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Conserved domains on  [gi|506380944|ref|WP_015900663|]
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DNA repair exonuclease [Staphylococcus carnosus]

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];
2-249 1.54e-69

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


:

Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 219.40  E-value: 1.54e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   2 VKFIHCADLHLDSPFKSHShlspnIYEDvkksTYESFKSIIDHALREEVDFIVIAGDLFDKENRSLRAEVFLKEQFERLE 81
Cdd:COG0420    1 MRFLHTADWHLGKPLHGAS-----RRED----QLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLS 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944  82 KEQIFVYISHGNHDPLSEL-ITTEWPAK--VSVFDKNVETYQTItKHGEKILLHGFSYQN---DESYENKLDEYPSSQGE 155
Cdd:COG0420   72 EAGIPVVLIAGNHDSPSRLsAGSPLLENlgVHVFGSVEPEPVEL-EDGLGVAVYGLPYLRpsdEEALRDLLERLPRALDP 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944 156 KGMHIGVLHGT---YSKTSDNHRYtEFLLEDLNTKLYHYWALGHIHERSQLNDMPPIFYPGNIQGRHFNEQGEKGFLLVE 232
Cdd:COG0420  151 GGPNILLLHGFvagASGSRDIYVA-PVPLSALPAAGFDYVALGHIHRPQVLGGDPRIRYSGSPEPRSFSEAGGKGVLLVE 229

                        250
                 ....*....|....*...
gi 506380944 233 -GDELKLDITFVPTQYIR 249
Cdd:COG0420  230 lDAGGLVSVEFVPLPATR 247
 
Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
2-249 1.54e-69

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


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 219.40  E-value: 1.54e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   2 VKFIHCADLHLDSPFKSHShlspnIYEDvkksTYESFKSIIDHALREEVDFIVIAGDLFDKENRSLRAEVFLKEQFERLE 81
Cdd:COG0420    1 MRFLHTADWHLGKPLHGAS-----RRED----QLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLS 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944  82 KEQIFVYISHGNHDPLSEL-ITTEWPAK--VSVFDKNVETYQTItKHGEKILLHGFSYQN---DESYENKLDEYPSSQGE 155
Cdd:COG0420   72 EAGIPVVLIAGNHDSPSRLsAGSPLLENlgVHVFGSVEPEPVEL-EDGLGVAVYGLPYLRpsdEEALRDLLERLPRALDP 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944 156 KGMHIGVLHGT---YSKTSDNHRYtEFLLEDLNTKLYHYWALGHIHERSQLNDMPPIFYPGNIQGRHFNEQGEKGFLLVE 232
Cdd:COG0420  151 GGPNILLLHGFvagASGSRDIYVA-PVPLSALPAAGFDYVALGHIHRPQVLGGDPRIRYSGSPEPRSFSEAGGKGVLLVE 229

                        250
                 ....*....|....*...
gi 506380944 233 -GDELKLDITFVPTQYIR 249
Cdd:COG0420  230 lDAGGLVSVEFVPLPATR 247
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 3-221 1.24e-52

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: 173.61  E-value: 1.24e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   3 KFIHCADLHLDSPFKSHSHLspniyedvKKSTYESFKSIIDHALREEVDFIVIAGDLFDKENRSLRAEVFLKEQFERLEK 82
Cdd:cd00840    1 RFLHTADWHLGYPLYGLSRR--------EEDFFKAFEEIVDLAIEEKVDFVLIAGDLFDSNNPSPEALKLAIEGLRRLCE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944  83 EQIFVYISHGNHDPLSelittewpakvsvfdknvetyqtitkhgeKILLHGFSYQNDESYEN---KLDEYPSSQGEKGMH 159
Cdd:cd00840   73 AGIPVFVIAGNHDSPA-----------------------------RVAIYGLPYLRDERLERlfeDLELRPRLLKPDWFN 123

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 506380944 160 IGVLHGTYSKTSDNHRYTEFLLEDLNTKLYHYWALGHIHERSQLND-MPPIFYPGNIQGRHFN 221
Cdd:cd00840  124 ILLLHQGVDGAGPSDSERPIVPEDLLPDGFDYVALGHIHKPQIIEGgGPPIVYPGSPEPTSFS 186
sbcd TIGR00619
exonuclease SbcD; All proteins in this family for which functions are known are ...
 3-225 1.30e-08

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: 55.12  E-value: 1.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944    3 KFIHCADLHLDSPFKSHSHLspniyEDVKKSTYEsfksIIDHALREEVDFIVIAGDLFDKENRSLRAEVFLKEQFERLEK 82
Cdd:TIGR00619   2 RILHTSDWHLGKTLEGVSRL-----AEQKAFLDD----LLEFAKAEQVDALLVAGDVFDTANPPAEAQELFNAFFVNLSD 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   83 EQIF--VYIShGNHDPLSELittEWPAKVSVFdKNVETYQTITkHGEKIL----------------------LHGFSYQN 138
Cdd:TIGR00619  73 TGIRpiVVIS-GNHDSAQRL---SAAKKLLAE-LGVFVVGSPG-HDPQILllkdgtngeglcvglfllpreaILTRAGLD 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944  139 DES-------YENKLDEYPSSQGEKG----MHIGVLHGTY--SKTSDNHR------YTEFLLEDLNTKLYHywALGHIHE 199
Cdd:TIGR00619 147 GFGlelllahTDVKLRQAAEALKLRLdqdlPKILLAHLFTagATKSDAERriyigtLYAFPLQNFPEADYI--ALGHIHI 224

                         250       260
                  ....*....|....*....|....*.
gi 506380944  200 RSQLNDMPPIFYPGNIQGRHFNEQGE 225
Cdd:TIGR00619 225 HKISKGRERVRYSGSPFPLSFDEAGK 250
Metallophos pfam00149
Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, ...
 3-95 2.26e-06

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: 46.05  E-value: 2.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944    3 KFIHCADLHLDSPFkshshlspniyedvkkstyESFKSIIDHALREE-VDFIVIAGDLFDKENRSLRAEVFLKEQFERLE 81
Cdd:pfam00149   2 RILVIGDLHLPGQL-------------------DDLLELLKKLLEEGkPDLVLHAGDLVDRGPPSEEVLELLERLIKYVP 62

                          90
                  ....*....|....
gi 506380944   82 keqifVYISHGNHD 95
Cdd:pfam00149  63 -----VYLVRGNHD 71
 
Name Accession Description Interval E-value
SbcD COG0420
DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair];
2-249 1.54e-69

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


Pssm-ID: 440189 [Multi-domain]  Cd Length: 250  Bit Score: 219.40  E-value: 1.54e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   2 VKFIHCADLHLDSPFKSHShlspnIYEDvkksTYESFKSIIDHALREEVDFIVIAGDLFDKENRSLRAEVFLKEQFERLE 81
Cdd:COG0420    1 MRFLHTADWHLGKPLHGAS-----RRED----QLAALDRLVDLAIEEKVDAVLIAGDLFDSANPSPEAVRLLAEALRRLS 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944  82 KEQIFVYISHGNHDPLSEL-ITTEWPAK--VSVFDKNVETYQTItKHGEKILLHGFSYQN---DESYENKLDEYPSSQGE 155
Cdd:COG0420   72 EAGIPVVLIAGNHDSPSRLsAGSPLLENlgVHVFGSVEPEPVEL-EDGLGVAVYGLPYLRpsdEEALRDLLERLPRALDP 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944 156 KGMHIGVLHGT---YSKTSDNHRYtEFLLEDLNTKLYHYWALGHIHERSQLNDMPPIFYPGNIQGRHFNEQGEKGFLLVE 232
Cdd:COG0420  151 GGPNILLLHGFvagASGSRDIYVA-PVPLSALPAAGFDYVALGHIHRPQVLGGDPRIRYSGSPEPRSFSEAGGKGVLLVE 229

                        250
                 ....*....|....*...
gi 506380944 233 -GDELKLDITFVPTQYIR 249
Cdd:COG0420  230 lDAGGLVSVEFVPLPATR 247
MPP_Mre11_N cd00840
Mre11 nuclease, N-terminal metallophosphatase domain; Mre11 (also known as SbcD in Escherichia ...
 3-221 1.24e-52

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: 173.61  E-value: 1.24e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   3 KFIHCADLHLDSPFKSHSHLspniyedvKKSTYESFKSIIDHALREEVDFIVIAGDLFDKENRSLRAEVFLKEQFERLEK 82
Cdd:cd00840    1 RFLHTADWHLGYPLYGLSRR--------EEDFFKAFEEIVDLAIEEKVDFVLIAGDLFDSNNPSPEALKLAIEGLRRLCE 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944  83 EQIFVYISHGNHDPLSelittewpakvsvfdknvetyqtitkhgeKILLHGFSYQNDESYEN---KLDEYPSSQGEKGMH 159
Cdd:cd00840   73 AGIPVFVIAGNHDSPA-----------------------------RVAIYGLPYLRDERLERlfeDLELRPRLLKPDWFN 123

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 506380944 160 IGVLHGTYSKTSDNHRYTEFLLEDLNTKLYHYWALGHIHERSQLND-MPPIFYPGNIQGRHFN 221
Cdd:cd00840  124 ILLLHQGVDGAGPSDSERPIVPEDLLPDGFDYVALGHIHKPQIIEGgGPPIVYPGSPEPTSFS 186
sbcd TIGR00619
exonuclease SbcD; All proteins in this family for which functions are known are ...
 3-225 1.30e-08

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: 55.12  E-value: 1.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944    3 KFIHCADLHLDSPFKSHSHLspniyEDVKKSTYEsfksIIDHALREEVDFIVIAGDLFDKENRSLRAEVFLKEQFERLEK 82
Cdd:TIGR00619   2 RILHTSDWHLGKTLEGVSRL-----AEQKAFLDD----LLEFAKAEQVDALLVAGDVFDTANPPAEAQELFNAFFVNLSD 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   83 EQIF--VYIShGNHDPLSELittEWPAKVSVFdKNVETYQTITkHGEKIL----------------------LHGFSYQN 138
Cdd:TIGR00619  73 TGIRpiVVIS-GNHDSAQRL---SAAKKLLAE-LGVFVVGSPG-HDPQILllkdgtngeglcvglfllpreaILTRAGLD 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944  139 DES-------YENKLDEYPSSQGEKG----MHIGVLHGTY--SKTSDNHR------YTEFLLEDLNTKLYHywALGHIHE 199
Cdd:TIGR00619 147 GFGlelllahTDVKLRQAAEALKLRLdqdlPKILLAHLFTagATKSDAERriyigtLYAFPLQNFPEADYI--ALGHIHI 224

                         250       260
                  ....*....|....*....|....*.
gi 506380944  200 RSQLNDMPPIFYPGNIQGRHFNEQGE 225
Cdd:TIGR00619 225 HKISKGRERVRYSGSPFPLSFDEAGK 250
CpdA COG1409
3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms];
2-95 3.64e-08

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


Pssm-ID: 441019 [Multi-domain]  Cd Length: 234  Bit Score: 53.54  E-value: 3.64e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   2 VKFIHCADLHLDSPFKSHshlspniyedvkksTYESFKSIIDHALREEVDFIVIAGDLFDkenRSLRAEV-FLKEQFERL 80
Cdd:COG1409    1 FRFAHISDLHLGAPDGSD--------------TAEVLAAALADINAPRPDFVVVTGDLTD---DGEPEEYaAAREILARL 63

                         90
                 ....*....|....*
gi 506380944  81 ekeQIFVYISHGNHD 95
Cdd:COG1409   64 ---GVPVYVVPGNHD 75
Metallophos pfam00149
Calcineurin-like phosphoesterase; This family includes a diverse range of phosphoesterases, ...
 3-95 2.26e-06

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: 46.05  E-value: 2.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944    3 KFIHCADLHLDSPFkshshlspniyedvkkstyESFKSIIDHALREE-VDFIVIAGDLFDKENRSLRAEVFLKEQFERLE 81
Cdd:pfam00149   2 RILVIGDLHLPGQL-------------------DDLLELLKKLLEEGkPDLVLHAGDLVDRGPPSEEVLELLERLIKYVP 62

                          90
                  ....*....|....
gi 506380944   82 keqifVYISHGNHD 95
Cdd:pfam00149  63 -----VYLVRGNHD 71
COG2129 COG2129
Predicted phosphoesterase, related to the Icc protein [General function prediction only];
3-96 2.77e-05

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


Pssm-ID: 441732 [Multi-domain]  Cd Length: 211  Bit Score: 44.62  E-value: 2.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   3 KFIHCADLHLDspfkshshlspniyedvkkstYESFKSIIDHALREEVDFIVIAGDLFDKENRSLRAEVFlkEQFERLEK 82
Cdd:COG2129    1 KILAVSDLHGN---------------------FDLLEKLLELARAEDADLVILAGDLTDFGTAEEAREVL--EELAALGV 57

                         90
                 ....*....|....
gi 506380944  83 EQIFVyisHGNHDP 96
Cdd:COG2129   58 PVLAV---PGNHDD 68
YaeI COG1408
Predicted phosphohydrolase, MPP superfamily [General function prediction only];
2-95 4.01e-04

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


Pssm-ID: 441018 [Multi-domain]  Cd Length: 268  Bit Score: 41.70  E-value: 4.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   2 VKFIHCADLHLDsPFKSHSHLspniyedvkkstyesfKSIIDHALREEVDFIVIAGDLFDKENRSLRAevfLKEQFERLe 81
Cdd:COG1408   43 LRIVQLSDLHLG-PFIGGERL----------------ERLVEKINALKPDLVVLTGDLVDGSVAELEA---LLELLKKL- 101

                         90
                 ....*....|....
gi 506380944  82 KEQIFVYISHGNHD 95
Cdd:COG1408  102 KAPLGVYAVLGNHD 115
MPP_superfamily cd00838
metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also ...
 45-95 1.14e-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: 38.79  E-value: 1.14e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 506380944  45 ALREEVDFIVIAGDLFDKENRSLRAEvflkEQFERLEKEQIFVYISHGNHD 95
Cdd:cd00838   22 AKAEKPDLVICLGDLVDYGPDPEEVE----LKALRLLLAGIPVYVVPGNHD 68
MPP_YkuE_C cd07385
Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; YkuE is an ...
 21-95 1.87e-03

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: 39.57  E-value: 1.87e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 506380944  21 HLSPNIYEDVkkstyesFKSIIDHALREEVDFIVIAGDLFDKENRSLRAEVflkEQFERLEKEQ--IFVYishGNHD 95
Cdd:cd07385   11 HLGPFVGRTR-------LQKVVRKVNELNPDLIVITGDLVDGDVSVLRLLA---SPLSKLKAPLgvYFVL---GNHD 74
MPP_YbbF-LpxH cd07398
Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; YbbF/LpxH is an ...
 4-133 2.62e-03

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: 38.88  E-value: 2.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   4 FIhcADLHLDSPFKSHSHLSpniyedvkkstyESFKsiidHALREEVDFIVIAGDLFD--KENRSLRAEVFLKEQFERLE 81
Cdd:cd07398    2 FI--SDLHLGLRGCRADRLL------------DFLL----VEELDEADALYLLGDIFDlwIGDDSVVWPGAHRALARLLR 63

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 506380944  82 KEQ--IFVYISHGNHDPLseliTTEWPAKVSVFDKNVETYQTITKHGEKILL-HG 133
Cdd:cd07398   64 LADrgTEVIYVPGNHDFL----LGRFFAEALGAILLPEPAEHLELDGKRLLVlHG 114
MPP_GpdQ cd07402
Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; GpdQ ...
 4-95 3.11e-03

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: 38.80  E-value: 3.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   4 FIHCADLHLDSPfkshshLSPNIY-EDvkksTYESFKSIIDH--ALREEVDFIVIAGDLFDK-ENRSLRAevfLKEQFER 79
Cdd:cd07402    1 IAQISDTHLFAP------GEGALLgVD----TAARLAAAVAQvnALHPRPDLVVVTGDLSDDgSPESYER---LRELLAP 67

                         90
                 ....*....|....*.
gi 506380944  80 LEKEqifVYISHGNHD 95
Cdd:cd07402   68 LPAP---VYWIPGNHD 80
mre11 TIGR00583
DNA repair protein (mre11); All proteins in this family for which functions are known are ...
 24-199 3.49e-03

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: 39.43  E-value: 3.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   24 PNIYEDvkksTYESFKSIIDHALREEVDFIVIAGDLFDKEN----------RSLR-----------------AEVFLKEQ 76
Cdd:TIGR00583  21 PVRGDD----SWNTFEEVLQIAKEQDVDMILLGGDLFHENKpsrkslyqvlRSLRlyclgdkpceleflsdaSVVFNQSA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506380944   77 FERLEKEQ------IFVYISHGNHDPLS------ELITTEWPAKVSVFDKNVETYQTIT------KHGEKILLHGFSYQN 138
Cdd:TIGR00583  97 FGNVNYEDpninvaIPVFSIHGNHDDPSgdgllcALDLLHATGLVNYFGKVPEIDNIIVspillqKGETKLALYGISNVR 176

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 506380944  139 DESY-----ENKLD-EYPSSQGEKGMHIGVLHGTYSKtsdnHRYTEFLLEDLNTKLYHYWALGHIHE 199
Cdd:TIGR00583 177 DERLvrtfkDNKVSfLRPNAGAEDWFNLLVLHQNHAA----HTSTSFLPESFIPDFFDLVIWGHEHE 239
 
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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