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Conserved domains on  [gi|2535604632|ref|WP_292409442|]
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MULTISPECIES: PHP domain-containing protein [unclassified Methanoculleus]

Protein Classification

PHP domain-containing protein( domain architecture ID 11427581)

PHP (Polymerase and Histidinol Phosphatase) domain-containing protein has an invariant histidine that is involved in metal ion coordination, similar to Bifidobacterium adolescentis metal-dependent phosphoesterase

CATH:  3.20.20.140
Gene Ontology:  GO:0046872
PubMed:  9685491
SCOP:  4000443

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 23-211 1.41e-31

5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];


:

Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 115.78  E-value: 1.41e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  23 LPADLHFHTRHSDSATRVRDALKLAARQGI-GLAITDHNQASGVVEAR--GQKINVPLVPGIEVSANDG---PHILLYF- 95
Cdd:COG0613     2 MKIDLHVHTTASDGSLSPEELVARAKAAGLdVLAITDHDTVAGYEEAAeaAKELGLLVIPGVEISTRWEgreVHILGYGi 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  96 -YSVSDLLDFYRRHIEKNRRNgpftaiRLSTPEILERREDYSCIAAEAHPCGYAFlnrgveRCVAGACIGEEVFSRLDAL 174
Cdd:COG0613    82 dPEDPALEALLGIPVEKAERE------WLSLEEAIDLIREAGGVAVLAHPFRYKR------GRWLDDLLEELADAGLDGI 149

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2535604632 175 EVICGGMARSHNLKAAGLAVAHGLGRTGGTDGHLLHE 211
Cdd:COG0613   150 EVYNGRHSPEDNERAAELAEEYGLLATGGSDAHGPEK 186
 
Name Accession Description Interval E-value
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 23-211 1.41e-31

5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];


Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 115.78  E-value: 1.41e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  23 LPADLHFHTRHSDSATRVRDALKLAARQGI-GLAITDHNQASGVVEAR--GQKINVPLVPGIEVSANDG---PHILLYF- 95
Cdd:COG0613     2 MKIDLHVHTTASDGSLSPEELVARAKAAGLdVLAITDHDTVAGYEEAAeaAKELGLLVIPGVEISTRWEgreVHILGYGi 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  96 -YSVSDLLDFYRRHIEKNRRNgpftaiRLSTPEILERREDYSCIAAEAHPCGYAFlnrgveRCVAGACIGEEVFSRLDAL 174
Cdd:COG0613    82 dPEDPALEALLGIPVEKAERE------WLSLEEAIDLIREAGGVAVLAHPFRYKR------GRWLDDLLEELADAGLDGI 149

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2535604632 175 EVICGGMARSHNLKAAGLAVAHGLGRTGGTDGHLLHE 211
Cdd:COG0613   150 EVYNGRHSPEDNERAAELAEEYGLLATGGSDAHGPEK 186
PHP_HisPPase_AMP cd07438
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ...
 25-207 1.21e-17

Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; The PHP domain of this HisPPase family has an unknown function. It has a second domain inserted in the middle that binds adenosine 5-monophosphate (AMP). The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to give histidinol. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to the other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.


Pssm-ID: 213993 [Multi-domain]  Cd Length: 155  Bit Score: 77.82  E-value: 1.21e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  25 ADLHFHTRHSDSATRVRDALKLAARQGI-GLAITDHNQASGVVEAR--GQKINVPLVPGIEVSANDGP---HILlyfysv 98
Cdd:cd07438     1 IDLHTHSTASDGTLSPEELVELAKEAGLkVLAITDHDTVAGLEEALaaAKELGIELIPGVEISTEYEGrevHIL------ 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  99 sdlldfyrrhieknrrnG-PFTAIRLstpeILErredysC--IAAEAHPCGYAFLNRGVERCVagacigEEVFSR-LDAL 174
Cdd:cd07438    75 -----------------GsPEEAIEL----IHA------AggVAVLAHPGLYKLSRKKLEELI------EELKEAgLDGI 121

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2535604632 175 EVICGGMARSHNLKAAGLAVAHGLGRTGGTDGH 207
Cdd:cd07438   122 EVYHPYHSPEDRERLLELAKEYGLLVTGGSDFH 154
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 21-254 2.03e-12

CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is found in several partially characterized metallohydrolases, including McbA and CehA. Both were studied as hydrolases of carbaryl, a xenobiotic compound that does not contain a phosphate group, suggesting that presuming members of this family to be phosphoesterases (like many PHP domain-containing proteins) may be incorrect.


Pssm-ID: 468321 [Multi-domain]  Cd Length: 315  Bit Score: 66.19  E-value: 2.03e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  21 GLLPADLHFHTRHSDSATRVRDALKLAARQGI-GLAITDHNQASGVVEARG---QKINVPLVPGIEVSANDGpHILLYfy 96
Cdd:NF038032    1 GWYSGDLHIHTNHSDGPTTPEELARAALAEGLdVIALTDHNTISGRAYFAEllaSERGLLVIPGMEVTTFWG-HMNLL-- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  97 svsdlldfyrrhiekNRRNGPFTAIRLSTPEIlerrEDYSCIAAEAHP----CGYA--FlNRGVERC-VAGACIGEEVFS 169
Cdd:NF038032   78 ---------------GLDLDPYIDWRNTDPGS----PDIDEVIDEAHRqgglVGIAhpF-SPGGPLCtGCGWEALIDDLG 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632 170 RLDALEVICGGMARSHNLKAAG-----LAVAHGLGRTGGTDGHLL-HELGG----VVTCAEADTVEELLDAVRMKNTVV- 238
Cdd:NF038032  138 KVDAIEVWNTPDPAPTNERALAlwyhlLNEGFRITATGGSDAHDDfDERPGlprtYVYVDGELSYEAILAALKAGRTYVt 217

                         250
                  ....*....|....*.
gi 2535604632 239 IGrerPLVEKAVMGTA 254
Cdd:NF038032  218 TG---PLLELTVNGTA 230
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 26-87 1.04e-09

DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family of hypothetical proteins


Pssm-ID: 197753 [Multi-domain]  Cd Length: 67  Bit Score: 53.81  E-value: 1.04e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2535604632   26 DLHFHTRHS--DSATRVRDALKLAARQGI-GLAITDHNQASGVVEAR--GQKINVPLVPGIEVSAND 87
Cdd:smart00481   1 DLHVHSDYSllDGALSPEELVKRAKELGLkAIAITDHGNLFGAVEFYkaAKKAGIKPIIGLEANIVD 67
PHP pfam02811
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ...
 26-83 6.13e-07

PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain.


Pssm-ID: 460705 [Multi-domain]  Cd Length: 171  Bit Score: 48.31  E-value: 6.13e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2535604632  26 DLHFHTRHS--DSATRVRDALKLAARQGI-GLAITDHNQASGVVE----ARGQKINvPLVpGIEV 83
Cdd:pfam02811   1 HLHVHSEYSllDGAARIEELVKRAKELGMpAIAITDHGNLFGAVEfykaAKKAGIK-PII-GCEV 63
dnaE PRK05673
DNA polymerase III subunit alpha; Validated
 27-83 2.73e-04

DNA polymerase III subunit alpha; Validated


Pssm-ID: 235554 [Multi-domain]  Cd Length: 1135  Bit Score: 42.40  E-value: 2.73e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2535604632   27 LHFHTRHS--DSATRVRDALKLAARQGIG-LAITDHNQASGVVE----ARGQKINvPLVpGIEV 83
Cdd:PRK05673     5 LHVHSEYSllDGAAKIKPLVKKAAELGMPaVALTDHGNLFGAVEfykaAKGAGIK-PII-GCEA 66
 
Name Accession Description Interval E-value
YciV COG0613
5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and ...
 23-211 1.41e-31

5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism];


Pssm-ID: 440378 [Multi-domain]  Cd Length: 188  Bit Score: 115.78  E-value: 1.41e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  23 LPADLHFHTRHSDSATRVRDALKLAARQGI-GLAITDHNQASGVVEAR--GQKINVPLVPGIEVSANDG---PHILLYF- 95
Cdd:COG0613     2 MKIDLHVHTTASDGSLSPEELVARAKAAGLdVLAITDHDTVAGYEEAAeaAKELGLLVIPGVEISTRWEgreVHILGYGi 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  96 -YSVSDLLDFYRRHIEKNRRNgpftaiRLSTPEILERREDYSCIAAEAHPCGYAFlnrgveRCVAGACIGEEVFSRLDAL 174
Cdd:COG0613    82 dPEDPALEALLGIPVEKAERE------WLSLEEAIDLIREAGGVAVLAHPFRYKR------GRWLDDLLEELADAGLDGI 149

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2535604632 175 EVICGGMARSHNLKAAGLAVAHGLGRTGGTDGHLLHE 211
Cdd:COG0613   150 EVYNGRHSPEDNERAAELAEEYGLLATGGSDAHGPEK 186
PHP_HisPPase_AMP cd07438
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) ...
 25-207 1.21e-17

Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; The PHP domain of this HisPPase family has an unknown function. It has a second domain inserted in the middle that binds adenosine 5-monophosphate (AMP). The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to give histidinol. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to the other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.


Pssm-ID: 213993 [Multi-domain]  Cd Length: 155  Bit Score: 77.82  E-value: 1.21e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  25 ADLHFHTRHSDSATRVRDALKLAARQGI-GLAITDHNQASGVVEAR--GQKINVPLVPGIEVSANDGP---HILlyfysv 98
Cdd:cd07438     1 IDLHTHSTASDGTLSPEELVELAKEAGLkVLAITDHDTVAGLEEALaaAKELGIELIPGVEISTEYEGrevHIL------ 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  99 sdlldfyrrhieknrrnG-PFTAIRLstpeILErredysC--IAAEAHPCGYAFLNRGVERCVagacigEEVFSR-LDAL 174
Cdd:cd07438    75 -----------------GsPEEAIEL----IHA------AggVAVLAHPGLYKLSRKKLEELI------EELKEAgLDGI 121

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2535604632 175 EVICGGMARSHNLKAAGLAVAHGLGRTGGTDGH 207
Cdd:cd07438   122 EVYHPYHSPEDRERLLELAKEYGLLVTGGSDFH 154
PHP_HisPPase cd07432
Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase ...
 25-207 8.94e-13

Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase; HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. HisPPase can be classified into two types: the bifunctional HisPPase found in proteobacteria that belongs to the DDDD superfamily and the monofunctional Bacillus subtilis type that is a member of the PHP family. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.


Pssm-ID: 213987 [Multi-domain]  Cd Length: 129  Bit Score: 63.80  E-value: 8.94e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  25 ADLHFHTRHS-DSATRVRDALKLAARQGI-GLAITDHNQASGVVEAR--GQKINVPLVPGIEVSAndgphillyfysvsd 100
Cdd:cd07432     1 ADLHIHSVFSpDSDMTPEEIVERAIELGLdGIAITDHNTIDGAEEALkeAYKDGLLVIPGVEVTL--------------- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632 101 lldfyrrhieknrrngpftairlstpeilerredysCIAaeAHPCGYAFLNRGVErcvagacIGEEVFSRLDALEVICGG 180
Cdd:cd07432    66 ------------------------------------VVL--AHPDRPSRYGLSDL-------ILKPLIKNGDAIEVNNSR 100

                         170       180
                  ....*....|....*....|....*...
gi 2535604632 181 MARSHNLKAAG-LAVAHGLGRTGGTDGH 207
Cdd:cd07432   101 LRYGLNNLAAKrYAELGGLPITGGSDAH 128
CehA_McbA_metalo NF038032
CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is ...
 21-254 2.03e-12

CehA/McbA family metallohydrolase domain; This domain, a branch of the PHP superfamily, is found in several partially characterized metallohydrolases, including McbA and CehA. Both were studied as hydrolases of carbaryl, a xenobiotic compound that does not contain a phosphate group, suggesting that presuming members of this family to be phosphoesterases (like many PHP domain-containing proteins) may be incorrect.


Pssm-ID: 468321 [Multi-domain]  Cd Length: 315  Bit Score: 66.19  E-value: 2.03e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  21 GLLPADLHFHTRHSDSATRVRDALKLAARQGI-GLAITDHNQASGVVEARG---QKINVPLVPGIEVSANDGpHILLYfy 96
Cdd:NF038032    1 GWYSGDLHIHTNHSDGPTTPEELARAALAEGLdVIALTDHNTISGRAYFAEllaSERGLLVIPGMEVTTFWG-HMNLL-- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  97 svsdlldfyrrhiekNRRNGPFTAIRLSTPEIlerrEDYSCIAAEAHP----CGYA--FlNRGVERC-VAGACIGEEVFS 169
Cdd:NF038032   78 ---------------GLDLDPYIDWRNTDPGS----PDIDEVIDEAHRqgglVGIAhpF-SPGGPLCtGCGWEALIDDLG 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632 170 RLDALEVICGGMARSHNLKAAG-----LAVAHGLGRTGGTDGHLL-HELGG----VVTCAEADTVEELLDAVRMKNTVV- 238
Cdd:NF038032  138 KVDAIEVWNTPDPAPTNERALAlwyhlLNEGFRITATGGSDAHDDfDERPGlprtYVYVDGELSYEAILAALKAGRTYVt 217

                         250
                  ....*....|....*.
gi 2535604632 239 IGrerPLVEKAVMGTA 254
Cdd:NF038032  218 TG---PLLELTVNGTA 230
POLIIIAc smart00481
DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family ...
 26-87 1.04e-09

DNA polymerase alpha chain like domain; DNA polymerase alpha chain like domain, incl. family of hypothetical proteins


Pssm-ID: 197753 [Multi-domain]  Cd Length: 67  Bit Score: 53.81  E-value: 1.04e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2535604632   26 DLHFHTRHS--DSATRVRDALKLAARQGI-GLAITDHNQASGVVEAR--GQKINVPLVPGIEVSAND 87
Cdd:smart00481   1 DLHVHSDYSllDGALSPEELVKRAKELGLkAIAITDHGNLFGAVEFYkaAKKAGIKPIIGLEANIVD 67
PHP pfam02811
PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative ...
 26-83 6.13e-07

PHP domain; The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain.


Pssm-ID: 460705 [Multi-domain]  Cd Length: 171  Bit Score: 48.31  E-value: 6.13e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2535604632  26 DLHFHTRHS--DSATRVRDALKLAARQGI-GLAITDHNQASGVVE----ARGQKINvPLVpGIEV 83
Cdd:pfam02811   1 HLHVHSEYSllDGAARIEELVKRAKELGMpAIAITDHGNLFGAVEfykaAKKAGIK-PII-GCEV 63
DnaE COG0587
DNA polymerase III, alpha subunit [Replication, recombination and repair];
27-94 8.06e-07

DNA polymerase III, alpha subunit [Replication, recombination and repair];


Pssm-ID: 440352 [Multi-domain]  Cd Length: 1050  Bit Score: 50.07  E-value: 8.06e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632   27 LHFHTRHS--DSATRVRDALKLAARQGI-GLAITDHNQASGVVE----ARGQkiNVPLVPGIEVS------ANDGPHILL 93
Cdd:COG0587      8 LHVHSEYSllDGASRPEELVARAAELGMpALAITDHGNLFGAVRfykaAKKA--GIKPIIGCELYvapgsrDDAGYHLVL 85


                   .
gi 2535604632   94 Y 94
Cdd:COG0587     86 L 86
PHP_C pfam13263
PHP-associated; This is a subunit, probably the alpha, of bacterial and eukaryotic DNA ...
 185-236 5.62e-06

PHP-associated; This is a subunit, probably the alpha, of bacterial and eukaryotic DNA polymerase III, associated with the PHP domain, pfam02811.


Pssm-ID: 433069 [Multi-domain]  Cd Length: 56  Bit Score: 42.94  E-value: 5.62e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2535604632 185 HNLKAAGLAVAHGLGRTGGTDGHLLHELGGVVT--CAEADTVEELLDAVRMKNT 236
Cdd:pfam13263   3 ANRKARRLAEKLGLPGTGGSDAHVLEEVGRAYTefEEDIRTEEDLLEAIRKGRT 56
PHP cd07309
Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2 ...
 25-84 5.75e-05

Polymerase and Histidinol Phosphatase domain; The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP in polymerases has trinuclear zinc/magnesium dependent proofreading activity. It has also been shown that the PHP domain functions in DNA repair. The PHP structures have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.


Pssm-ID: 213985 [Multi-domain]  Cd Length: 88  Bit Score: 40.87  E-value: 5.75e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2535604632  25 ADLHFHTRHSDSA-TRVRDALKLAARQGI-GLAITDHNQASGVVEAR----------GQKINVPLVPGIEVS 84
Cdd:cd07309     1 VDLHTHTVFSDGDhAKLTELVDKAKELGPdALAITDHGNLRGLAEFNtagk*nhikaAEAAGIKIIIGSEVN 72
dnaE PRK05673
DNA polymerase III subunit alpha; Validated
 27-83 2.73e-04

DNA polymerase III subunit alpha; Validated


Pssm-ID: 235554 [Multi-domain]  Cd Length: 1135  Bit Score: 42.40  E-value: 2.73e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2535604632   27 LHFHTRHS--DSATRVRDALKLAARQGIG-LAITDHNQASGVVE----ARGQKINvPLVpGIEV 83
Cdd:PRK05673     5 LHVHSEYSllDGAAKIKPLVKKAAELGMPaVALTDHGNLFGAVEfykaAKGAGIK-PII-GCEA 66
PHP_PolIIIA_DnaE3 cd12113
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ...
 27-83 1.16e-03

Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, the PolIIIA PHP exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such an activity has not been found. It has been shown that the PHP of PolIIIA has a trinuclear metal complex and is capable of proofreading activity. Bacterial genome replication and DNA repair mechanisms is related to the GC content of its genomes. There is a correlation between GC content variations and the dimeric combinations of PolIIIA subunits. Eubacteria can be grouped into different GC variable groups: the full-spectrum or dnaE1 group, the high-GC or dnaE2-dnaE1 group, and the low GC or polC-dnaE3 group.


Pssm-ID: 213997 [Multi-domain]  Cd Length: 283  Bit Score: 39.73  E-value: 1.16e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2535604632  27 LHFHTRHS--DSATRVRDALKLAARQGI-GLAITDHNQASGVVE----ARGQKINvPLVpGIEV 83
Cdd:cd12113     5 LHVHTEYSllDGAIRIKDLVKRAKELGMpALAITDHGNMFGAIEfykaAKKAGIK-PII-GCEV 66
HIS2 COG1387
Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and ...
 23-66 1.30e-03

Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and metabolism, General function prediction only]; Histidinol phosphatase or related hydrolase of the PHP family is part of the Pathway/BioSystem: Histidine biosynthesis


Pssm-ID: 440997 [Multi-domain]  Cd Length: 232  Bit Score: 39.37  E-value: 1.30e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2535604632  23 LPADLHFHTRHSDSATRVRDALKLAARQGI-GLAITDHNQASGVV 66
Cdd:COG1387     1 MRGDLHTHTTYSDGEGTIEEMVEAAIELGLeYIAITDHSPSLFVA 45
dnaE PRK06826
DNA polymerase III DnaE; Reviewed
 27-83 2.54e-03

DNA polymerase III DnaE; Reviewed


Pssm-ID: 235868 [Multi-domain]  Cd Length: 1151  Bit Score: 39.49  E-value: 2.54e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2535604632   27 LHFHTRHS--DSATRVRDALKLAARQGI-GLAITDHNQASGVVE----ARGQKINvPLVpGIEV 83
Cdd:PRK06826     8 LHVHTEYSllDGSARIKDLIKRAKELGMdSIAITDHGVMYGVVDfykaAKKQGIK-PII-GCEV 69
dnaE2 PRK05672
error-prone DNA polymerase; Validated
 25-94 2.90e-03

error-prone DNA polymerase; Validated


Pssm-ID: 235553 [Multi-domain]  Cd Length: 1046  Bit Score: 39.07  E-value: 2.90e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632   25 ADLHFHTRHS--DSATRVRDALKLAARQGI-GLAITDHNQASGVVEA--RGQKINVPLVPGIEVS-----ANDGPHILLY 94
Cdd:PRK05672     6 AELHCHSNFSflDGASHPEELVERAARLGLrALAITDECGLAGVVRAaeAAKELGLRLVIGAELSlgpdpDPGGPHLLVL 85
PHP_PolIIIA_DnaE2 cd07434
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ...
 47-94 2.93e-03

Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; PolIIIA DnaE2 plays a role in SOS mutagenesis/translesion synthesis and has dominant effects in determining GC variability in the bacterial genome. PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. PolC PHP is located in a different location compared to dnaE1, 2, and 3. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP domains found in DnaEs of thermophilic origin exhibit 3'-5' exonuclease activity.


Pssm-ID: 213989 [Multi-domain]  Cd Length: 260  Bit Score: 38.21  E-value: 2.93e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2535604632  47 AARQGI-GLAITDHNQASGVVEARG--QKINVPLVPGIEVSANDGPHILLY 94
Cdd:cd07434    26 AAELGYrALAITDECSLAGVVRAHAaaKELGLKLIVGSELVLADGTRLVLL 76
CFEM pfam05730
CFEM domain; This fungal specific cysteine rich domain is found in some proteins with proposed ...
 134-179 3.45e-03

CFEM domain; This fungal specific cysteine rich domain is found in some proteins with proposed roles in fungal pathogenesis. The structure of the CFEM domain containing protein 'Surface antigen protein 2' from Candida albicans has been solved.


Pssm-ID: 399033 [Multi-domain]  Cd Length: 66  Bit Score: 35.51  E-value: 3.45e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2535604632 134 DYSCIaaeahpCGYAFLNRGVERCVAGACIGEEVFSRLDALEVICG 179
Cdd:pfam05730  27 DFACL------CTNPNFQGAITDCVASACTADDALAAINAASSICS 66
PRK08392 PRK08392
hypothetical protein; Provisional
 26-59 3.99e-03

hypothetical protein; Provisional


Pssm-ID: 169423 [Multi-domain]  Cd Length: 215  Bit Score: 37.84  E-value: 3.99e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2535604632  26 DLHFHTRHSDSATRVRDALKLAARQGIGL-AITDH 59
Cdd:PRK08392    2 DLHTHTVYSDGIGSVRDNIAEAERKGLRLvGISDH 36
PHP_HisPPase_Chlorobi_like cd12112
Polymerase and Histidinol Phosphatase domain of Chlorobi like; The PHP (also called histidinol ...
 23-91 8.67e-03

Polymerase and Histidinol Phosphatase domain of Chlorobi like; The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. Chlorobi PHP is uncharacterized protein. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. The HisPPase can be classified into two types: the bifunctional Hisppase found in proteobacteria that belongs to the DDDD superfamily and the monofunctional Bacillus subtilis type that is a member of the PHP family. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel.


Pssm-ID: 213996 [Multi-domain]  Cd Length: 235  Bit Score: 36.92  E-value: 8.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535604632  23 LPADLHFHTRHSDSA----TRVRDALklaaRQGI-GLAITDH---------------NQASGVVEARGQKINVPLVPGIE 82
Cdd:cd12112    13 LKCDFHTHTVFSDGHvwpeIRVREAW----REGLdAIAITEHieyrphkediphpdrNRSYKIAKEAAESKGLLIIPGAE 88

                          90
                  ....*....|
gi 2535604632  83 VSANDGP-HI 91
Cdd:cd12112    89 ITREKPPgHL 98
 
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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