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Conserved domains on  [gi|880818269|ref|WP_048665974|]
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MULTISPECIES: exonuclease SbcCD subunit D [Enterobacteriaceae]

Protein Classification

metallophosphoesterase family protein( domain architecture ID 11417965)

metallophosphoesterase family protein may contain an active site consisting of two metal ions (usually manganese, iron, or zinc), such as exonuclease SbcCD subunit D is a component of SbcCD, which is involved in double-strand DNA break detection and repair by homologous recombination and non-homologous end joining of damaged DNA

CATH:  3.60.21.10
EC:  3.1.-.-
Gene Ontology:  GO:0042578|GO:0046872|GO:0003677
PubMed:  25837850|8003970
SCOP:  3001067

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
54-208 8.55e-13

DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];


:

Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 67.25  E-value: 8.55e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269  54 LVAGDTFHvRGAISPSVLHFVTETYEWIiKELGLEVVMLAGNHdletnDSVYSANAAASL-RSIGVEIVCGK--RPHSIK 130
Cdd:COG0420   44 LIAGDLFD-SANPSPEAVRLLAEALRRL-SEAGIPVVLIAGNH-----DSPSRLSAGSPLlENLGVHVFGSVepEPVELE 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269 131 MG-DVTVHLISWRNNHAE--LISDLKTLRSGLDGDNHDVVV-HTSINKAIPTMPDVG--IDAQELKDIGFRLLLSGHYHN 204
Cdd:COG0420  117 DGlGVAVYGLPYLRPSDEeaLRDLLERLPRALDPGGPNILLlHGFVAGASGSRDIYVapVPLSALPAAGFDYVALGHIHR 196


                 ....
gi 880818269 205 HKEV 208
Cdd:COG0420  197 PQVL 200
 
Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
54-208 8.55e-13

DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 67.25  E-value: 8.55e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269  54 LVAGDTFHvRGAISPSVLHFVTETYEWIiKELGLEVVMLAGNHdletnDSVYSANAAASL-RSIGVEIVCGK--RPHSIK 130
Cdd:COG0420   44 LIAGDLFD-SANPSPEAVRLLAEALRRL-SEAGIPVVLIAGNH-----DSPSRLSAGSPLlENLGVHVFGSVepEPVELE 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269 131 MG-DVTVHLISWRNNHAE--LISDLKTLRSGLDGDNHDVVV-HTSINKAIPTMPDVG--IDAQELKDIGFRLLLSGHYHN 204
Cdd:COG0420  117 DGlGVAVYGLPYLRPSDEeaLRDLLERLPRALDPGGPNILLlHGFVAGASGSRDIYVapVPLSALPAAGFDYVALGHIHR 196


                 ....
gi 880818269 205 HKEV 208
Cdd:COG0420  197 PQVL 200
47 PHA02546
endonuclease subunit; Provisional
 56-288 1.65e-09

endonuclease subunit; Provisional


Pssm-ID: 222867 [Multi-domain]  Cd Length: 340  Bit Score: 58.47  E-value: 1.65e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269  56 AGDTFHVRGAISPSVLHFVTETYEWIIKELGLEVVMLAGNHDLETNDSVySANAAASLRSIGVEIVCGKRPHSIKMGDVT 135
Cdd:PHA02546  46 LGDTFDVRKAITQNTMNFVREKIFDLLKEAGITLHVLVGNHDMYYKNTI-RPNAPTELLGQYDNITVIDEPTTVDFDGCS 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269 136 VHLISWRN--NHAELISDLKTLRSgldgdnhDVVV-HTSIN--KAIPTMP-DVGIDAQELKDigFRLLLSGHYHnHKEVL 209
Cdd:PHA02546 125 IDLIPWICkeNTEEILEFIKNSKS-------EYCVgHWELNgfYFYKGMKsDHGLDPDFLKK--YKQVWSGHFH-TISEK 194

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269 210 PGVVSIGALTHQNWGDVGSLAGF-----------MIVNPdgtFTHHE-TSAPKFvnleDDVEDDQIRGNYVRFrAVVESD 277
Cdd:PHA02546 195 GNVTYIGTPYTLTAGDENDPRGFwvfdtethkleFIANP---TTWHRrITYPDY----DKIDIKDFKGKSVRL-IVTEVD 266

                        250
                 ....*....|.
gi 880818269 278 EEGIKIQNVLK 288
Cdd:PHA02546 267 DDLTKFESELE 277
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 52-207 2.75e-07

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: 50.35  E-value: 2.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269  52 YMLVAGDTFHVRgAISPSVLHFVTETYEwIIKELGLEVVMLAGNHDletndsvysanaaaSLRSigveivcgkrphsikm 131
Cdd:cd00840   42 FVLIAGDLFDSN-NPSPEALKLAIEGLR-RLCEAGIPVFVIAGNHD--------------SPAR---------------- 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 880818269 132 gdVTVHLISWRNNH--AELISDLK-TLRSGLDGDNHDVVVHTSINKAIPTMPDVGIDAQELKDIGFRLLLSGHYHNHKE 207
Cdd:cd00840   90 --VAIYGLPYLRDErlERLFEDLElRPRLLKPDWFNILLLHQGVDGAGPSDSERPIVPEDLLPDGFDYVALGHIHKPQI 166
 
Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
54-208 8.55e-13

DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 67.25  E-value: 8.55e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269  54 LVAGDTFHvRGAISPSVLHFVTETYEWIiKELGLEVVMLAGNHdletnDSVYSANAAASL-RSIGVEIVCGK--RPHSIK 130
Cdd:COG0420   44 LIAGDLFD-SANPSPEAVRLLAEALRRL-SEAGIPVVLIAGNH-----DSPSRLSAGSPLlENLGVHVFGSVepEPVELE 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269 131 MG-DVTVHLISWRNNHAE--LISDLKTLRSGLDGDNHDVVV-HTSINKAIPTMPDVG--IDAQELKDIGFRLLLSGHYHN 204
Cdd:COG0420  117 DGlGVAVYGLPYLRPSDEeaLRDLLERLPRALDPGGPNILLlHGFVAGASGSRDIYVapVPLSALPAAGFDYVALGHIHR 196


                 ....
gi 880818269 205 HKEV 208
Cdd:COG0420  197 PQVL 200
47 PHA02546
endonuclease subunit; Provisional
 56-288 1.65e-09

endonuclease subunit; Provisional


Pssm-ID: 222867 [Multi-domain]  Cd Length: 340  Bit Score: 58.47  E-value: 1.65e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269  56 AGDTFHVRGAISPSVLHFVTETYEWIIKELGLEVVMLAGNHDLETNDSVySANAAASLRSIGVEIVCGKRPHSIKMGDVT 135
Cdd:PHA02546  46 LGDTFDVRKAITQNTMNFVREKIFDLLKEAGITLHVLVGNHDMYYKNTI-RPNAPTELLGQYDNITVIDEPTTVDFDGCS 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269 136 VHLISWRN--NHAELISDLKTLRSgldgdnhDVVV-HTSIN--KAIPTMP-DVGIDAQELKDigFRLLLSGHYHnHKEVL 209
Cdd:PHA02546 125 IDLIPWICkeNTEEILEFIKNSKS-------EYCVgHWELNgfYFYKGMKsDHGLDPDFLKK--YKQVWSGHFH-TISEK 194

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269 210 PGVVSIGALTHQNWGDVGSLAGF-----------MIVNPdgtFTHHE-TSAPKFvnleDDVEDDQIRGNYVRFrAVVESD 277
Cdd:PHA02546 195 GNVTYIGTPYTLTAGDENDPRGFwvfdtethkleFIANP---TTWHRrITYPDY----DKIDIKDFKGKSVRL-IVTEVD 266

                        250
                 ....*....|.
gi 880818269 278 EEGIKIQNVLK 288
Cdd:PHA02546 267 DDLTKFESELE 277
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 52-207 2.75e-07

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: 50.35  E-value: 2.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 880818269  52 YMLVAGDTFHVRgAISPSVLHFVTETYEwIIKELGLEVVMLAGNHDletndsvysanaaaSLRSigveivcgkrphsikm 131
Cdd:cd00840   42 FVLIAGDLFDSN-NPSPEALKLAIEGLR-RLCEAGIPVFVIAGNHD--------------SPAR---------------- 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 880818269 132 gdVTVHLISWRNNH--AELISDLK-TLRSGLDGDNHDVVVHTSINKAIPTMPDVGIDAQELKDIGFRLLLSGHYHNHKE 207
Cdd:cd00840   90 --VAIYGLPYLRDErlERLFEDLElRPRLLKPDWFNILLLHQGVDGAGPSDSERPIVPEDLLPDGFDYVALGHIHKPQI 166
 
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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