2YPN,1AH5


Conserved Protein Domain Family
HMBS
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cd00494: HMBS (this model, PSSM-Id:29604 is obsolete and has been replaced by 270213)
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Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II. HMBS is found in all organisms except viruses.
Links
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Statistics
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PSSM-Id: 29604
Aligned: 22 rows
Threshold Bit Score: -1
Created: 6-Mar-2002
Updated: 9-Mar-2011
Structure
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Program:
Drawing:
Aligned Rows:
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active sitedomain
Conserved site includes 21 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:2YPN_A: binds 3-{2-[4-(2-carboxyethyl)-3-carboxymethyl-5H-pyrrol-2-ylmethyl]-4-carboxymethyl-5-methyl-2H-pyrrol-3-yl}-propionic acid
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1              #   #                                                                  
2YPN_A      6 LRIATRQSPLALWQAHYVKDKLMAshpglVVELVPMVTRGDVIlDTPLAKVg---gKGLFVKELEVALLEN-----RADI 77  Escherichia coli
2495174     4 LVIGSRGSELALWQANHIKERLKKec-liESEIQIVKTKGDKIlDTPLNKIg---gKGLFTKELEELLLKG-----AIDL 74  Helicobacter pylori
11269706    3 LIIATRKSKLAQVQTEKVMELLKEke-nvDSKKLLVMTEGDRRlDVSLNKIg---gKGLFVKEIELALLNK-----EAHG 73  Clostridium perfri...
11386862    5 IRIGTRNSTLALIQTNLVIEQIKQifpdiNCEIVPIITSGDLIqNKPLYDIg---gKALFLKEIEQALLDK-----KIDL 76  Rickettsia prowazekii
12644400    7 FPIGTRKSKLAVIQSEIIREELEKhyphlEFPIISRDTIGDEIlSKALFEFkrqlaKSLWTRELEALLVTN-----QCRI 81  fission yeast
122846      6 LHIGGRKSKLAVIQSNHVLKLIEEkypdyDCKVFTLQTLGDQIqFKPLYSFg---gKALWTKELEDHLYHDdp-skKLDL 81  baker's yeast
10720013   14 VQIGGRKSKLAVVQSEIVKKVIEDtfpnlSCSILALSTLGDKVqTQPLYTFg---gKSLWTKELEILLLDSvdefpKLDL 90  Candida albicans
2495178     2 IRIGTRGSKLALYQANKVAELLKNlg--yKVEIKIIKTTGDRVlDKKLSDIg----IGVFTKELDLAMLNN-----EIDI 70  Methanococcus jann...
6225498     3 LIVGTRGSKLALAQTNKVAERLKEr---yEVEIRIVKTAGDIMkDKPLYEFk---gMGAFVRALDTALAEG-----KVDV 71  Archaeoglobus fulg...
11386772    1 MIAGTRGSRLALVQTNHVIEMLSEvc-keKIEKKIIKTKGDRIrDSQLYSMd---sRGLFTRELDMAVLNE-----EVDL 71  Methanothermobacte...

Feature 1        # ##                                             ### ##               #      
2YPN_A     78 AVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNyds---ldaLPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGT 154 Escherichia coli
2495174    75 AVHSLKDVPVVFEKGLDLACITKRADVRDTFLSVKfpd---lmsLPKGAKVGTTSLRRSMQIKLKRQDLDTESLRGNVQT 151 Helicobacter pylori
11269706   74 AVHSMKDVPFELPSEFELVAMPEREDIRDAFVSLNgst---lsnLRKGARIGTSSIRRAEQLKLFRDDLEIVPIRGNVQT 150 Clostridium perfri...
11386862   77 AVHSLKDIPGKIPVELVIAAVLEREDPRDVLVCLNyqs---ietLPQNAVIGSSAVRRKAFIKKIRPDLNIKVFRGNVDS 153 Rickettsia prowazekii
12644400   82 LVHSLKDLPSEMPDGMVIACIPKRSCPLDAIVFKAgshyktvadLPPGSVVGTSSIRRRALLARNFPHLRFVDIRGNVGT 161 fission yeast
122846     82 IVHSLKDMPTLLPEGFELGGITKRVDPTDCLVMPFysaykslddLPDGGIVGTSSVRRSAQLKRKYPHLKFESVRGNIQT 161 baker's yeast
10720013   91 IVHSLKDMPTNLPEEFELGCIFQREDPRDAIVMKQgssykslkdLPAGAIVGTSSIRRSSQLIKNYPHLRFESVRGNIQT 170 Candida albicans
2495178    71 AVHSLKDIPTIWNENLMVGAVLERDSYHDLLIWNKdid----fnEDSKIVIGTSSMRRRAFLKFIYPNAKFELLRGNVDT 146 Methanococcus jann...
6225498    72 AVHSFKDVPSQRVEGTVVAAVIERDSPCDVLISRDgst---leeLDEGAVVGTSSLRRRAQLSRLRGDLRFENLRGNLDT 148 Archaeoglobus fulg...
11386772   72 AVHSLKDVPSDLDPDLAIAAVPPRESPAEVLVSRLdw-----edLPQGSKLGTSSLRREAFCNHHQKNFKMEPLRGNIDT 146 Methanothermobacte...

Feature 1     #              ###  #  #                   #  ##                                
2YPN_A    155 RLSKLDNG--EYDAIILAVAGLKRLGLes-riRAALPPeiSLPAVGQGAVGIECRLDDsRTRELLAalnhheTALRVTAE 231 Escherichia coli
2495174   152 RLKKLECG--EFDAIILAEAGLCRLEIqgakyRKAFSVeeMIPSMGQGALGVEMLKNHkHFATLQKlnd-ekSAFCCRLE 228 Helicobacter pylori
11269706  151 RIKKITEE--NLDGIILAAAGLKRLGMed-viSDYFDPkvFLPAIGQGALGIECLKGG-EFNDYFKaldskeVRTTVEAE 226 Clostridium perfri...
11386862  154 RIKKLMTG--EVDAIILSYAGLKRLNVfnqkyCHLIEYskMLPCIGQGVIAVEIRKDDnAMFNICSqinhlpTFELIKPE 231 Rickettsia prowazekii
12644400  162 RLAKLDAPdsQFDCLVLAAAGLFRLGLkd-riAQMLTApfVYYAVGQGALAVEVRADDkEMIEMLKplqhqeTLYACLAE 240 fission yeast
122846    162 RLQKLDDPksPYQCIILASAGLMRMGLen-riTQRFHSdtMYHAVGQGALGIEIRKGDtKMMKILDeicdlnATICCLSE 240 baker's yeast
10720013  171 RLNKLDQPnnEYCCLILASAGLIRLGLgh-riTSYLDD--MYYAVGQGALGIEIRKGDdNIKSILKkiedpiATICCLAE 247 Candida albicans
2495178   147 RLRKLKEG--LYDAIVLSEAGIIRLGVsl-edFNYKRLd-ILPAPAQGIIAVACKRDDeEMKSILKeinherTYLESLCE 222 Methanococcus jann...
6225498   149 RLRKLREG--NYDAIVVAEAGLKRLGLdreveYQPFPPevIVPPANQGIIAIATRKGEeDLVAFLNde---kTWLEAMVE 223 Archaeoglobus fulg...
11386772  147 RIRKVMDG--EVHATIMAEAGLKRLGLee-hiKRRFPVeyFTPAAGQGALAVITRADS-ELISSIGrithhpSLQEVTAE 222 Methanothermobacte...

Feature 1               #                                                                
2YPN_A    232 RAMNTRLEGGCQVPIGSYAELIdg-----eIWLRALVGAP-DGSQIIRGERRGap----qDAEQMGISLAEELLN 296 Escherichia coli
2495174   229 REFIKGLNGGCQIPIGVHASLMgd-----rVKIQAVLGLP-NGKEVITKEKQGdk----tKAFDLVQELLEEFLQ 293 Helicobacter pylori
11269706  227 RSFMKVLNGGCHSLIGAYSEVK--------DNDLYMIGTFtVNNRIVKKDILGnk----eDNILLGKKLAEKILG 289 Clostridium perfringens
11386862  232 RAFLEYLDANCSTPIAAYAQYLda----ynIQIDFMLGNLdCTKIIFQTEITNi-----kTSKICGIKAAKMMLA 297 Rickettsia prowazekii
12644400  241 RALMKRLQGGCAIPIGVQTDVLaisnssyrISLLGTVLSA-DGLRAAFGNAEAvvs-seeEAEELGITVALALLK 313 fission yeast
122846    241 RALMRTLEGGCSVPIGVESKYNeet---kkLLLKAIVVDV-EGTEAVEDEIEMlienvkeDSMACGKILAERMIA 311 baker's yeast
10720013  248 RSLMRYLEGGCSVPLGVHSDYNesk---qeLTLKGIIVSP-DGTVSIEDEVIKrit-cdeDCEQVGIELGDKLKA 317 Candida albicans
2495178   223 RTALNEFGGGCSVPFGALAVYDekn---elLKLKAAVVTN-DELKNASGEVKCkid-eidKAVELGKKIGLKLKN 292 Methanococcus jannaschii
6225498   224 RAVIKELGVGCAVPVGVYAEAQs------rVRLICEILDK-KYLRVEEKLSKDta---veEAAEIGKDLRKEIYG 288 Archaeoglobus fulgidus
11386772  223 KTLLRELGAGCQCPLGVIGRATgn-----qLTLYAVLLTR-EGEMLRKVTVRGpl----aEAEDIGKKAAKEMED 287 Methanothermobacter the...

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