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(-) Description

Title :  STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE BOUND WITH HISTIDINE METHYL ESTER AT 25 C
 
Authors :  S. Worley, E. Schelp, A. F. Monzingo, S. Ernst, J. D. Robertus
Date :  29 Mar 01  (Deposition) - 13 Mar 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (2x)
Keywords :  Substrate-Induced Activation, Active Form, Site-Directed Mutant, Pyruvoyl, Carboxy-Lyase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Worley, E. Schelp, A. F. Monzingo, S. Ernst, J. D. Robertus
Structure And Cooperativity Of A T-State Mutant Of Histidin Decarboxylase From Lactobacillus 30A.
Proteins V. 46 321 2002
PubMed-ID: 11835507  |  Reference-DOI: 10.1002/PROT.10042

(-) Compounds

Molecule 1 - HISTIDINE DECARBOXYLASE BETA CHAIN
    Chains: A, C, E
    EC Number: 4.1.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: BETA CHAIN (RESIDUES 1-81)
    Gene: HDCA
    Mutation: YES
    Organism Scientific: LACTOBACILLUS SP.
    Organism Taxid: 1593
    Strain: 30A
    Synonym: PI CHAIN
 
Molecule 2 - HISTIDINE DECARBOXYLASE ALPHA CHAIN
    Chains: B, D, F
    EC Number: 4.1.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: ALPHA CHAIN (RESIDUES 82-310)
    Gene: HDCA
    Organism Scientific: LACTOBACILLUS SP.
    Organism Taxid: 1593
    Strain: 30A
    Synonym: PI CHAIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1PVH3Ligand/IonHISTIDINE-METHYL-ESTER
2PYR3Ligand/IonPYRUVIC ACID
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1PVH6Ligand/IonHISTIDINE-METHYL-ESTER
2PYR6Ligand/IonPYRUVIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:81 , PHE B:83 , MET B:194 , PHE B:195 , PVH B:482 , ASN C:76BINDING SITE FOR RESIDUE PYR B 82
2AC2SOFTWARESER C:81 , PHE D:83 , MET D:194 , PHE D:195 , PVH D:482 , ASN E:76BINDING SITE FOR RESIDUE PYR D 82
3AC3SOFTWAREASN A:76 , SER E:81 , PHE F:83 , MET F:194 , PHE F:195 , PVH F:482BINDING SITE FOR RESIDUE PYR F 82
4AC4SOFTWAREALA A:80 , SER A:81 , PYR B:82 , PHE B:83 , ALA B:153 , ASN B:154 , PHE B:195 , VAL B:196 , GLU B:197 , TYR C:62 , ASP C:63 , GLU C:66BINDING SITE FOR RESIDUE PVH B 482
5AC5SOFTWAREALA C:80 , SER C:81 , PYR D:82 , PHE D:83 , ASN D:154 , PHE D:195 , VAL D:196 , GLU D:197 , TYR E:62 , ASP E:63 , GLU E:66BINDING SITE FOR RESIDUE PVH D 482
6AC6SOFTWARETYR A:62 , ASP A:63 , GLU A:66 , ALA E:80 , SER E:81 , PYR F:82 , PHE F:83 , ASN F:154 , PHE F:195 , VAL F:196 , GLU F:197BINDING SITE FOR RESIDUE PVH F 482

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IBW)

(-) Sequences/Alignments

Asymmetric 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 d1ibw.1 A:,B: Histidine decarboxylase                                             SCOP domains
               CATH domains 1ibwA00 A:1-81 Pyruvoyl-Dependent Histidine Decarboxylas, subunit A               CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.......eee.............eee..eeeeeeeeeeeeee..hhhhhhhhhhhhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1ibw A   1 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDNNVLDGIVSYDRAETKNAYIGQINMTTAS  81
                                    10        20        30        40        50        60        70        80 


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:228
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303        
           DCHS_LACS3    84 FTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 311
               SCOP domains d1ibw.1 A:,B: Histidine decarboxylase                                                                                                                                                                                                SCOP domains
               CATH domains 1ibwB00 B:83-310 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ......eee........hhhhh....eeee..--------hhhhhhhhhhhhh-..eee.....eeeeeeeeeeeeeee............eeeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..eeeeeeeeeeeeeee..hhh......hhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------eeeeeeeee----------eee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ibw B  83 FTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 310
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        


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 d1ibw.2 C:,D: Histidine decarboxylase                                             SCOP domains
               CATH domains 1ibwC00 C:1-81 Pyruvoyl-Dependent Histidine Decarboxylas, subunit A               CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.......eee.............eee..eeeeeeeeeeeeee..hhhhhhhhhhhhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1ibw C   1 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDNNVLDGIVSYDRAETKNAYIGQINMTTAS  81
                                    10        20        30        40        50        60        70        80 


Chain D from PDB  Type:PROTEIN  Length:228
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:228
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303        
           DCHS_LACS3    84 FTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 311
               SCOP domains d1ibw.2 C:,D: Histidine decarboxylase                                                                                                                                                                                                SCOP domains
               CATH domains 1ibwD00 D:83-310 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ......eee........hhhhh....eeee..--------hhhhhhhhhhhhh-..eee.....eeeeeeeeeeeeeee............eeeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..eeeeeeeeeeeeeee..hhh......hhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------eeeeeeeee----------eee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ibw D  83 FTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 310
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        


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 d1ibw.3 E:,F: Histidine decarboxylase                                             SCOP domains
               CATH domains 1ibwE00 E:1-81 Pyruvoyl-Dependent Histidine Decarboxylas, subunit A               CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.......eee.............eee..eeeeeeeeeeeeee..hhhhhhhhhhhhhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1ibw E   1 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDNNVLDGIVSYDRAETKNAYIGQINMTTAS  81
                                    10        20        30        40        50        60        70        80 


Chain F from PDB  Type:PROTEIN  Length:228
 aligned with DCHS_LACS3 | P00862 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:228
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303        
           DCHS_LACS3    84 FTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 311
               SCOP domains d1ibw.3 E:,F: Histidine decarboxylase                                                                                                                                                                                                SCOP domains
               CATH domains 1ibwF00 F:83-310 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ......eee......hhhhhhh....eeee..--------hhhhhhhhhhhhh-..eee.....eeeeeeeeeeeeeee............eeeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..eeeeeeeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------eeeeeeeee----------eee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ibw F  83 FTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY 310
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IBW)

(-) Gene Ontology  (5, 5)

Asymmetric 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 1pya

(-) Related Entries Specified in the PDB File

1hq6 STRUCTURE OF PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE AT PH 8
1ibt STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE AT -170 C
1ibu STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE AT 25 C
1ibv STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE BOUND WITH HISTIDINE METHYL ESTER AT -170 C
1pya STRUCTURE OF PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE AT PH 4.8