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Conserved domains on  [gi|186972951|pdb|2ZIU|B]
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Chain B, Crossover junction endonuclease EME1

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
XPF_nuclease_EME1 cd20081
XPF-like nuclease domain of crossover junction endonuclease EME1; EME1, also called MMS4 ...
17-223 3.95e-104

XPF-like nuclease domain of crossover junction endonuclease EME1; EME1, also called MMS4 homolog (hMMS4), interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Its typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. EME1 may be required in mitosis for the processing of stalled or collapsed replication forks. The nuclease domain of EME1 is a nuclease-like domain which is involved in targeting the MUS81-EME1 heterodimer complex to DNA.


:

Pssm-ID: 410857  Cd Length: 179  Bit Score: 302.83  E-value: 3.95e-104
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       17 EECLKHIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRAGPSE-DREDWVEEPTVLVLLRAEAFVSM 95
Cdd:cd20081   3 EECLKHIVVVLDPGLLQMEGGGQLLSALQAMECSCVIEAQAIPRSVTWRRRAAPSQvDEEDWVEEPTVLVLLPAEEFVSM 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       96 IDNGKQGSLDSTMKGKETLQGFVTDITAKTAGKALSLVIVDQEKCFSaqnpprrgkqgankqtkkqqqrqpeasigsmVS 175
Cdd:cd20081  83 VHNYKQESLGSTTEGKETLQSFVTDITAKTAGKALSLVVVDMEKYFR-------------------------------VS 131
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
2ZIU_B      176 RVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFKKLR 223
Cdd:cd20081 132 RVDVEEALVDLQLHTGVQVQFLETWKEFADFICMFTKAVAEAPFKKLR 179
 
Name Accession Description Interval E-value
XPF_nuclease_EME1 cd20081
XPF-like nuclease domain of crossover junction endonuclease EME1; EME1, also called MMS4 ...
17-223 3.95e-104

XPF-like nuclease domain of crossover junction endonuclease EME1; EME1, also called MMS4 homolog (hMMS4), interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Its typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. EME1 may be required in mitosis for the processing of stalled or collapsed replication forks. The nuclease domain of EME1 is a nuclease-like domain which is involved in targeting the MUS81-EME1 heterodimer complex to DNA.


Pssm-ID: 410857  Cd Length: 179  Bit Score: 302.83  E-value: 3.95e-104
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       17 EECLKHIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRAGPSE-DREDWVEEPTVLVLLRAEAFVSM 95
Cdd:cd20081   3 EECLKHIVVVLDPGLLQMEGGGQLLSALQAMECSCVIEAQAIPRSVTWRRRAAPSQvDEEDWVEEPTVLVLLPAEEFVSM 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       96 IDNGKQGSLDSTMKGKETLQGFVTDITAKTAGKALSLVIVDQEKCFSaqnpprrgkqgankqtkkqqqrqpeasigsmVS 175
Cdd:cd20081  83 VHNYKQESLGSTTEGKETLQSFVTDITAKTAGKALSLVVVDMEKYFR-------------------------------VS 131
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
2ZIU_B      176 RVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFKKLR 223
Cdd:cd20081 132 RVDVEEALVDLQLHTGVQVQFLETWKEFADFICMFTKAVAEAPFKKLR 179
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
43-210 1.27e-04

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: 41.65  E-value: 1.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B         43 ALQTMECRCVIEAQAVPCSVtWRRRAGPSEDredwveEPTVLVLLRAEAFVSMIDNGKQGSLDStmkgketlqgfvtDIT 122
Cdd:pfam02732  14 LLEELGVEVVVETLPVGDYL-WVPREYDLEL------EVVLDVIVERKSLDDLVSSIIDGRLFE-------------QKS 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B        123 AKTAGKALSLVIVDQEKCFSAQNPPRRgkqgankqtkkqqqrqpeasigSMVSRVDAEEALVDLQLHTEAQAQIVQSWKE 202
Cdd:pfam02732  74 RLKRGYKKPILLVEGLDLFSRKLKNKR----------------------RDINPNAIEGALASLQVDYGVRIIRTRSAEE 131

                  ....*...
2ZIU_B        203 LADFTCAF 210
Cdd:pfam02732 132 TAEWLASL 139
 
Name Accession Description Interval E-value
XPF_nuclease_EME1 cd20081
XPF-like nuclease domain of crossover junction endonuclease EME1; EME1, also called MMS4 ...
17-223 3.95e-104

XPF-like nuclease domain of crossover junction endonuclease EME1; EME1, also called MMS4 homolog (hMMS4), interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Its typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. EME1 may be required in mitosis for the processing of stalled or collapsed replication forks. The nuclease domain of EME1 is a nuclease-like domain which is involved in targeting the MUS81-EME1 heterodimer complex to DNA.


Pssm-ID: 410857  Cd Length: 179  Bit Score: 302.83  E-value: 3.95e-104
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       17 EECLKHIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRAGPSE-DREDWVEEPTVLVLLRAEAFVSM 95
Cdd:cd20081   3 EECLKHIVVVLDPGLLQMEGGGQLLSALQAMECSCVIEAQAIPRSVTWRRRAAPSQvDEEDWVEEPTVLVLLPAEEFVSM 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       96 IDNGKQGSLDSTMKGKETLQGFVTDITAKTAGKALSLVIVDQEKCFSaqnpprrgkqgankqtkkqqqrqpeasigsmVS 175
Cdd:cd20081  83 VHNYKQESLGSTTEGKETLQSFVTDITAKTAGKALSLVVVDMEKYFR-------------------------------VS 131
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
2ZIU_B      176 RVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFKKLR 223
Cdd:cd20081 132 RVDVEEALVDLQLHTGVQVQFLETWKEFADFICMFTKAVAEAPFKKLR 179
XPF_nuclease_EME-like cd20080
XPF-like nuclease domain of the family of Essential Meiotic Endonucleases (EMEs) and similar ...
22-220 2.74e-87

XPF-like nuclease domain of the family of Essential Meiotic Endonucleases (EMEs) and similar proteins; The family of EMEs includes EME1 and EME2. EME1, also called MMS4 homolog (hMMS4), interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Its typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. EME1 may be required in mitosis for the processing of stalled or collapsed replication forks. EME2 interacts with MUS81 to form a DNA structure-specific endonuclease which cleaves substrates such as 3'-flap structures. MUS81-EME2 is responsible for fork cleavage and restart in human cells. The MUS81-EME2 protein, whose actions are restricted to S phase, is also responsible for telomere maintenance in telomerase-negative ALT (Alternative Lengthening of Telomeres) cells. The nuclease domain of EMEs is a nuclease-like domain which is involved in targeting the MUS81-EME heterodimer complex to DNA. The family also includes budding yeast Mms4 (also known as Eme1 in other organisms), a putative transcriptional (co)activator that protects Saccharomyces cerevisiae cells from endogenous and environmental DNA damage. It interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. The nuclease domain of Mms4 lacks the catalytic motif.


Pssm-ID: 410856  Cd Length: 164  Bit Score: 259.63  E-value: 2.74e-87
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       22 HIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRAGPSEDREDWVEEPTVLVLLRAEAFVSMIDNGKQ 101
Cdd:cd20080   1 HIIVVLDPVLLQLEGGGQLLGALQTAECRCVIEAQAVPCSVTWRRRAGPSEDREDWVEEPTVLVLLRAEAFVSYIDNGKQ 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B      102 GSLDSTMKGKETLQGFVTDITAKTAGKALSLVIVDQEKCfsaqnpprrgkqgankqtkkqqqrqpeasigsmvsRVDAEE 181
Cdd:cd20080  81 GSLDSTMKGKETLQGFVTDITAKTAGKALSLVIVDQEKI-----------------------------------RVDAEE 125
                       170       180       190
                ....*....|....*....|....*....|....*....
2ZIU_B      182 ALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFK 220
Cdd:cd20080 126 ALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFK 164
XPF_nuclease_EME cd20083
XPF-like nuclease domain of crossover junction endonucleases, EME1, EME2 and similar proteins; ...
22-220 1.66e-54

XPF-like nuclease domain of crossover junction endonucleases, EME1, EME2 and similar proteins; The Mus81-EME1 complex is a structure-selective endonuclease with a critical role in the resolution of recombination intermediates during DNA repair after interstrand cross-links, replication fork collapse, or double-strand breaks. ERCC4 domain of Eme1 is a nuclease-like domain which is involved in targeting the MUS81-EME1 heterodimer complex to DNA.


Pssm-ID: 410859  Cd Length: 179  Bit Score: 176.32  E-value: 1.66e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       22 HIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRAGP-------SEDREDWVEEPTVLVLLRAEAFVS 94
Cdd:cd20083   1 FIRVVIDPKILEESYGGELLSALQEKGLKYEIESQPIPNSITWTRNVPEdtvadneVALEESEEDEPYVLLILSAEEFVK 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       95 MIDNGkqgsldstmkgkeTLQGFVTDITAKTAGKALSLVIVDQEKCFSAQNPPRRGKQgankqtkkqqqrqpEASIGSMV 174
Cdd:cd20083  81 MVKNG-------------TLLDHISSVKSLFPNYPITLVIYGLNKYKRYHKKKEQSKK--------------KKKNLKNV 133
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*.
2ZIU_B      175 SRVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFK 220
Cdd:cd20083 134 SRPPVEEALIELQLHAKCSSRLCETEAELALHVAQLTKAIAEAPYK 179
XPF_nuclease_EME2 cd20082
XPF-like nuclease domain of crossover junction endonuclease EME2; EME2 interacts with MUS81 to ...
17-220 1.21e-37

XPF-like nuclease domain of crossover junction endonuclease EME2; EME2 interacts with MUS81 to form a DNA structure-specific endonuclease which cleaves substrates such as 3'-flap structures. MUS81-EME2 is responsible for fork cleavage and restart in human cells. The MUS81-EME2 protein, whose actions are restricted to S phase, is also responsible for telomere maintenance in telomerase-negative ALT (Alternative Lengthening of Telomeres) cells. The nuclease domain of EME2 is a nuclease-like domain which is involved in targeting the MUS81-EME2 heterodimer complex to DNA.


Pssm-ID: 410858  Cd Length: 195  Bit Score: 133.22  E-value: 1.21e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       17 EECLKHIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRA-GPSEDREDW-VEEPTVLVLLRAEAFVS 94
Cdd:cd20082   3 EQCLKSLTVCVDPALLQDAGSDVLLEALSSLEWRYSIEPQSLPHSITWRRELpQDEPCCEAGtVEEDQVLMVLEPNEFLD 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       95 MIDNGKQGSL-DSTMKGKETLQGFVTDITAKTAGKALSLVIV--DQEKCFSAQNPPRRGKQGANKQtkkqqqrqpeasig 171
Cdd:cd20082  83 MVASLKQVPNgDGSSGEMESLLGPLFEYLNKDPTKVVTLLVIglDAYSWSNQLSGQKQKQLGSELG-------------- 148
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*....
2ZIU_B      172 smVSRVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFK 220
Cdd:cd20082 149 --MTDLDIEEALVFLQLHKNVSVLFLESWQELTDHVCAVTKALSKRPFK 195
XPF_nuclease-like cd19940
nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap ...
24-212 1.09e-25

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: 99.76  E-value: 1.09e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       24 IVVLDPVLLqmegGGQLLGALQTMECRCVIEAQAvPCSVTWRRRagpsedredwveepTVLVLLRAEAFVSMIDNGKqgs 103
Cdd:cd19940   1 SIVVDPRER----RSELLSELQRLGVQVEFEDLA-VGDYVLSNR--------------TCVERKSLSDLVSSINKGR--- 58
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B      104 ldstmkgketLQGFVTDITAKtaGKALSLVIVDQEKCFsaqnpprrgkqgankqtkkqqqrqpeasiGSMVSRVDAEEAL 183
Cdd:cd19940  59 ----------LREQLQRLTRK--FERRVLLVEKDRSKF-----------------------------RSMVSSVQALSAL 97
                       170       180
                ....*....|....*....|....*....
2ZIU_B      184 VDLQLHTEAQAQIVQSWKELADFTCAFTK 212
Cdd:cd19940  98 TKLQLLTGIRLLIVASPKETADLLEELTQ 126
XPF_nuclease_Mms4 cd20085
XPF-like nuclease domain of Saccharomyces cerevisiae crossover junction endonuclease Mms4 and ...
15-220 8.52e-10

XPF-like nuclease domain of Saccharomyces cerevisiae crossover junction endonuclease Mms4 and similar proteins; Budding yeast Mms4, also known as Eme1 in other organisms, is a putative transcriptional (co)activator that protects Saccharomyces cerevisiae cells from endogenous and environmental DNA damage. It interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Typical substrates include 3'-flap structures, D-loops, replication forks with regressed leading strands and nicked Holliday junctions. The nuclease domain of Mms4 lacks the catalytic motif.


Pssm-ID: 410860  Cd Length: 220  Bit Score: 57.99  E-value: 8.52e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       15 NSEECLKHIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRR--------AG---PSEDREdwVEEPTV 83
Cdd:cd20085  10 DKEESTPEMIVDIPSSLLSSSLGSQLEELLKPLGVEHSTWDSPVPNIIRWRRKvtaeyddeLDhwePIPERI--EEEKHV 87
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B       84 LVLLRAEAFVSMIdngkqgsldstmKGKETLQGFVTDITAKTAGKALSLVIVD-----------QEKCFSAQnppRRGKQ 152
Cdd:cd20085  88 LLYLTAKEFVELA------------LGGNDLDSHVSKIKSLFPGKKVIYLIEGltawlrknknlRNRQFAAA---VRSQL 152
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
2ZIU_B      153 GANKQTKKQQQRQPEASIGSMVSRVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFK 220
Cdd:cd20085 153 SGSETSSRSAKSKKKALSAEYIDEDDIEDALLRLQVEHNVLIHHTNSPLETAEWIANFTQHISTIPYK 220
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
43-210 1.27e-04

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: 41.65  E-value: 1.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B         43 ALQTMECRCVIEAQAVPCSVtWRRRAGPSEDredwveEPTVLVLLRAEAFVSMIDNGKQGSLDStmkgketlqgfvtDIT 122
Cdd:pfam02732  14 LLEELGVEVVVETLPVGDYL-WVPREYDLEL------EVVLDVIVERKSLDDLVSSIIDGRLFE-------------QKS 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2ZIU_B        123 AKTAGKALSLVIVDQEKCFSAQNPPRRgkqgankqtkkqqqrqpeasigSMVSRVDAEEALVDLQLHTEAQAQIVQSWKE 202
Cdd:pfam02732  74 RLKRGYKKPILLVEGLDLFSRKLKNKR----------------------RDINPNAIEGALASLQVDYGVRIIRTRSAEE 131

                  ....*...
2ZIU_B        203 LADFTCAF 210
Cdd:pfam02732 132 TAEWLASL 139
 
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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