1M65


Conserved Protein Domain Family
PHP_HisPPase_Ycdx_like

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cd07437: PHP_HisPPase_Ycdx_like 
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Polymerase and Histidinol Phosphatase domain of Ycdx like
PHP Ycdx-like is a stand alone PHP domain similar to Ycdx E. coli protein with an unknown physiological role. 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. 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. YcdX may be involved in swarming.
Statistics
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PSSM-Id: 213992
Aligned: 108 rows
Threshold Bit Score: 287.802
Created: 14-Dec-2011
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
active site
Conserved site includes 9 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:The active site of PHP is characterized by a trinuclear metal cluster liganded by histidines, aspartate and glutamate.
  • Structure:1M65; Escherichia coli YcdX PHP domain binds Zn2+ and 2Na2+ ions

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1             # #     #                        #                                         
1M65_A         2 YPVDLHMHTVASTHAYSTLSDYIAQAKQKGIKLFAITDHGPDMed------------aPHHWHFINMRI-WPRVVDGVGI 68  Escherichia coli
ZP_03568246    3 ILCDVHTHTMYSRHAYSTMEENVREAASQGFELLGLTDHFSSMlyee--------qilKNFQFFLNLNV-IPEVWHGVRV 73  Atopobium rimae...
YP_003800108  27 IACDVHTHTLFSRHAYSTIEENVRAAAGRHIELLGSTDHFSSMlhreatgerasgydlRDNQYFLNYAV-WPRTWHGVRL 105 Olsenella uli D...
YP_003829525   4 IECDTHTHTLYSRHAYSTIEENIRSASEKGIKLLASTDHFSDMlfgd-------yenvKNYQYFFCCNN-WPRQWKGVTL 75  Butyrivibrio pr...
ZP_04452483    4 IKTDTHTHTLASGHAYSTIEENLRAGKEQGLELVGTTDHFSSFfvps--------ttfACYGFFINRGD-LPEIWHGVRL 74  Abiotrophia def...
ZP_02860859    3 IVADLHTHTSVSHHAYSTIVEMCKGAKKAGHIALGTTDHGPALqd------------gAHQWHFQSLEMfIPRILEGVYV 70  Anaerofustis st...
CBL33324       3 FVADMHTHTLASDHAYSTISENAASAAKAGLSYLGMTDHCINMed------------sPHIWHFCNMGV-IPHFLSGVRI 69  Eubacterium sir...
ZP_02861170    3 IIADLHTHTNISEHAFSTLEENCIAGNKIGLDAVGITNHGPALed------------gASHWHFKSLGKnNPGKMHGVYL 70  Anaerofustis st...
YP_003786586   3 IIADLHTHTIVSQHAFSTVDEIINAAKDKGFLAVAITDHGPKSsd------------gAKPVHFRSMHN-IPEYVNGIRV 69  Brachyspira pil...
ZP_07664377    4 IACDTHSHTLLSRHAFSTIQENVHAAAIARLELLGCTDHFSSMitkevdleraqtydlRDFQHFINYSA-WPSSWEGVRV 82  Atopobium vagin...
Feature 1            #                                               #                           
1M65_A        69 LRGIEANiKNVDGEID--------------------CSGKMFDSLDLIIAGFHEPVFAPHDk-ATNTQAMIATIASGNVH 127 Escherichia coli
ZP_03568246   74 LHGCEVDiVDLEGNLFghdivvdtsingdklahpryLGNLVLSRCDYAVASIHGKDWARSAtpAQVTRMYVNVLDNPHVL 153 Atopobium rimae...
YP_003800108 106 LHGCEADiVDLDGRLFgydapvayeingaslgcattLKERVFRDCDYVIASVHNAEFAHGAslARTTAMYVHALEDPKVL 185 Olsenella uli D...
YP_003829525  76 LRGCEADiVDMEGNFFghdiairksvigdtydpeknLQEMVFEKLDFVIASVHAKRHTIGKsvAENTNMYIKALENPKVF 155 Butyrivibrio pr...
ZP_04452483   75 LFGAEVDiVDLKGNLFghdiyipfp---ykngnkvtYEEGILNRLDYLIASVHFKEFTANStvVENTELYIKALEHDKVK 151 Abiotrophia def...
ZP_02860859   71 LRGAEANiLQPDGRLD--------------------IPDHVLDTLDYVVASIHNETFLERDp-DRITEIMLKVLENPRID 129 Anaerofustis st...
CBL33324      70 IKGVEADlTGYNGELD--------------------INDDIYYNVEWINASMHNPCIIPGTa-EQHTNAYIKVMDNPKVC 128 Eubacterium sir...
ZP_02861170   71 ISGIELN-IMQDGSID--------------------LEEEYLSNLDLVIASFHQEVFYPKDk-NHVNDMLNEAITNKNIN 128 Anaerofustis st...
YP_003786586  70 LRGAEANiIDYDGNID--------------------LRKNVLECLDFVIASYHEDSITPSNi-ESHTNGYIGLIKNSYVD 128 Brachyspira pil...
ZP_07664377   83 LHGCEVDiVDMEGHIFgenipvryqiggrlydhvesLADKVCSQCDYALASLHNIDFARQAskSEVTRMYMKTLDNPYVL 162 Atopobium vagin...
Feature 1           #                                                             # #            
1M65_A       128 IISHPGNPKYEIDVKAVAEAAAKHQVALEINNSSFlh-sRKGSEDNCREVAAAVRDAGgWVALGSDSHTAFTMGEFEECL 206 Escherichia coli
ZP_03568246  154 ILGHLGRSFLDFDVDALVCECRDRGKLIEINEATYaeghATEQQDRCRRIAERCAELGcMVSFGSDAHIATRIAHADCVS 233 Atopobium rimae...
YP_003800108 186 ILGHTGRSAVPFDMDEVLAVAKDLGKLIEINEATLv--sHQEASGACRRIAERCAELGvMVSTGTDAHISCDIGRLDRVR 263 Olsenella uli D...
YP_003829525 156 FIGHIGRAGVPFEMDEVLKRARDLHKPIEINEHSFs--wEGHHQMVCRELAVRCAELGvSICVNTDAHMALEIGETGRAQ 233 Butyrivibrio pr...
ZP_04452483  152 ILGHIGRSGLEFDVEEVVRAAKAMNKMIEINEASFg--hGDIIKERCRRIAVTCAETGtKIAVNSDAHCSFKIGKYPNAI 229 Abiotrophia def...
ZP_02860859  130 ILGHLGAPIFKFDYETLISKCNEYDKVVEVNNNSFy--aRKGSKENCLEIAKLCKKYDvPISVNSDAHFCLGVGKIDRAK 207 Anaerofustis st...
CBL33324     129 VLGHTESADYPYDYDAVTKACKEKNVAMEFNVSRFr--sQTSVQRLHDIILPTCAKNGcYVIVDSDAHFCDKIGAFKKAE 206 Eubacterium sir...
ZP_02861170  129 VFGHLGNEIFKFDYEDIISKCNKYDKVVEVNNHSFv--qRPGSDVNCLEIIKLCKKYEvPIMVNSDAHISSSIGHFEDAI 206 Anaerofustis st...
YP_003786586 129 CLGHVGNPKFAFDMEKIIKLCKDYNKLIEINSASFk--vRKGSDTNCKEVALLCKKYNlNIVVTSDSHSKYNVGNHEAAL 206 Brachyspira pil...
ZP_07664377  163 ILGHTGRYGVDFDIKELCAYAKEKGKLIEINEATL----AGYPTNTCKEIALCCAETEtMITTGSDSHISMHIGQFSHVK 238 Atopobium vagin...
Feature 1                                    
1M65_A       207 KILDAVDFPPERILNVSPRRLLNFLESR 234 Escherichia coli
ZP_03568246  234 RLLDEIHFPEELMACRDAATFLKVKEAA 261 Atopobium rimae ATCC 49626
YP_003800108 264 SLLGEIGFPQRLVATRDAETFMGVLSRA 291 Olsenella uli DSM 7084
YP_003829525 234 AMLEEIGFPQELIINRTRESFLQGLSEC 261 Butyrivibrio proteoclasticus B316
ZP_04452483  230 KMLEEIDFPEELIGNRDAETFLSMVCPK 257 Abiotrophia defectiva ATCC 49176
ZP_02860859  208 GIIEASDFPEELIINASPENLQKYFMRK 235 Anaerofustis stercorihominis DSM 17244
CBL33324     207 ALLKDIDFPEELIVNADLERFENFLRLR 234 Eubacterium siraeum V10Sc8a
ZP_02861170  207 AVIEKAGYPEELIVNSSMDRLQDYFKHI 234 Anaerofustis stercorihominis DSM 17244
YP_003786586 207 NMLEDINFPEDLILNADFDRLMNYLNSR 234 Brachyspira pilosicoli 95/1000
ZP_07664377  239 KLLEEIHFPQKLIATTDSSTFLRVMHHA 266 Atopobium vaginae DSM 15829

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