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Conserved domains on  [gi|664281569|ref|WP_030811703|]
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MULTISPECIES: exonuclease SbcCD subunit D [Streptomyces]

Protein Classification

exonuclease SbcCD subunit D( domain architecture ID 11417993)

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|3.30.160.210
Gene Ontology:  GO:0003677|GO:0004529|GO:0006281|GO:0004519|GO:0006310
PubMed:  9653124|24531464

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];
1-271 1.17e-80

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


:

Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 247.52  E-value: 1.17e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   1 MRLLHTSDWHLGRSFHRVSLLDAQAAYLDHLVATVEEREVDAVLVAGDVYDRAVPPLTAVELFDRALHRLAAVGVPTVMI 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLSEAGIPVVLI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  81 SGNHDSARRLGVGAGLFERAGIHLRTDPEgcATPVVLaDDHGDVAFYGLPYLEPAlvkdvlgagkagHEAVLTAAMDRVR 160
Cdd:COG0420   81 AGNHDSPSRLSAGSPLLENLGVHVFGSVE--PEPVEL-EDGLGVAVYGLPYLRPS------------DEEALRDLLERLP 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569 161 ADLAtrpAETRSVVLAHAFVAGGEPSdseRDITvggVAAVPAGVF--DGVDYAALGHLHGSQRV--TARVRYSGSPLAYS 236
Cdd:COG0420  146 RALD---PGGPNILLLHGFVAGASGS---RDIY---VAPVPLSALpaAGFDYVALGHIHRPQVLggDPRIRYSGSPEPRS 216

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 664281569 237 FSEAdHRKTMWLIDLDADGCIAAeERIDCPVERPL 271
Cdd:COG0420  217 FSEA-GGKGVLLVELDAGGLVSV-EFVPLPATRRF 249
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 269-358 5.69e-11

Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and archaea. This domain is about 90 amino acids in length. This domain is found associated with pfam00149. SbcD works in complex with SbdC (SbcDC) which is a transcription regulator. It down-regulates transcription of arl and mgr to inhibit type 5 capsule protein production. It acts as part of the SOS pathway of bacteria.


:

Pssm-ID: 463533  Cd Length: 100  Bit Score: 58.85  E-value: 5.69e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  269 RPLARLRGRLDTLLEDPAL----DRHEHAWVEATLTDPVRPADPMARLARRFPHT----LSLVFDPERPPDDPGASYAQR 340
Cdd:pfam12320   3 RDLRRIKGSLEELLAALAYleeePADREDYLEVELTDEEPIPDLMERLREAYPNIpvelLRIRRTREERQAEEEEEAAED 82

                          90
                  ....*....|....*...
gi 664281569  341 LKGRDDHQIAEDFVAHVR 358
Cdd:pfam12320  83 LEELSPLELFERFYEEQT 100
 
Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
1-271 1.17e-80

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


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 247.52  E-value: 1.17e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   1 MRLLHTSDWHLGRSFHRVSLLDAQAAYLDHLVATVEEREVDAVLVAGDVYDRAVPPLTAVELFDRALHRLAAVGVPTVMI 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLSEAGIPVVLI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  81 SGNHDSARRLGVGAGLFERAGIHLRTDPEgcATPVVLaDDHGDVAFYGLPYLEPAlvkdvlgagkagHEAVLTAAMDRVR 160
Cdd:COG0420   81 AGNHDSPSRLSAGSPLLENLGVHVFGSVE--PEPVEL-EDGLGVAVYGLPYLRPS------------DEEALRDLLERLP 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569 161 ADLAtrpAETRSVVLAHAFVAGGEPSdseRDITvggVAAVPAGVF--DGVDYAALGHLHGSQRV--TARVRYSGSPLAYS 236
Cdd:COG0420  146 RALD---PGGPNILLLHGFVAGASGS---RDIY---VAPVPLSALpaAGFDYVALGHIHRPQVLggDPRIRYSGSPEPRS 216

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 664281569 237 FSEAdHRKTMWLIDLDADGCIAAeERIDCPVERPL 271
Cdd:COG0420  217 FSEA-GGKGVLLVELDAGGLVSV-EFVPLPATRRF 249
sbcd TIGR00619
exonuclease SbcD; All proteins in this family for which functions are known are ...
 1-244 4.60e-54

exonuclease SbcD; All proteins in this family for which functions are known are double-stranded DNA exonuclease (as part of a complex with SbcC homologs). This complex functions in the initiation of recombination and recombinational repair and is particularly important in regulating the stability of DNA sections that can form secondary structures. This family is likely homologous to the MRE11 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273178 [Multi-domain]  Cd Length: 253  Bit Score: 179.15  E-value: 4.60e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569    1 MRLLHTSDWHLGRSFHRVSLLDAQAAYLDHLVATVEEREVDAVLVAGDVYDRAVPPLTAVELFDRALHRLAAVGV-PTVM 79
Cdd:TIGR00619   1 MRILHTSDWHLGKTLEGVSRLAEQKAFLDDLLEFAKAEQVDALLVAGDVFDTANPPAEAQELFNAFFVNLSDTGIrPIVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   80 ISGNHDSARRLGVGAGLFERAGIHLRTDPEGcATPVVLADDHGDVAFY-------------GLPYLEPALVKDVLGAGKA 146
Cdd:TIGR00619  81 ISGNHDSAQRLSAAKKLLAELGVFVVGSPGH-DPQILLLKDGTNGEGLcvglfllpreailTRAGLDGFGLELLLAHTDV 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  147 GHEAVLTAAMDRVRADLATrpaetrsVVLAHAFVAGGEPSDSERDITVGGVAAVPAGVFDGVDYAALGHLHGSQR--VTA 224
Cdd:TIGR00619 160 KLRQAAEALKLRLDQDLPK-------ILLAHLFTAGATKSDAERRIYIGTLYAFPLQNFPEADYIALGHIHIHKIskGRE 232

                         250       260
                  ....*....|....*....|
gi 664281569  225 RVRYSGSPLAYSFSEADHRK 244
Cdd:TIGR00619 233 RVRYSGSPFPLSFDEAGKDK 252
PRK10966 PRK10966
exonuclease subunit SbcD; Provisional
 1-281 1.07e-48

exonuclease subunit SbcD; Provisional


Pssm-ID: 182871 [Multi-domain]  Cd Length: 407  Bit Score: 169.73  E-value: 1.07e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   1 MRLLHTSDWHLGRSFHRVSLLDAQAAYLDHLVATVEEREVDAVLVAGDVYDRAVPPLTAVELFDRALHRLAAVGVPTVMI 80
Cdd:PRK10966   1 MRILHTSDWHLGQNFYSKSRAAEHQAFLDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCQLVVL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  81 SGNHDSARRLGVGAGLFEragiHLRTDPEGCAT------PVVLADDHGDVA--FYGLPYLEPalvKDVLG--AGKAGHE- 149
Cdd:PRK10966  81 AGNHDSVATLNESRDLLA----FLNTTVIASASddlghqVIILPRRDGTPGavLCAIPFLRP---RDVITsqAGQSGIEk 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569 150 --AVLTAAMDRVR----ADLATRPAETRSV-VLA--HAFVAGGEPSDSERDITVGGVAAVPAGVFDGVDYAALGHLHGSQ 220
Cdd:PRK10966 154 qqALQAAIADHYQqlyqLACELRDELGQPLpIIAtgHLTTVGASKSDSVRDIYIGTLDAFPAQAFPPADYIALGHIHRAQ 233

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 664281569 221 RV--TARVRYSGSPLAYSFSEADHRKTMWLIDLDADGCIAAEErIDCPVERPLARLRGRLDTL 281
Cdd:PRK10966 234 KVggTEHIRYSGSPIPLSFDELGKSKSVHLVEFDQGKLQSVTP-LPVPVFQPMAVLKGDLASI 295
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 2-238 1.74e-45

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: 154.73  E-value: 1.74e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   2 RLLHTSDWHLGRSFHRVS-LLDAQAAYLDHLVATVEEREVDAVLVAGDVYDRAVPPLTAVELFDRALHRLAAVGVPTVMI 80
Cdd:cd00840    1 RFLHTADWHLGYPLYGLSrREEDFFKAFEEIVDLAIEEKVDFVLIAGDLFDSNNPSPEALKLAIEGLRRLCEAGIPVFVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  81 SGNHDSARRlgvgaglferagihlrtdpegcatpvvladdhgdVAFYGLPYLepalvkdvlgagkagHEAVLTAAMDRVR 160
Cdd:cd00840   81 AGNHDSPAR----------------------------------VAIYGLPYL---------------RDERLERLFEDLE 111

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569 161 ADLATRPAETRSVVLAHAFVAGGEPSDSERDITVGGVAavpagvFDGVDYAALGHLHGSQRV---TARVRYSGSPLAYSF 237
Cdd:cd00840  112 LRPRLLKPDWFNILLLHQGVDGAGPSDSERPIVPEDLL------PDGFDYVALGHIHKPQIIeggGPPIVYPGSPEPTSF 185


                 .
gi 664281569 238 S 238
Cdd:cd00840  186 S 186
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 269-358 5.69e-11

Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and archaea. This domain is about 90 amino acids in length. This domain is found associated with pfam00149. SbcD works in complex with SbdC (SbcDC) which is a transcription regulator. It down-regulates transcription of arl and mgr to inhibit type 5 capsule protein production. It acts as part of the SOS pathway of bacteria.


Pssm-ID: 463533  Cd Length: 100  Bit Score: 58.85  E-value: 5.69e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  269 RPLARLRGRLDTLLEDPAL----DRHEHAWVEATLTDPVRPADPMARLARRFPHT----LSLVFDPERPPDDPGASYAQR 340
Cdd:pfam12320   3 RDLRRIKGSLEELLAALAYleeePADREDYLEVELTDEEPIPDLMERLREAYPNIpvelLRIRRTREERQAEEEEEAAED 82

                          90
                  ....*....|....*...
gi 664281569  341 LKGRDDHQIAEDFVAHVR 358
Cdd:pfam12320  83 LEELSPLELFERFYEEQT 100
Metallophos pfam00149
Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, ...
 1-86 1.69e-10

Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD or yeast MRE11. The most conserved regions in this superfamily centre around the metal chelating residues.


Pssm-ID: 459691 [Multi-domain]  Cd Length: 114  Bit Score: 57.99  E-value: 1.69e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569    1 MRLLHTSDWHLGRSFHRVslldaqAAYLDHLvatVEEREVDAVLVAGDVYDRAVPPLTAVELFDRALHRlaavgVPTVMI 80
Cdd:pfam00149   1 MRILVIGDLHLPGQLDDL------LELLKKL---LEEGKPDLVLHAGDLVDRGPPSEEVLELLERLIKY-----VPVYLV 66


                  ....*.
gi 664281569   81 SGNHDS 86
Cdd:pfam00149  67 RGNHDF 72
 
Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
1-271 1.17e-80

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


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 247.52  E-value: 1.17e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   1 MRLLHTSDWHLGRSFHRVSLLDAQAAYLDHLVATVEEREVDAVLVAGDVYDRAVPPLTAVELFDRALHRLAAVGVPTVMI 80
Cdd:COG0420    1 MRFLHTADWHLGKPLHGASRREDQLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLSEAGIPVVLI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  81 SGNHDSARRLGVGAGLFERAGIHLRTDPEgcATPVVLaDDHGDVAFYGLPYLEPAlvkdvlgagkagHEAVLTAAMDRVR 160
Cdd:COG0420   81 AGNHDSPSRLSAGSPLLENLGVHVFGSVE--PEPVEL-EDGLGVAVYGLPYLRPS------------DEEALRDLLERLP 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569 161 ADLAtrpAETRSVVLAHAFVAGGEPSdseRDITvggVAAVPAGVF--DGVDYAALGHLHGSQRV--TARVRYSGSPLAYS 236
Cdd:COG0420  146 RALD---PGGPNILLLHGFVAGASGS---RDIY---VAPVPLSALpaAGFDYVALGHIHRPQVLggDPRIRYSGSPEPRS 216

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 664281569 237 FSEAdHRKTMWLIDLDADGCIAAeERIDCPVERPL 271
Cdd:COG0420  217 FSEA-GGKGVLLVELDAGGLVSV-EFVPLPATRRF 249
sbcd TIGR00619
exonuclease SbcD; All proteins in this family for which functions are known are ...
 1-244 4.60e-54

exonuclease SbcD; All proteins in this family for which functions are known are double-stranded DNA exonuclease (as part of a complex with SbcC homologs). This complex functions in the initiation of recombination and recombinational repair and is particularly important in regulating the stability of DNA sections that can form secondary structures. This family is likely homologous to the MRE11 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273178 [Multi-domain]  Cd Length: 253  Bit Score: 179.15  E-value: 4.60e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569    1 MRLLHTSDWHLGRSFHRVSLLDAQAAYLDHLVATVEEREVDAVLVAGDVYDRAVPPLTAVELFDRALHRLAAVGV-PTVM 79
Cdd:TIGR00619   1 MRILHTSDWHLGKTLEGVSRLAEQKAFLDDLLEFAKAEQVDALLVAGDVFDTANPPAEAQELFNAFFVNLSDTGIrPIVV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   80 ISGNHDSARRLGVGAGLFERAGIHLRTDPEGcATPVVLADDHGDVAFY-------------GLPYLEPALVKDVLGAGKA 146
Cdd:TIGR00619  81 ISGNHDSAQRLSAAKKLLAELGVFVVGSPGH-DPQILLLKDGTNGEGLcvglfllpreailTRAGLDGFGLELLLAHTDV 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  147 GHEAVLTAAMDRVRADLATrpaetrsVVLAHAFVAGGEPSDSERDITVGGVAAVPAGVFDGVDYAALGHLHGSQR--VTA 224
Cdd:TIGR00619 160 KLRQAAEALKLRLDQDLPK-------ILLAHLFTAGATKSDAERRIYIGTLYAFPLQNFPEADYIALGHIHIHKIskGRE 232

                         250       260
                  ....*....|....*....|
gi 664281569  225 RVRYSGSPLAYSFSEADHRK 244
Cdd:TIGR00619 233 RVRYSGSPFPLSFDEAGKDK 252
PRK10966 PRK10966
exonuclease subunit SbcD; Provisional
 1-281 1.07e-48

exonuclease subunit SbcD; Provisional


Pssm-ID: 182871 [Multi-domain]  Cd Length: 407  Bit Score: 169.73  E-value: 1.07e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   1 MRLLHTSDWHLGRSFHRVSLLDAQAAYLDHLVATVEEREVDAVLVAGDVYDRAVPPLTAVELFDRALHRLAAVGVPTVMI 80
Cdd:PRK10966   1 MRILHTSDWHLGQNFYSKSRAAEHQAFLDWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCQLVVL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  81 SGNHDSARRLGVGAGLFEragiHLRTDPEGCAT------PVVLADDHGDVA--FYGLPYLEPalvKDVLG--AGKAGHE- 149
Cdd:PRK10966  81 AGNHDSVATLNESRDLLA----FLNTTVIASASddlghqVIILPRRDGTPGavLCAIPFLRP---RDVITsqAGQSGIEk 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569 150 --AVLTAAMDRVR----ADLATRPAETRSV-VLA--HAFVAGGEPSDSERDITVGGVAAVPAGVFDGVDYAALGHLHGSQ 220
Cdd:PRK10966 154 qqALQAAIADHYQqlyqLACELRDELGQPLpIIAtgHLTTVGASKSDSVRDIYIGTLDAFPAQAFPPADYIALGHIHRAQ 233

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 664281569 221 RV--TARVRYSGSPLAYSFSEADHRKTMWLIDLDADGCIAAEErIDCPVERPLARLRGRLDTL 281
Cdd:PRK10966 234 KVggTEHIRYSGSPIPLSFDELGKSKSVHLVEFDQGKLQSVTP-LPVPVFQPMAVLKGDLASI 295
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 2-238 1.74e-45

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: 154.73  E-value: 1.74e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   2 RLLHTSDWHLGRSFHRVS-LLDAQAAYLDHLVATVEEREVDAVLVAGDVYDRAVPPLTAVELFDRALHRLAAVGVPTVMI 80
Cdd:cd00840    1 RFLHTADWHLGYPLYGLSrREEDFFKAFEEIVDLAIEEKVDFVLIAGDLFDSNNPSPEALKLAIEGLRRLCEAGIPVFVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  81 SGNHDSARRlgvgaglferagihlrtdpegcatpvvladdhgdVAFYGLPYLepalvkdvlgagkagHEAVLTAAMDRVR 160
Cdd:cd00840   81 AGNHDSPAR----------------------------------VAIYGLPYL---------------RDERLERLFEDLE 111

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569 161 ADLATRPAETRSVVLAHAFVAGGEPSDSERDITVGGVAavpagvFDGVDYAALGHLHGSQRV---TARVRYSGSPLAYSF 237
Cdd:cd00840  112 LRPRLLKPDWFNILLLHQGVDGAGPSDSERPIVPEDLL------PDGFDYVALGHIHKPQIIeggGPPIVYPGSPEPTSF 185


                 .
gi 664281569 238 S 238
Cdd:cd00840  186 S 186
CpdA COG1409
3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms];
1-264 3.25e-12

3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms];


Pssm-ID: 441019 [Multi-domain]  Cd Length: 234  Bit Score: 65.48  E-value: 3.25e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   1 MRLLHTSDWHLGRSFHRVslldaQAAYLDHLVATVEEREVDAVLVAGDVYDRAVPpltavELFDRALHRLAAVGVPTVMI 80
Cdd:COG1409    1 FRFAHISDLHLGAPDGSD-----TAEVLAAALADINAPRPDFVVVTGDLTDDGEP-----EEYAAAREILARLGVPVYVV 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  81 SGNHDsarRLGVGAGLFERagiHLRTDPEGCATPVVladDHGDVAFYGLPYLEPALVKDVLGAgkagheavltAAMDRVR 160
Cdd:COG1409   71 PGNHD---IRAAMAEAYRE---YFGDLPPGGLYYSF---DYGGVRFIGLDSNVPGRSSGELGP----------EQLAWLE 131

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569 161 ADLATRPAETRSVVLAHAFVAGGEPSDSERDITVGGVAAVPAGVfdGVDYAALGHLHGSQRVTAR-VRYSGSP-LAYSFS 238
Cdd:COG1409  132 EELAAAPAKPVIVFLHHPPYSTGSGSDRIGLRNAEELLALLARY--GVDLVLSGHVHRYERTRRDgVPYIVAGsTGGQVR 209

                        250       260
                 ....*....|....*....|....*.
gi 664281569 239 EADHrktMWLIDLDADGCIAAEERID 264
Cdd:COG1409  210 LPPG---YRVIEVDGDGLTVEVRRVD 232
SbcD_C pfam12320
Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and ...
 269-358 5.69e-11

Type 5 capsule protein repressor C-terminal domain; This domain is found in bacteria and archaea. This domain is about 90 amino acids in length. This domain is found associated with pfam00149. SbcD works in complex with SbdC (SbcDC) which is a transcription regulator. It down-regulates transcription of arl and mgr to inhibit type 5 capsule protein production. It acts as part of the SOS pathway of bacteria.


Pssm-ID: 463533  Cd Length: 100  Bit Score: 58.85  E-value: 5.69e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569  269 RPLARLRGRLDTLLEDPAL----DRHEHAWVEATLTDPVRPADPMARLARRFPHT----LSLVFDPERPPDDPGASYAQR 340
Cdd:pfam12320   3 RDLRRIKGSLEELLAALAYleeePADREDYLEVELTDEEPIPDLMERLREAYPNIpvelLRIRRTREERQAEEEEEAAED 82

                          90
                  ....*....|....*...
gi 664281569  341 LKGRDDHQIAEDFVAHVR 358
Cdd:pfam12320  83 LEELSPLELFERFYEEQT 100
Metallophos pfam00149
Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, ...
 1-86 1.69e-10

Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD or yeast MRE11. The most conserved regions in this superfamily centre around the metal chelating residues.


Pssm-ID: 459691 [Multi-domain]  Cd Length: 114  Bit Score: 57.99  E-value: 1.69e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569    1 MRLLHTSDWHLGRSFHRVslldaqAAYLDHLvatVEEREVDAVLVAGDVYDRAVPPLTAVELFDRALHRlaavgVPTVMI 80
Cdd:pfam00149   1 MRILVIGDLHLPGQLDDL------LELLKKL---LEEGKPDLVLHAGDLVDRGPPSEEVLELLERLIKY-----VPVYLV 66


                  ....*.
gi 664281569   81 SGNHDS 86
Cdd:pfam00149  67 RGNHDF 72
YaeI COG1408
Predicted phosphohydrolase, MPP superfamily [General function prediction only];
1-104 2.97e-09

Predicted phosphohydrolase, MPP superfamily [General function prediction only];


Pssm-ID: 441018 [Multi-domain]  Cd Length: 268  Bit Score: 57.50  E-value: 2.97e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   1 MRLLHTSDWHLGRSFHRvslldaqaAYLDHLVATVEEREVDAVLVAGDVYDRAVPPLTAVElfdRALHRLAAVGvPTVMI 80
Cdd:COG1408   43 LRIVQLSDLHLGPFIGG--------ERLERLVEKINALKPDLVVLTGDLVDGSVAELEALL---ELLKKLKAPL-GVYAV 110

                         90       100
                 ....*....|....*....|....
gi 664281569  81 SGNHDSARRLGVGAGLFERAGIHL 104
Cdd:COG1408  111 LGNHDYYAGLEELRAALEEAGVRV 134
COG2129 COG2129
Predicted phosphoesterase, related to the Icc protein [General function prediction only];
2-104 1.31e-07

Predicted phosphoesterase, related to the Icc protein [General function prediction only];


Pssm-ID: 441732 [Multi-domain]  Cd Length: 211  Bit Score: 51.55  E-value: 1.31e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   2 RLLHTSDWHLGRSfhrvslldaqaaYLDHLVATVEEREVDAVLVAGDVYDRAvppltAVELFDRALHRLAAVGVPTVMIS 81
Cdd:COG2129    1 KILAVSDLHGNFD------------LLEKLLELARAEDADLVILAGDLTDFG-----TAEEAREVLEELAALGVPVLAVP 63

                         90       100
                 ....*....|....*....|...
gi 664281569  82 GNHDSARRLgvgaGLFERAGIHL 104
Cdd:COG2129   64 GNHDDPEVL----DALEESGVHN 82
MPP_YkuE_C cd07385
Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; YkuE is an ...
 2-104 1.98e-06

Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; YkuE is an uncharacterized Bacillus subtilis protein with a C-terminal metallophosphatase domain and an N-terminal twin-arginine (RR) motif. An RR-signal peptide derived from the Bacillus subtilis YkuE protein can direct Tat-dependent secretion of agarase in Streptomyces lividans. This is an indication that YkuE is transported by the Bacillus subtilis Tat (Twin-arginine translocation) pathway machinery. YkuE 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: 277331 [Multi-domain]  Cd Length: 224  Bit Score: 48.43  E-value: 1.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   2 RLLHTSDWHLGRSFHRvslldaqaAYLDHLVATVEEREVDAVLVAGDVYDRAVPPLTAVElfdRALHRLAAvGVPTVMIS 81
Cdd:cd07385    3 RIVQLSDIHLGPFVGR--------TRLQKVVRKVNELNPDLIVITGDLVDGDVSVLRLLA---SPLSKLKA-PLGVYFVL 70

                         90       100
                 ....*....|....*....|....
gi 664281569  82 GNHDSARRL-GVGAGLFERAGIHL 104
Cdd:cd07385   71 GNHDYYSGDvEVWIAALEKAGITV 94
MPP_1 cd07400
Uncharacterized subfamily, metallophosphatase domain; Uncharacterized subfamily of the MPP ...
 3-85 1.08e-04

Uncharacterized subfamily, metallophosphatase domain; Uncharacterized subfamily of the 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: 277345 [Multi-domain]  Cd Length: 138  Bit Score: 41.90  E-value: 1.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   3 LLHTSDWHLGRSFHRVSLLDAqaayldhLVATVEEREVDAVLVAGDVYDRAVPpltavELFDRALHRLAAVGV-PTVMIS 81
Cdd:cd07400    1 IAHISDLHFGEERKPEVLELN-------LLDEINALKPDLVVVTGDLTQRARP-----AEFEEAREFLDALEPePVVVVP 68


                 ....
gi 664281569  82 GNHD 85
Cdd:cd07400   69 GNHD 72
MPP_GpdQ cd07402
Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; GpdQ ...
 3-87 1.91e-04

Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; GpdQ (glycerophosphodiesterase Q, also known as Rv0805 in Mycobacterium tuberculosis) is a binuclear metallophosphoesterase from Enterobacter aerogenes that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents. The GpdQ homolog, Rv0805, has 2',3'-cyclic nucleotide phosphodiesterase activity. GpdQ and Rv0805 belong 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: 277347 [Multi-domain]  Cd Length: 240  Bit Score: 42.65  E-value: 1.91e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   3 LLHTSDWHLGRSFHRVSLLDAQAAYLDHLVATVEER--EVDAVLVAGDVYDRAVPPltAVELFDRALHRLAAvgvPTVMI 80
Cdd:cd07402    1 IAQISDTHLFAPGEGALLGVDTAARLAAAVAQVNALhpRPDLVVVTGDLSDDGSPE--SYERLRELLAPLPA---PVYWI 75


                 ....*..
gi 664281569  81 SGNHDSA 87
Cdd:cd07402   76 PGNHDDR 82
MPP_YbbF-LpxH cd07398
Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; YbbF/LpxH is an ...
 7-123 2.46e-04

Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; YbbF/LpxH is an Escherichia coli UDP-2,3-diacylglucosamine hydrolase thought to catalyze the fourth step of lipid A biosynthesis, in which a precursor UDP-2,3-diacylglucosamine is hydrolyzed to yield 2,3-diacylglucosamine 1-phosphate and UMP. YbbF 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: 277343 [Multi-domain]  Cd Length: 217  Bit Score: 41.96  E-value: 2.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   7 SDWHLGRSfhrvsllDAQAAYLDHLVATVEEREVDAVLVAGDVYD----RAVPPLTAVELFDRALHRLAAVGVPTVMISG 82
Cdd:cd07398    4 SDLHLGLR-------GCRADRLLDFLLVEELDEADALYLLGDIFDlwigDDSVVWPGAHRALARLLRLADRGTEVIYVPG 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 664281569  83 NHDSarrlGVGAGLFERAGIHLRTDPEGCAT----PVVLAddHGD 123
Cdd:cd07398   77 NHDF----LLGRFFAEALGAILLPEPAEHLEldgkRLLVL--HGD 115
47 PHA02546
endonuclease subunit; Provisional
 1-85 2.84e-04

endonuclease subunit; Provisional


Pssm-ID: 222867 [Multi-domain]  Cd Length: 340  Bit Score: 42.68  E-value: 2.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   1 MRLLHTSDWHLGRSFHRVSLLDAQAAYLDHLVATVEEREVDAVLVAGDVYD--RAVPPLTAVELFDRALHRLAAVGVPTV 78
Cdd:PHA02546   1 MKILLIGDQHLGVRKDDPWFQNYQLKFIKQAIEYSKAHGITTWIQLGDTFDvrKAITQNTMNFVREKIFDLLKEAGITLH 80


                 ....*..
gi 664281569  79 MISGNHD 85
Cdd:PHA02546  81 VLVGNHD 87
MPP_superfamily cd00838
metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also ...
 4-85 9.31e-03

metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing 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. This superfamily includes: the phosphoprotein phosphatases (PPPs), 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: 277317 [Multi-domain]  Cd Length: 130  Bit Score: 36.09  E-value: 9.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 664281569   4 LHTSDWHLGrsfhrvslLDAQAAYLDHLVAtvEEREVDAVLVAGDVYDRAVPPLTAVELFDRALHRlaavGVPTVMISGN 83
Cdd:cd00838    1 LVISDIHGN--------LEALEAVLEAALA--KAEKPDLVICLGDLVDYGPDPEEVELKALRLLLA----GIPVYVVPGN 66


                 ..
gi 664281569  84 HD 85
Cdd:cd00838   67 HD 68
 
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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