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Conserved domains on  [gi|260764007|ref|NP_689676|]
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crossover junction endonuclease EME1 isoform 2 [Homo sapiens]

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 ...
 244-452 1.42e-103

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: 309.76  E-value: 1.42e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 244 RPEECLKHIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRAGPSE-DREDWVEEPTVLVLLRAEAFV 322
Cdd:cd20081    1 RPEECLKHIVVVLDPGLLQMEGGGQLLSALQAMECSCVIEAQAIPRSVTWRRRAAPSQvDEEDWVEEPTVLVLLPAEEFV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 323 SMIDNGKQGSLDSTMKGKETLQGFVTDITAKTAGKALSLVIVDQEKCFSaqnpprrgkqgankqtkkqqqrqpeasigsm 402
Cdd:cd20081   81 SMVHNYKQESLGSTTEGKETLQSFVTDITAKTAGKALSLVVVDMEKYFR------------------------------- 129

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 260764007 403 VSRVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFKKLR 452
Cdd:cd20081  130 VSRVDVEEALVDLQLHTGVQVQFLETWKEFADFICMFTKAVAEAPFKKLR 179
 
Name Accession Description Interval E-value
XPF_nuclease_EME1 cd20081
XPF-like nuclease domain of crossover junction endonuclease EME1; EME1, also called MMS4 ...
 244-452 1.42e-103

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: 309.76  E-value: 1.42e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 244 RPEECLKHIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRAGPSE-DREDWVEEPTVLVLLRAEAFV 322
Cdd:cd20081    1 RPEECLKHIVVVLDPGLLQMEGGGQLLSALQAMECSCVIEAQAIPRSVTWRRRAAPSQvDEEDWVEEPTVLVLLPAEEFV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 323 SMIDNGKQGSLDSTMKGKETLQGFVTDITAKTAGKALSLVIVDQEKCFSaqnpprrgkqgankqtkkqqqrqpeasigsm 402
Cdd:cd20081   81 SMVHNYKQESLGSTTEGKETLQSFVTDITAKTAGKALSLVVVDMEKYFR------------------------------- 129

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 260764007 403 VSRVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFKKLR 452
Cdd:cd20081  130 VSRVDVEEALVDLQLHTGVQVQFLETWKEFADFICMFTKAVAEAPFKKLR 179
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
 272-439 1.48e-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: 42.03  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007  272 ALQTMECRCVIEAQAVPCSVtWRRRAGPSEDredwveEPTVLVLLRAEAFVSMIDNGKQGSLDStmkgketlqgfvtDIT 351
Cdd:pfam02732  14 LLEELGVEVVVETLPVGDYL-WVPREYDLEL------EVVLDVIVERKSLDDLVSSIIDGRLFE-------------QKS 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007  352 AKTAGKALSLVIVDQEKCFSAQNPPRRgkqgankqtkkqqqrqpeasigSMVSRVDAEEALVDLQLHTEAQAQIVQSWKE 431
Cdd:pfam02732  74 RLKRGYKKPILLVEGLDLFSRKLKNKR----------------------RDINPNAIEGALASLQVDYGVRIIRTRSAEE 131


                  ....*...
gi 260764007  432 LADFTCAF 439
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 ...
 244-452 1.42e-103

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: 309.76  E-value: 1.42e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 244 RPEECLKHIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRAGPSE-DREDWVEEPTVLVLLRAEAFV 322
Cdd:cd20081    1 RPEECLKHIVVVLDPGLLQMEGGGQLLSALQAMECSCVIEAQAIPRSVTWRRRAAPSQvDEEDWVEEPTVLVLLPAEEFV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 323 SMIDNGKQGSLDSTMKGKETLQGFVTDITAKTAGKALSLVIVDQEKCFSaqnpprrgkqgankqtkkqqqrqpeasigsm 402
Cdd:cd20081   81 SMVHNYKQESLGSTTEGKETLQSFVTDITAKTAGKALSLVVVDMEKYFR------------------------------- 129

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 260764007 403 VSRVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFKKLR 452
Cdd:cd20081  130 VSRVDVEEALVDLQLHTGVQVQFLETWKEFADFICMFTKAVAEAPFKKLR 179
XPF_nuclease_EME-like cd20080
XPF-like nuclease domain of the family of Essential Meiotic Endonucleases (EMEs) and similar ...
 251-449 6.71e-84

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: 258.47  E-value: 6.71e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 251 HIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRAGPSEDREDWVEEPTVLVLLRAEAFVSMIDNGKQ 330
Cdd:cd20080    1 HIIVVLDPVLLQLEGGGQLLGALQTAECRCVIEAQAVPCSVTWRRRAGPSEDREDWVEEPTVLVLLRAEAFVSYIDNGKQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 331 GSLDSTMKGKETLQGFVTDITAKTAGKALSLVIVDQEKCfsaqnpprrgkqgankqtkkqqqrqpeasigsmvsRVDAEE 410
Cdd:cd20080   81 GSLDSTMKGKETLQGFVTDITAKTAGKALSLVIVDQEKI-----------------------------------RVDAEE 125

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 260764007 411 ALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFK 449
Cdd:cd20080  126 ALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFK 164
XPF_nuclease_EME cd20083
XPF-like nuclease domain of crossover junction endonucleases, EME1, EME2 and similar proteins; ...
 251-449 4.25e-52

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: 175.94  E-value: 4.25e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 251 HIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRR-------RAGPSEDREDWVEEPTVLVLLRAEAFVS 323
Cdd:cd20083    1 FIRVVIDPKILEESYGGELLSALQEKGLKYEIESQPIPNSITWTRnvpedtvADNEVALEESEEDEPYVLLILSAEEFVK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 324 MIDNGkqgsldstmkgkeTLQGFVTDITAKTAGKALSLVIVDQEKCFSAQNPPRRGKQgankqtkkqqqrqpEASIGSMV 403
Cdd:cd20083   81 MVKNG-------------TLLDHISSVKSLFPNYPITLVIYGLNKYKRYHKKKEQSKK--------------KKKNLKNV 133

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 260764007 404 SRVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFK 449
Cdd:cd20083  134 SRPPVEEALIELQLHAKCSSRLCETEAELALHVAQLTKAIAEAPYK 179
XPF_nuclease_EME2 cd20082
XPF-like nuclease domain of crossover junction endonuclease EME2; EME2 interacts with MUS81 to ...
 244-449 5.39e-38

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: 138.62  E-value: 5.39e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 244 RPEECLKHIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRRA-GPSEDREDW-VEEPTVLVLLRAEAF 321
Cdd:cd20082    1 RPEQCLKSLTVCVDPALLQDAGSDVLLEALSSLEWRYSIEPQSLPHSITWRRELpQDEPCCEAGtVEEDQVLMVLEPNEF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 322 VSMIDNGKQGSL-DSTMKGKETLQGFVTDITAKTAGKALSLVIV--DQEKCFSAQNPPRRGKQGANKQtkkqqqrqpeas 398
Cdd:cd20082   81 LDMVASLKQVPNgDGSSGEMESLLGPLFEYLNKDPTKVVTLLVIglDAYSWSNQLSGQKQKQLGSELG------------ 148

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 260764007 399 igsmVSRVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFK 449
Cdd:cd20082  149 ----MTDLDIEEALVFLQLHKNVSVLFLESWQELTDHVCAVTKALSKRPFK 195
XPF_nuclease-like cd19940
nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap ...
 253-441 4.50e-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: 100.53  E-value: 4.50e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 253 IVVLDPVLLqmegGGQLLGALQTMECRCVIEAQAvPCSVTWRRRagpsedredwveepTVLVLLRAEAFVSMIDNGKqgs 332
Cdd:cd19940    1 SIVVDPRER----RSELLSELQRLGVQVEFEDLA-VGDYVLSNR--------------TCVERKSLSDLVSSINKGR--- 58

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 333 ldstmkgketLQGFVTDITAKtaGKALSLVIVDQEKCFsaqnpprrgkqgankqtkkqqqrqpeasiGSMVSRVDAEEAL 412
Cdd:cd19940   59 ----------LREQLQRLTRK--FERRVLLVEKDRSKF-----------------------------RSMVSSVQALSAL 97

                        170       180
                 ....*....|....*....|....*....
gi 260764007 413 VDLQLHTEAQAQIVQSWKELADFTCAFTK 441
Cdd:cd19940   98 TKLQLLTGIRLLIVASPKETADLLEELTQ 126
XPF_nuclease_Mms4 cd20085
XPF-like nuclease domain of Saccharomyces cerevisiae crossover junction endonuclease Mms4 and ...
 246-449 2.02e-09

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: 2.02e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 246 EECLKHIIVVLDPVLLQMEGGGQLLGALQTMECRCVIEAQAVPCSVTWRRR--------AG---PSEDREdwVEEPTVLV 314
Cdd:cd20085   12 EESTPEMIVDIPSSLLSSSLGSQLEELLKPLGVEHSTWDSPVPNIIRWRRKvtaeyddeLDhwePIPERI--EEEKHVLL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007 315 LLRAEAFVSMIdngkqgsldstmKGKETLQGFVTDITAKTAGKALSLVIVD-----------QEKCFSAQnppRRGKQGA 383
Cdd:cd20085   90 YLTAKEFVELA------------LGGNDLDSHVSKIKSLFPGKKVIYLIEGltawlrknknlRNRQFAAA---VRSQLSG 154

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 260764007 384 NKQTKKQQQRQPEASIGSMVSRVDAEEALVDLQLHTEAQAQIVQSWKELADFTCAFTKAVAEAPFK 449
Cdd:cd20085  155 SETSSRSAKSKKKALSAEYIDEDDIEDALLRLQVEHNVLIHHTNSPLETAEWIANFTQHISTIPYK 220
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
 272-439 1.48e-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: 42.03  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007  272 ALQTMECRCVIEAQAVPCSVtWRRRAGPSEDredwveEPTVLVLLRAEAFVSMIDNGKQGSLDStmkgketlqgfvtDIT 351
Cdd:pfam02732  14 LLEELGVEVVVETLPVGDYL-WVPREYDLEL------EVVLDVIVERKSLDDLVSSIIDGRLFE-------------QKS 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260764007  352 AKTAGKALSLVIVDQEKCFSAQNPPRRgkqgankqtkkqqqrqpeasigSMVSRVDAEEALVDLQLHTEAQAQIVQSWKE 431
Cdd:pfam02732  74 RLKRGYKKPILLVEGLDLFSRKLKNKR----------------------RDINPNAIEGALASLQVDYGVRIIRTRSAEE 131


                  ....*...
gi 260764007  432 LADFTCAF 439
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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