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Conserved domains on  [gi|924477250|ref|WP_053500351|]
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MULTISPECIES: ligase-associated DNA damage response endonuclease PdeM [Stenotrophomonas]

Protein Classification

metallophosphoesterase family protein( domain architecture ID 46112)

metallophosphoesterase family protein may contain an active site consisting of two metal ions (usually manganese, iron, or zinc)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MPP_superfamily super family cl13995
metallophosphatase superfamily, metallophosphatase domain; Metallophosphatases (MPPs), also ...
 10-208 2.41e-63

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.


The actual alignment was detected with superfamily member TIGR04123:

Pssm-ID: 472684  Cd Length: 208  Bit Score: 195.47  E-value: 2.41e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250   10 AGESLVLLGARALYWPARQALLLADLHLGKADVFRRAGIALPSGGTGKDLQRLQGLLDRHACRELWILGDILHGPAHRAA 89
Cdd:TIGR04123   4 AGETLVLLPSGALYWPAERLLVVADLHLGKAAHFRARGIPLPPYDTRATLERLAALIQRYQPRRLIVLGDLFHDRIGAER 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250   90 WYQQ-WLAWRERNAALDVHVLRGNHDRQLPH--AELQVQIHDEVRLPPFLLRHEPVPDAELHVIAGHLHPQIALPALRRR 166
Cdd:TIGR04123  84 LTWEdFAAWRRLHAGRDWVLIEGNHDRLAPDppEDLGGEVVDELRLGPLTFRHEPEPGPGGFEIAGHLHPGARLRGRGRR 163

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 924477250  167 F--PAFWLRDRMTLLPAFSAFTAGIVPVPAAGEQMVACVDNGLV 208
Cdd:TIGR04123 164 LrlPCFAFDGNRLILPAFGAFTGGLNVDPEAGDRVFAVAEGRVV 207
 
Name Accession Description Interval E-value
P_estr_lig_assc TIGR04123
metallophosphoesterase, DNA ligase-associated; Members of this protein family are an ...
 10-208 2.41e-63

metallophosphoesterase, DNA ligase-associated; Members of this protein family are an uncharacterized putative metallophosphoesterase associated with a DNA ligase, a helicase, and a putative exonuclease. It may play a role in DNA repair. Its system is present in about 12 % of prokaryotic reference genomes.


Pssm-ID: 274996  Cd Length: 208  Bit Score: 195.47  E-value: 2.41e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250   10 AGESLVLLGARALYWPARQALLLADLHLGKADVFRRAGIALPSGGTGKDLQRLQGLLDRHACRELWILGDILHGPAHRAA 89
Cdd:TIGR04123   4 AGETLVLLPSGALYWPAERLLVVADLHLGKAAHFRARGIPLPPYDTRATLERLAALIQRYQPRRLIVLGDLFHDRIGAER 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250   90 WYQQ-WLAWRERNAALDVHVLRGNHDRQLPH--AELQVQIHDEVRLPPFLLRHEPVPDAELHVIAGHLHPQIALPALRRR 166
Cdd:TIGR04123  84 LTWEdFAAWRRLHAGRDWVLIEGNHDRLAPDppEDLGGEVVDELRLGPLTFRHEPEPGPGGFEIAGHLHPGARLRGRGRR 163

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 924477250  167 F--PAFWLRDRMTLLPAFSAFTAGIVPVPAAGEQMVACVDNGLV 208
Cdd:TIGR04123 164 LrlPCFAFDGNRLILPAFGAFTGGLNVDPEAGDRVFAVAEGRVV 207
COG1407 COG1407
Metallophosphoesterase superfamily enzyme [General function prediction only];
5-188 9.77e-60

Metallophosphoesterase superfamily enzyme [General function prediction only];


Pssm-ID: 441017  Cd Length: 224  Bit Score: 186.62  E-value: 9.77e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250   5 LPLLRAGESLVLLGARALYWPARQALLLADLHLGKADVFRRAGIALPSGGTGKDLQRLQGLLDRHACRELWILGDILHG- 83
Cdd:COG1407    1 MEIELAGETLVLLPEGALYWPAERTLVVADLHLGKESAFRRRGIPLPPYDTRETLERLEALIERTGPDRLIILGDLFHDf 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250  84 PAHRAAWYQQWLAWRERNAALDVHVLRGNHDRQLPH--AELQVQIHD-EVRLPPFLLRHEPVPDAELHVIAGHLHPQIAL 160
Cdd:COG1407   81 GGPSRQEWEELERLLALHAGVEVILVRGNHDPGLPDllEDLGGEVVDeELVLGGLLFRHEPEPEAADGEIAGHEHPAVRL 160

                        170       180       190
                 ....*....|....*....|....*....|.
gi 924477250 161 PAL---RRRFPAFWLRDRMTLLPAFSAFTAG 188
Cdd:COG1407  161 RDRvgrSLRLPCFLRDGRRLVLPAFGAFTGG 191
MPP_PF1019 cd07391
Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; This family ...
 30-189 6.85e-33

Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; This family includes bacterial and archeal proteins homologous to PF1019, an uncharacterized Pyrococcus furiosus protein. The domain present in members of this family 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: 277337  Cd Length: 175  Bit Score: 116.64  E-value: 6.85e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250  30 LLLADLHLGKADVFRRAGIALPSGGTGKDLQRLQGLLDRHACRELWILGDILHGPAHRAAWYQQWLA-WRERNAALDVHV 108
Cdd:cd07391    1 LVIADLHLGYEEELRRQGINLPRRQKERLLERLDRLLEELGPDRLVILGDLKHSFGRVSRQERREVPfFRLLAKDVDVIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250 109 LRGNHDRQLPHAELQVQIH--DEVRLPPFLLRHEPVPDAEL---HVIAGHLHPQIALP---ALRRRFPAFWLRDRMTL-- 178
Cdd:cd07391   81 IRGNHDGGLEEILSDVNVVvvEGYLLGGYLIFHGHKEPDPLdakLVIMGHEHPAIKLRdgvGASRKLPCFLRGEGEDGdv 160

                        170
                 ....*....|...
gi 924477250 179 --LPAFSAFTAGI 189
Cdd:cd07391  161 ivLPAFNPLTGGV 173
 
Name Accession Description Interval E-value
P_estr_lig_assc TIGR04123
metallophosphoesterase, DNA ligase-associated; Members of this protein family are an ...
 10-208 2.41e-63

metallophosphoesterase, DNA ligase-associated; Members of this protein family are an uncharacterized putative metallophosphoesterase associated with a DNA ligase, a helicase, and a putative exonuclease. It may play a role in DNA repair. Its system is present in about 12 % of prokaryotic reference genomes.


Pssm-ID: 274996  Cd Length: 208  Bit Score: 195.47  E-value: 2.41e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250   10 AGESLVLLGARALYWPARQALLLADLHLGKADVFRRAGIALPSGGTGKDLQRLQGLLDRHACRELWILGDILHGPAHRAA 89
Cdd:TIGR04123   4 AGETLVLLPSGALYWPAERLLVVADLHLGKAAHFRARGIPLPPYDTRATLERLAALIQRYQPRRLIVLGDLFHDRIGAER 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250   90 WYQQ-WLAWRERNAALDVHVLRGNHDRQLPH--AELQVQIHDEVRLPPFLLRHEPVPDAELHVIAGHLHPQIALPALRRR 166
Cdd:TIGR04123  84 LTWEdFAAWRRLHAGRDWVLIEGNHDRLAPDppEDLGGEVVDELRLGPLTFRHEPEPGPGGFEIAGHLHPGARLRGRGRR 163

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 924477250  167 F--PAFWLRDRMTLLPAFSAFTAGIVPVPAAGEQMVACVDNGLV 208
Cdd:TIGR04123 164 LrlPCFAFDGNRLILPAFGAFTGGLNVDPEAGDRVFAVAEGRVV 207
COG1407 COG1407
Metallophosphoesterase superfamily enzyme [General function prediction only];
5-188 9.77e-60

Metallophosphoesterase superfamily enzyme [General function prediction only];


Pssm-ID: 441017  Cd Length: 224  Bit Score: 186.62  E-value: 9.77e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250   5 LPLLRAGESLVLLGARALYWPARQALLLADLHLGKADVFRRAGIALPSGGTGKDLQRLQGLLDRHACRELWILGDILHG- 83
Cdd:COG1407    1 MEIELAGETLVLLPEGALYWPAERTLVVADLHLGKESAFRRRGIPLPPYDTRETLERLEALIERTGPDRLIILGDLFHDf 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250  84 PAHRAAWYQQWLAWRERNAALDVHVLRGNHDRQLPH--AELQVQIHD-EVRLPPFLLRHEPVPDAELHVIAGHLHPQIAL 160
Cdd:COG1407   81 GGPSRQEWEELERLLALHAGVEVILVRGNHDPGLPDllEDLGGEVVDeELVLGGLLFRHEPEPEAADGEIAGHEHPAVRL 160

                        170       180       190
                 ....*....|....*....|....*....|.
gi 924477250 161 PAL---RRRFPAFWLRDRMTLLPAFSAFTAG 188
Cdd:COG1407  161 RDRvgrSLRLPCFLRDGRRLVLPAFGAFTGG 191
MPP_PF1019 cd07391
Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; This family ...
 30-189 6.85e-33

Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; This family includes bacterial and archeal proteins homologous to PF1019, an uncharacterized Pyrococcus furiosus protein. The domain present in members of this family 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: 277337  Cd Length: 175  Bit Score: 116.64  E-value: 6.85e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250  30 LLLADLHLGKADVFRRAGIALPSGGTGKDLQRLQGLLDRHACRELWILGDILHGPAHRAAWYQQWLA-WRERNAALDVHV 108
Cdd:cd07391    1 LVIADLHLGYEEELRRQGINLPRRQKERLLERLDRLLEELGPDRLVILGDLKHSFGRVSRQERREVPfFRLLAKDVDVIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250 109 LRGNHDRQLPHAELQVQIH--DEVRLPPFLLRHEPVPDAEL---HVIAGHLHPQIALP---ALRRRFPAFWLRDRMTL-- 178
Cdd:cd07391   81 IRGNHDGGLEEILSDVNVVvvEGYLLGGYLIFHGHKEPDPLdakLVIMGHEHPAIKLRdgvGASRKLPCFLRGEGEDGdv 160

                        170
                 ....*....|...
gi 924477250 179 --LPAFSAFTAGI 189
Cdd:cd07391  161 ivLPAFNPLTGGV 173
COG4186 COG4186
Uncharacterized conserved protein MJ1445, calcineurin-like phosphoesterase superfamily ...
 73-167 4.95e-03

Uncharacterized conserved protein MJ1445, calcineurin-like phosphoesterase superfamily [General function prediction only];


Pssm-ID: 443340  Cd Length: 167  Bit Score: 36.40  E-value: 4.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250  73 ELWILGDILHGPAhraawYQQWLAWRERnaaL--DVHVLRGNHDRQLPH------AELQVQIHDEVRLPPFLLRHEP--V 142
Cdd:COG4186   46 TVYHLGDFAFGGS-----AEEAREILRR---LngRKHLIRGNHDGKLLLrlpagfASVQDYAEIKLGGRRLLLCHYPlrT 117

                         90       100
                 ....*....|....*....|....*...
gi 924477250 143 PDAELH---VIAGHLHPQIALPALRRRF 167
Cdd:COG4186  118 WNGADRgawHLHGHVHGNRLLKPTRRSI 145
MPP_AQ1575 cd07390
Aquifex aeolicus AQ1575 and related proteins, metallophosphatase domain; This family includes ...
 73-175 7.91e-03

Aquifex aeolicus AQ1575 and related proteins, metallophosphatase domain; This family includes bacterial and archeal proteins homologous to AQ1575, an uncharacterized Aquifex aeolicus protein. AQ1575 may play an accessory role in DNA repair, based on the close proximity of its gene to Holliday junction resolvasome genes. The domain present in members of this family 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: 277336  Cd Length: 170  Bit Score: 35.80  E-value: 7.91e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924477250  73 ELWILGDILHGpaHRAAWyqQWLAWRERNAAlDVHVLRGNHD---------RQLPHAELQVQIHDEVRlppFLLRHEPVP 143
Cdd:cd07390   45 IVYHLGDFALG--TNKAN--EALEILSLLNG-HIHLIRGNHDksllmyrplFFESVQQYVRIEHGGRR---FYLSHYPYR 116

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 924477250 144 DAELH-----VIAGHLHpqialpALRRRFPAFWLRDR 175
Cdd:cd07390  117 GPDSPdfdgwLIHGHVH------SNSPDEGPFVYDPR 147
 
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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