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(-) Description

Title :  STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE AT-170 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 :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (2x)
Biol. Unit 2:  A,B,C,D,E,F  (1x)
Keywords :  Helix Disorder, Less 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
    ChainsA, C, E
    EC Number4.1.1.22
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentBETA CHAIN (RESIDUES 1-81)
    GeneHDCA
    MutationYES
    Organism ScientificLACTOBACILLUS SP.
    Organism Taxid1593
    Strain30A
    SynonymPI CHAIN
 
Molecule 2 - HISTIDINE DECARBOXYLASE ALPHA CHAIN
    ChainsB, D, F
    EC Number4.1.1.22
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentALPHA CHAIN (RESIDUES 82-310)
    GeneHDCA
    Organism ScientificLACTOBACILLUS SP.
    Organism Taxid1593
    Strain30A

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1PYR3Mod. Amino AcidPYRUVIC ACID
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1PYR6Mod. Amino AcidPYRUVIC ACID
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1PYR3Mod. Amino AcidPYRUVIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 1IBT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IBT)

(-) 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 d1ibt.1 A:,B: Histidine decarboxylase                                             SCOP domains
               CATH domains 1ibtA00 A:1-81 Pyruvoyl-Dependent Histidine Decarboxylas, subunit A               CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh......eee.............eee..eeeeeeeeeeeeee...hhhhhhhhhhhhhh......eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1ibt A   1 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDNNVLDGIVSYDRAETKNAYIGQINMTTAS  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 d1ibt.1 A:,B: Histidine decarboxylase                                                                                                                                                                                                 SCOP domains
               CATH domains -1ibtB00 B:83-310 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) eee....eee......hhhhhhh....eeee..--------hhhhhhhhhhhh--..eee.....eeeeeeeeeeeeeee............eeeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....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
                 1ibt 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:76
 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 d1ibt.2 C:,D: Histidine decarboxylase                                             SCOP domains
               CATH domains 1ibtC00 C:1-81 Pyruvoyl-Dependent Histidine Decar     boxylas, subunit A          CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh......eee.............eee..eeeeeeeeeeeee-----hhhhhhhhhhhhh......eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1ibt C   1 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRD-----VLDGIVSYDRAETKNAYIGQINMTTAS  81
                                    10        20        30        40        |-    |   60        70        80 
                                                                           49    55                          

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 d1ibt.2 C:,D: Histidine decarboxylase                                                                                                                                                                                                 SCOP domains
               CATH domains -1ibtD00 D:83-310 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) eee....eee......hhhhhhh....eeee..--------hhhhhhhhhhhh--..eee.....eeeeeeeeeeeeeee............eeeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....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
                 1ibt 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 d1ibt.3 E:,F: Histidine decarboxylase                                             SCOP domains
               CATH domains 1ibtE00 E:1-81 Pyruvoyl-Dependent Histidine Decarboxylas, subunit A               CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh......eee.............eee..eeeeeeeeeeeeee..hhhhhhhhhhhhhhh......eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1ibt E   1 SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDNNVLDGIVSYDRAETKNAYIGQINMTTAS  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 d1ibt.3 E:,F: Histidine decarboxylase                                                                                                                                                                                                 SCOP domains
               CATH domains -1ibtF00 F:83-310 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) eee....eee......hhhhhhh....eeee..--------hhhhhhhhhhhh--..eee.....eeeeeeeeeeeeeee............eeeeeeeeeee........eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....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
                 1ibt 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)
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  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

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) 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 | P008621hq6 1ibu 1ibv 1ibw 1pya

(-) Related Entries Specified in the PDB File

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