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(-) Description

Title :  REFINED STRUCTURE OF THE PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE FROM LACTOBACILLUS 30A
 
Authors :  T. Gallagher, D. A. Rozwarski, S. R. Ernst, M. L. Hackert
Date :  18 Dec 92  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Carboxy-Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Gallagher, D. A. Rozwarski, S. R. Ernst, M. L. Hackert
Refined Structure Of The Pyruvoyl-Dependent Histidine Decarboxylase From Lactobacillus 30A.
J. Mol. Biol. V. 230 516 1993
PubMed-ID: 8464063  |  Reference-DOI: 10.1006/JMBI.1993.1168
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L- HISTIDINE CARBOXYLASE)
    Chains: A, C, E
    EC Number: 4.1.1.22
    Engineered: YES
    Organism Scientific: LACTOBACILLUS SP. 30A
    Organism Taxid: 1593
    Strain: 30A
 
Molecule 2 - PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L- HISTIDINE CARBOXYLASE)
    Chains: B, D, F
    EC Number: 4.1.1.22
    Engineered: YES
    Organism Scientific: LACTOBACILLUS SP. 30A
    Organism Taxid: 1593
    Strain: 30A

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PYR3Mod. Amino AcidPYRUVIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1ACBAUTHORPYR B:82ACTIVE SITE 1
2ACDAUTHORPYR D:82ACTIVE SITE 2
3ACFAUTHORPYR F:82ACTIVE SITE 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PYA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PYA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PYA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PYA)

(-) Exons   (0, 0)

(no "Exon" information available for 1PYA)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:81
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:81
                                    11        21        31        41        51        61        71        81 
           DCHS_LACS3     2 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDDDVLDGIVSYDRAETKNAYIGQINMTTAS  82
               SCOP domains d1pya.1 A:,B: Histidine decarboxylase                                             SCOP domains
               CATH domains 1pyaA00 A:1-81 Pyruvoyl-Dependent Histidine Decarboxylas, subunit A               CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh......eee.............eee..eeeeeeeeeeeeee..hhhhhhhhhhhhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1pya A   1 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDDDVLDGIVSYDRAETKNAYIGQINMTTAS  81
                                    10        20        30        40        50        60        70        80 


Chain B from PDB  Type:PROTEIN  Length:229
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:229
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302         
           DCHS_LACS3    83 SFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 311
               SCOP domains d1pya.1 A:,B: Histidine decarboxylase                                                                                                                                                                                                 SCOP domains
               CATH domains -1pyaB00 B:83-310 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) eee....eee.................eeee..--------hhhhhhhhhhhhh-..eee.....eeeeeeeeeeeeeee............eeeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..eeeeeeeeeeeeeee.............hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------eeeeeeeee----------eee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pya B  82 xFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 310
                            |       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
                           82-PYR                                                                                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:81
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:81
                                    11        21        31        41        51        61        71        81 
           DCHS_LACS3     2 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDDDVLDGIVSYDRAETKNAYIGQINMTTAS  82
               SCOP domains d1pya.2 C:,D: Histidine decarboxylase                                             SCOP domains
               CATH domains 1pyaC00 C:1-81 Pyruvoyl-Dependent Histidine Decarboxylas, subunit A               CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh......eee.............eee..eeeeeeeeeeeeee..hhhhhhhhhhhhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1pya C   1 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDDDVLDGIVSYDRAETKNAYIGQINMTTAS  81
                                    10        20        30        40        50        60        70        80 


Chain D from PDB  Type:PROTEIN  Length:229
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:229
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302         
           DCHS_LACS3    83 SFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 311
               SCOP domains d1pya.2 C:,D: Histidine decarboxylase                                                                                                                                                                                                 SCOP domains
               CATH domains -1pyaD00 D:83-310 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) eee....eee.................eeee..--------hhhhhhhhhhhhh-..eee.....eeeeeeeeeeeeeee............eeeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..eeeeeeeeeeeeeee.............hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------eeeeeeeee----------eee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pya D  82 xFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 310
                            |       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
                           82-PYR                                                                                                                                                                                                                                


Chain E from PDB  Type:PROTEIN  Length:81
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:81
                                    11        21        31        41        51        61        71        81 
           DCHS_LACS3     2 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDDDVLDGIVSYDRAETKNAYIGQINMTTAS  82
               SCOP domains d1pya.3 E:,F: Histidine decarboxylase                                             SCOP domains
               CATH domains 1pyaE00 E:1-81 Pyruvoyl-Dependent Histidine Decarboxylas, subunit A               CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh......eee.............eee..eeeeeeeeeeeeee..hhhhhhhhhhhhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1pya E   1 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDDDVLDGIVSYDRAETKNAYIGQINMTTAS  81
                                    10        20        30        40        50        60        70        80 


Chain F from PDB  Type:PROTEIN  Length:229
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:229
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302         
           DCHS_LACS3    83 SFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 311
               SCOP domains d1pya.3 E:,F: Histidine decarboxylase                                                                                                                                                                                                 SCOP domains
               CATH domains -1pyaF00 F:83-310 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                                                                                               CATH domains
           Pfam domains (1) -HDC-1pyaF01 F:83-309                                                                                                                                                                                                               - Pfam domains (1)
           Pfam domains (2) -HDC-1pyaF02 F:83-309                                                                                                                                                                                                               - Pfam domains (2)
           Pfam domains (3) -HDC-1pyaF03 F:83-309                                                                                                                                                                                                               - Pfam domains (3)
           Pfam domains (4) -HDC-1pyaF04 F:83-309                                                                                                                                                                                                               - Pfam domains (4)
           Pfam domains (5) -HDC-1pyaF05 F:83-309                                                                                                                                                                                                               - Pfam domains (5)
           Pfam domains (6) -HDC-1pyaF06 F:83-309                                                                                                                                                                                                               - Pfam domains (6)
     Sec.struct. author (1) eee....eee.................eeee..--------hhhhhhhhhhhhh-..eee.....eeeeeeeeeeeeeee............eeeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..eeeeeeeeeeeeeee.............hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------eeeeeeeee----------eee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pya F  82 xFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 310
                            |       91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301         
                           82-PYR
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: HDC] (1)
(-)
Family: HDC (1)
(-)
Lactobacillus sp. (strain 30a) (1)
1aHDC-1pyaF01F:83-309
1bHDC-1pyaF02F:83-309
1cHDC-1pyaF03F:83-309
1dHDC-1pyaF04F:83-309
1eHDC-1pyaF05F:83-309
1fHDC-1pyaF06F:83-309

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (DCHS_LACS3 | P00862)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0004398    histidine decarboxylase activity    Catalysis of the reaction: L-histidine = histamine + CO2.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0006547    histidine metabolic process    The chemical reactions and pathways involving histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DCHS_LACS3 | P00862: 1hq6 1ibt 1ibu 1ibv 1ibw

(-) Related Entries Specified in the PDB File

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