQAIVnTQVVD-GFFVKRVQDAKESAAYLTIMTRylqklyqnctlfcrsREL 495
Cdd:COG1948   70 EA-YERPVLIIEGDL-LYEERNIHPNAIRGALA-SLALDfGIPVLPTRDAEDTAELLVTLAR---------------REQ 131

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 496 EGDGeaesekmvanlscslmafTEFNYGAIKnKCQTVREvfaRQLMQISGVSG---DKAAAVLEHYSTVSSLLQAydkcs 572
Cdd:COG1948  132 EEEK------------------REVSLHGKK-KPKTLRE---QQLYVVESLPGigpKLARRLLEHFGSVEAVFNA----- 184

                        250       260       270
                 ....*....|....*....|....*....|..
gi 528484546 573 SETEkeklLSSVKygklkrNLGPALSRTIYQL 604
Cdd:COG1948  185 SEEE----LMKVE------GIGEKTAERIREV 206
PRK13766 PRK13766
Hef nuclease; Provisional
 342-477 1.26e-05

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 48.33  E-value: 1.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528484546 342 VKELQRNSVTFDVRKLNVGDFlwVARERVtpvpgqlrppvgkelvldyIIERKRMDDLCGSIIDGRFREQKFRLKRcGLR 421
Cdd:PRK13766 577 ARHLKRLGAEVELKTLEVGDY--VVSDRV-------------------AVERKTAEDFVDSIIDRRLFEQVKDLKR-AYE 634

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 528484546 422 KPIYLVEecGSAAAHLSIPESTLQQAIVnTQVVD-GFFVKRVQDAKESAAYL-TIMTR 477
Cdd:PRK13766 635 RPVLIIE--GDLYTIRNIHPNAIRGALA-SIAVDfGIPILFTRDEEETADLLkVIAKR 689
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 44-85 3.28e-04

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 42.95  E-value: 3.28e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 528484546  44 YQKAINSLKKYPLPLKNGKEAKILQNFGDGICKILDE-----RLQKH 85
Cdd:cd00141   27 YRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEiletgKLRKL 73
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
 44-80 8.27e-03

DNA polymerase X family; includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases


Pssm-ID: 214688  Cd Length: 334  Bit Score: 38.89  E-value: 8.27e-03
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 528484546    44 YQKAINSLKKYPLPLKNGKEAKILQNFGDGICKILDE 80
Cdd:smart00483  30 FRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEE 66
 
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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