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Conserved domains on  [gi|530396808|ref|XP_005274065|]
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double-strand break repair protein MRE11 isoform X4 [Homo sapiens]

Protein Classification

double-strand break repair protein MRE11( domain architecture ID 1903556)

double-strand break repair protein MRE11 is a component of the MRN complex, which plays a central role in double-strand break (DSB) repair, DNA recombination, maintenance of telomere integrity and meiosis

CATH:  3.30.110.110|3.60.21.10
EC:  3.1.-.-
Gene Ontology:  GO:0004519|GO:0006302|GO:0030145|GO:0004527|GO:0003690|GO:0005515

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
mre11 super family cl44331
DNA repair protein (mre11); All proteins in this family for which functions are known are ...
 4-246 3.63e-90

DNA repair protein (mre11); All proteins in this family for which functions are known are subunits of a nuclease complex made up of multiple proteins including MRE11 and RAD50 homologs. The functions of this nuclease complex include recombinational repair and non-homolgous end joining. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The proteins in this family are distantly related to proteins in the SbcCD complex of bacteria. [DNA metabolism, DNA replication, recombination, and repair]


The actual alignment was detected with superfamily member TIGR00583:

Pssm-ID: 273153 [Multi-domain]  Cd Length: 405  Bit Score: 282.88  E-value: 3.63e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808    4 EKIDISPVLLQKGSTKIALYGLGSIPDERLYRMFVNKKVTMLRPKEDENSWFNLFVIHQNRSKHGSTNFIPEQFLDDFID 83
Cdd:TIGR00583 151 DNIIVSPILLQKGETKLALYGISNVRDERLVRTFKDNKVSFLRPNAGAEDWFNLLVLHQNHAAHTSTSFLPESFIPDFFD 230

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808   84 LVIWGHEHECKIAPTKNEQQLFYISQPGSSVVTSLSPGEAVKKHVGLLRIKGRKMNMHKIPLHTVRQFFMEDIVLANHPD 163
Cdd:TIGR00583 231 LVIWGHEHECLPDPVYNPSDGFYVLQPGSTVATSLTPGEALPKHVFILNIKGRKFASKPIPLQTVRPFVMKEILLDKVPG 310

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808  164 IFNPDNPKVTQAIQSFCLEKIEEMLE--NAE-RERLGNSH-----QPEKPLVRLRVDYSG---GFEPFSVLRFSQKFVDR 232
Cdd:TIGR00583 311 SRPILKTDNKKETDKRLIDEVEEMINeaNAEwKAKRADGEgdeprEPPLPLIRLKVDYTGpwlNYQVENPKRFSNRFVGR 390

                         250
                  ....*....|....
gi 530396808  233 VANPKDIIHFFRHR 246
Cdd:TIGR00583 391 VANANDVVQFYKNN 404
 
Name Accession Description Interval E-value
mre11 TIGR00583
DNA repair protein (mre11); All proteins in this family for which functions are known are ...
 4-246 3.63e-90

DNA repair protein (mre11); All proteins in this family for which functions are known are subunits of a nuclease complex made up of multiple proteins including MRE11 and RAD50 homologs. The functions of this nuclease complex include recombinational repair and non-homolgous end joining. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The proteins in this family are distantly related to proteins in the SbcCD complex of bacteria. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273153 [Multi-domain]  Cd Length: 405  Bit Score: 282.88  E-value: 3.63e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808    4 EKIDISPVLLQKGSTKIALYGLGSIPDERLYRMFVNKKVTMLRPKEDENSWFNLFVIHQNRSKHGSTNFIPEQFLDDFID 83
Cdd:TIGR00583 151 DNIIVSPILLQKGETKLALYGISNVRDERLVRTFKDNKVSFLRPNAGAEDWFNLLVLHQNHAAHTSTSFLPESFIPDFFD 230

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808   84 LVIWGHEHECKIAPTKNEQQLFYISQPGSSVVTSLSPGEAVKKHVGLLRIKGRKMNMHKIPLHTVRQFFMEDIVLANHPD 163
Cdd:TIGR00583 231 LVIWGHEHECLPDPVYNPSDGFYVLQPGSTVATSLTPGEALPKHVFILNIKGRKFASKPIPLQTVRPFVMKEILLDKVPG 310

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808  164 IFNPDNPKVTQAIQSFCLEKIEEMLE--NAE-RERLGNSH-----QPEKPLVRLRVDYSG---GFEPFSVLRFSQKFVDR 232
Cdd:TIGR00583 311 SRPILKTDNKKETDKRLIDEVEEMINeaNAEwKAKRADGEgdeprEPPLPLIRLKVDYTGpwlNYQVENPKRFSNRFVGR 390

                         250
                  ....*....|....
gi 530396808  233 VANPKDIIHFFRHR 246
Cdd:TIGR00583 391 VANANDVVQFYKNN 404
Mre11_DNA_bind pfam04152
Mre11 DNA-binding presumed domain; The Mre11 complex is a multi-subunit nuclease that is ...
 138-305 1.11e-62

Mre11 DNA-binding presumed domain; The Mre11 complex is a multi-subunit nuclease that is composed of Mre11, Rad50 and Nbs1/Xrs2, and is involved in checkpoint signalling and DNA replication. Mre11 has an intrinsic DNA-binding activity that is stimulated by Rad50 on its own or in combination with Nbs1.


Pssm-ID: 461198  Cd Length: 175  Bit Score: 203.21  E-value: 1.11e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808  138 MNMHKIPLHTVRQFFMEDIVLANHPDIFNPDnPKVTQAIQSFCLEKIEEMLENAERERL--------GNSHQPEKPLVRL 209
Cdd:pfam04152   1 FKLEPIPLKTVRPFVMDEIVLSEVAEIKPPD-PDDKEEVTKFLREKVEELIEEAKEEWLereaddeeGEPEQPPLPLIRL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808  210 RVDYSGGFEPFSVLRFSQKFVDRVANPKDIIHFFRHREQKEKTGEEINFGK----LITKPSEGTTLRVEDLVKQYFQTAe 285
Cdd:pfam04152  80 RVEYTGGFEVENPQRFGQRFVGRVANPNDVVQFYRKKKARRKKKKDKAADGedeeLLDEPEKLDELRVEDLVKEYLAAQ- 158

                         170       180
                  ....*....|....*....|
gi 530396808  286 knvQLSLLTERGMGEAVQEF 305
Cdd:pfam04152 159 ---QLTLLPENGLGEAVEQF 175
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 17-119 1.81e-27

Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia coli) is a subunit of the MRX protein complex. This complex includes: Mre11, Rad50, and Xrs2/Nbs1, and plays a vital role in several nuclear processes including DNA double-strand break repair, telomere length maintenance, cell cycle checkpoint control, and meiotic recombination, in eukaryotes. During double-strand break repair, the MRX complex is required to hold the two ends of a broken chromosome together. In vitro studies show that Mre11 has 3'-5' exonuclease activity on dsDNA templates and endonuclease activity on dsDNA and ssDNA templates. In addition to the N-terminal phosphatase domain, the eukaryotic MRE11 members of this family have a C-terminal DNA binding domain (not included in this alignment model). MRE11-like proteins are found in prokaryotes and archaea was well as in eukaryotes. Mre11 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277319 [Multi-domain]  Cd Length: 186  Bit Score: 108.90  E-value: 1.81e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808  17 STKIALYGLGSIPDERLYRMFVNKKvtmLRPKEDENSWFNLFVIHQNRSKHGSTN----FIPEQFLDDFIDLVIWGHEHE 92
Cdd:cd00840   87 PARVAIYGLPYLRDERLERLFEDLE---LRPRLLKPDWFNILLLHQGVDGAGPSDserpIVPEDLLPDGFDYVALGHIHK 163

                         90       100
                 ....*....|....*....|....*..
gi 530396808  93 CKIaptkNEQQLFYISQPGSSVVTSLS 119
Cdd:cd00840  164 PQI----IEGGGPPIVYPGSPEPTSFS 186
 
Name Accession Description Interval E-value
mre11 TIGR00583
DNA repair protein (mre11); All proteins in this family for which functions are known are ...
 4-246 3.63e-90

DNA repair protein (mre11); All proteins in this family for which functions are known are subunits of a nuclease complex made up of multiple proteins including MRE11 and RAD50 homologs. The functions of this nuclease complex include recombinational repair and non-homolgous end joining. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The proteins in this family are distantly related to proteins in the SbcCD complex of bacteria. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273153 [Multi-domain]  Cd Length: 405  Bit Score: 282.88  E-value: 3.63e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808    4 EKIDISPVLLQKGSTKIALYGLGSIPDERLYRMFVNKKVTMLRPKEDENSWFNLFVIHQNRSKHGSTNFIPEQFLDDFID 83
Cdd:TIGR00583 151 DNIIVSPILLQKGETKLALYGISNVRDERLVRTFKDNKVSFLRPNAGAEDWFNLLVLHQNHAAHTSTSFLPESFIPDFFD 230

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808   84 LVIWGHEHECKIAPTKNEQQLFYISQPGSSVVTSLSPGEAVKKHVGLLRIKGRKMNMHKIPLHTVRQFFMEDIVLANHPD 163
Cdd:TIGR00583 231 LVIWGHEHECLPDPVYNPSDGFYVLQPGSTVATSLTPGEALPKHVFILNIKGRKFASKPIPLQTVRPFVMKEILLDKVPG 310

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808  164 IFNPDNPKVTQAIQSFCLEKIEEMLE--NAE-RERLGNSH-----QPEKPLVRLRVDYSG---GFEPFSVLRFSQKFVDR 232
Cdd:TIGR00583 311 SRPILKTDNKKETDKRLIDEVEEMINeaNAEwKAKRADGEgdeprEPPLPLIRLKVDYTGpwlNYQVENPKRFSNRFVGR 390

                         250
                  ....*....|....
gi 530396808  233 VANPKDIIHFFRHR 246
Cdd:TIGR00583 391 VANANDVVQFYKNN 404
Mre11_DNA_bind pfam04152
Mre11 DNA-binding presumed domain; The Mre11 complex is a multi-subunit nuclease that is ...
 138-305 1.11e-62

Mre11 DNA-binding presumed domain; The Mre11 complex is a multi-subunit nuclease that is composed of Mre11, Rad50 and Nbs1/Xrs2, and is involved in checkpoint signalling and DNA replication. Mre11 has an intrinsic DNA-binding activity that is stimulated by Rad50 on its own or in combination with Nbs1.


Pssm-ID: 461198  Cd Length: 175  Bit Score: 203.21  E-value: 1.11e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808  138 MNMHKIPLHTVRQFFMEDIVLANHPDIFNPDnPKVTQAIQSFCLEKIEEMLENAERERL--------GNSHQPEKPLVRL 209
Cdd:pfam04152   1 FKLEPIPLKTVRPFVMDEIVLSEVAEIKPPD-PDDKEEVTKFLREKVEELIEEAKEEWLereaddeeGEPEQPPLPLIRL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808  210 RVDYSGGFEPFSVLRFSQKFVDRVANPKDIIHFFRHREQKEKTGEEINFGK----LITKPSEGTTLRVEDLVKQYFQTAe 285
Cdd:pfam04152  80 RVEYTGGFEVENPQRFGQRFVGRVANPNDVVQFYRKKKARRKKKKDKAADGedeeLLDEPEKLDELRVEDLVKEYLAAQ- 158

                         170       180
                  ....*....|....*....|
gi 530396808  286 knvQLSLLTERGMGEAVQEF 305
Cdd:pfam04152 159 ---QLTLLPENGLGEAVEQF 175
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 17-119 1.81e-27

Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia coli) is a subunit of the MRX protein complex. This complex includes: Mre11, Rad50, and Xrs2/Nbs1, and plays a vital role in several nuclear processes including DNA double-strand break repair, telomere length maintenance, cell cycle checkpoint control, and meiotic recombination, in eukaryotes. During double-strand break repair, the MRX complex is required to hold the two ends of a broken chromosome together. In vitro studies show that Mre11 has 3'-5' exonuclease activity on dsDNA templates and endonuclease activity on dsDNA and ssDNA templates. In addition to the N-terminal phosphatase domain, the eukaryotic MRE11 members of this family have a C-terminal DNA binding domain (not included in this alignment model). MRE11-like proteins are found in prokaryotes and archaea was well as in eukaryotes. Mre11 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277319 [Multi-domain]  Cd Length: 186  Bit Score: 108.90  E-value: 1.81e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530396808  17 STKIALYGLGSIPDERLYRMFVNKKvtmLRPKEDENSWFNLFVIHQNRSKHGSTN----FIPEQFLDDFIDLVIWGHEHE 92
Cdd:cd00840   87 PARVAIYGLPYLRDERLERLFEDLE---LRPRLLKPDWFNILLLHQGVDGAGPSDserpIVPEDLLPDGFDYVALGHIHK 163

                         90       100
                 ....*....|....*....|....*..
gi 530396808  93 CKIaptkNEQQLFYISQPGSSVVTSLS 119
Cdd:cd00840  164 PQI----IEGGGPPIVYPGSPEPTSFS 186
 
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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