1PDA,3ECR,1YPN,4HTG


Conserved Protein Domain Family
PBP2_HMBS

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cd00494: PBP2_HMBS 
Click on image for an interactive view with Cn3D
Hydroxymethylbilane synthase possesses the type 2 periplasmic binding protein fold
Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, vitamin B12 and related macrocycles. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This family includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor.
Statistics
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PSSM-Id: 270213
View PSSM: cd00494
Aligned: 18 rows
Threshold Bit Score: 258.374
Threshold Setting Gi: 159483239
Created: 6-Mar-2002
Updated: 2-Mar-2014
Structure
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Program:
Drawing:
Aligned Rows:
 
ligand bindingdimer interface
Conserved site includes 18 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding site [chemical binding site]
Evidence:
  • Structure:1PDA; Escherichia coli porphobilinogen deaminase binds dipyrromethane cofactor, contacts at 4 A.
    View structure with Cn3D
  • Citation:PMID 1522882
  • Structure:3ECR; Human porphobilinogen deaminase binds dipyrromethane cofactor, contacts at 4 A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1              #   #                                                             #       
1PDA_A         5 VLRIATRqspLALWQAHYVKDKLMAShp----glVVELVPMVTRGDVIldtpl-----------akvggKGLFVKELEVA 69  Escherichia coli
Q59293         3 KIRIGSRdskLAIIQSELIMSAIRKYdp----diELELITMKTTGDKIldktl-----------dkiegKGLFVKELDNA 67  Clostridium josui
A9A1A1         2 KYIVGARgsqLSVAQTNLVIAELKKAhp----dtEYEIKTITTKGDTDsrplf------------tidqKGIFEKEIDRA 65  Nitrosopumilus ...
YP_002308952  10 NLRVISRnspLSLLQVKEVFSFFPNI--------DYQLITIESFGDKNkhvalfdisnvssffleeesiSDFFTRELDEA 81  Candidatus Azob...
EGB07188      17 HVKIATRpspLAVKQAERVAETLRRAdp----alTTELVRISSTGEYRnntplp----------laldpTVDFTGLLDDA 82  Aureococcus ano...
CAJ89766       6 LIRIVSRdspMALAQVERVRAGLAALhp----gvRTEVVPVKTTGDKWlgdls------------qvegKGAFTKEVDAA 69  Streptomyces am...
YP_003551802  42 PLVLASRastLAMAQAELVRVALKPV--------ASRIEPFTTKGDLIldrpl-----------vevggKGVFIKELERS 102 alpha proteobac...
XP_001699668  62 PLVIATRpskLAKEQTRQVQQLLLAAaqlkdeqlQLSTLELASRGDTTqgvsl------------rslgSGAFTEELDQA 129 Chlamydomonas r...
NP_787860      3 PLRIGTRsslLATAQTAQVQKTMRDVf-------LLDTQQVLIQTGSVrr------------------rDGSFVAALRTA 57  Tropheryma whip...
NP_867485     11 RLRIATRespLAMWQAEHVAKLLKKHg------fQTEIVPLVSKGDTDmrpid------------gtrqVGLFTKRIQQA 72  Rhodopirellula ...
Feature 1                     ##                                                         ### ##  
1PDA_A        70 LLenraDIAVHSMKDVP--VEFPQG-LGLVTICEREDp-rDAFVSNNyds-----------ldaLPAGSIVGTSSLRRQC 134 Escherichia coli
Q59293        68 LYnnevDITVHSYKDMP--LEENPE-LPVVALSKREDp-rDAFILPQn----------------GENGEPIGSSSLRRQL 127 Clostridium josui
A9A1A1        66 VAqkevDFAVHSLKDVP--SELDDN-LVLACIPKRETv-nDVFISPDgst-----------ldsIKPGSVIGTSSLRRAV 130 Nitrosopumilus ...
YP_002308952  82 LIynkaDIAVHSAKDLP--YPLPYD-LELFALFQAMDk-sDSLISRNnlt-----------leqLPPRARVGTSSQKRKT 146 Candidatus Azob...
EGB07188      83 VGsgavDVAVHSLKDLPp-ANRWRGdLRVACHLPRTEsaaDALVGYAsm-------------dlVPRGARVGTASQRRRA 148 Aureococcus ano...
CAJ89766      70 LLsdeaDLAVHCVKDVPadRPLPAG-TVFAAFLERDDv-rDALIHPDglt-----------ldeLPAGTRVGTSSVRRVA 136 Streptomyces am...
YP_003551802 103 LLagesDAAVHSMKDME--SDFAAG-TMIGAVLPREDr-rDALVGSYadl------------daLPDGAIVGTSSVRRRA 166 alpha proteobac...
XP_001699668 130 VLsgaaDMSVHSLKDCP--AALAPG-LLLAACLPRADp-rDVLIAPEats-----------lgeLVPGSRVGTSSSRRAA 194 Chlamydomonas r...
NP_787860     58 LLegecDLAVHSLKDIP--IAPHEG-TLITAVLPREDp-cDVLCARKdlt-----------lttLPSGAKVGTASARRRA 122 Tropheryma whip...
NP_867485     73 LVddeaDVAVHSLKDLP--TEPDSR-FVLAAVPPRESv-lDALVFADnsphlesqtgaespldyLPQGARVGTGSTRRLA 148 Rhodopirellula ...
Feature 1                     #####  #                                        #                  
1PDA_A       135 QLAERrpdLIIRSLRGNVGTRLSKLDNgeyDAIILAvAGLKRLGles-riRAALPPeisLPAVGQGAVGIECRLdd---- 209 Escherichia coli
Q59293       128 QLKELfpgCKTAPIRGNVQTRLKKLDSgefSAIVLAaAGIKRLGles-riGRYFSVdeiLPAASQGIIAVQGRVg----- 201 Clostridium josui
A9A1A1       131 QVSRKrpdVTVKPIRGNIETRIKKASGenyDAIVLAkAGISRLGvd--vkYTELSTddfSPSPGQGAIAIVARAdd---- 204 Nitrosopumilus ...
YP_002308952 147 ELLKIrpdLEVVSIRGNIEERIAKMDNgfiDALIVAtCALIRLGm----eARIACIlpfETHSLQGNLAIVGRKn----- 217 Candidatus Azob...
EGB07188     149 LLRCArpdLDVVTVRGNVHARLETLDRgdvDALILGaAGLQRLElldarrHAILSFdemLPAPAQGIVGAVARGdg---- 224 Aureococcus ano...
CAJ89766     137 QLAAThphLRCVPFRGNANRRLAKLAAgeaDALLLAvAGLERIGrrd-viSEVLSPetmMPPIGAGILALQCREgd---- 211 Streptomyces am...
YP_003551802 167 LLLHHrpdLRIKLLRGNINKRIAKLNQgdyDAIILAvAGLKRLKls--ldYTPLDEklmPTAAAQGALAVQLCDpslaqg 244 alpha proteobac...
XP_001699668 195 QIKHSfphLQVVQLRGNVDSRLGRIRSrdiGATVLAaAGLKRLG------VMNSDEgdtTATGAVGVVCRADDEwv---- 264 Chlamydomonas r...
NP_787860    123 QILNFrpdLDVVSLRGNIDKRLIHLDTl--DAIVLSaAGLKRIDred-aiTESFDIhdwPTAAGQGSLAIEVCRaqld-- 197 Tropheryma whip...
NP_867485    149 QLKQLrpdLEVLPIRGNVQTRLAKLNAgefDAIVLAhAGILRLEmtd-lpHRLFPLdemIPAPGQGALGIEVRSdd---- 223 Rhodopirellula ...
Feature 1                                                        #                               
1PDA_A       210 ------sRTRELLAaln------hheTALRVTAERAMNTRL----EGACQVP----IGSYAELIdg----eIWLRGLVGA 265 Escherichia coli
Q59293       202 -------ENFDFLKlfh------seeSLCISLAERTFVREM----NGGCSTP----IAAYATIQgs----eIILKGLYCN 256 Clostridium josui
A9A1A1       205 ------sKTIEMLKkie------dpdSRLEIEAERALSDFV----DSGCRFP----VGAYAKSNgs----eMTLTVTAFS 260 Nitrosopumilus ...
YP_002308952 218 ------dKNVKNLFciqdirkrygkvSLVGFGPGDPDLLTIgg-yKALLSAD----IIFYDDLLnq----eFLSRFLVEK 282 Candidatus Azob...
EGB07188     225 ------gALGDLLArad------drdARIAATAERAVLDVAdaasPGAGRPP----TSAAMTRDga----aWLLRARLTR 284 Aureococcus ano...
CAJ89766     212 ------tDLIEAVSglg------hpaTHREASAERMFLHVL----QGHCNSP----IAGYARVDrg---geLSLRACVFT 268 Streptomyces am...
YP_003551802 245 ekairqqAVFDAISpla------cvnSTIEVTAERAMLAHL----DGSCHTP----IAASARFVdd---ktLRLDGMVLS 307 alpha proteobac...
XP_001699668 265 ------vGLLDAIShr---------gTALEVAAERACLAALlg-gGGACQRSafpdIAWACHTRhdpdsntMDLDCLVAD 328 Chlamydomonas r...
NP_787860    198 ----dpqNRVAVTYrld------npmARVTTTAERGVLSLL----QADCFSP----IAVHAVYTand--ksLGLHAKVFS 257 Tropheryma whip...
NP_867485    224 ------aGAMDAIAnln------daaARLAATAERKVLSEL----HGGCLAP----IACHAKLEtsnhgteLCLRAIVMS 283 Rhodopirellula ...
Feature 1                       
1PDA_A       266 Pd--GSQIIRGERRG 278 Escherichia coli
Q59293       257 Et--TGELRKECVSG 269 Clostridium josui
A9A1A1       261 Vd--GKQFLHVSKTG 273 Nitrosopumilus maritimus SCM1
YP_002308952 283 VyvgKRKEVHRFHQG 297 Candidatus Azobacteroides pseudotrichonymphae genomovar. CFP2
EGB07188     285 Pd--GSRSAATTSTV 297 Aureococcus anophagefferens
CAJ89766     269 Pd--GKTRLNAHEWA 281 Streptomyces ambofaciens ATCC 23877
YP_003551802 308 Sd--GSAAFRRTMTA 320 alpha proteobacterium IMCC1322
XP_001699668 329 Le--GKELFRYTEFY 341 Chlamydomonas reinhardtii
NP_787860    258 Rd--GKIFCESIRFA 270 Tropheryma whipplei str. Twist
NP_867485    284 Ad--GEQRLQEDARI 296 Rhodopirellula baltica SH 1

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