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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRAZINAMIDASE OF PYROCOCCUS HORIKOSHII IN COMPLEX WITH ZINC
 
Authors :  X. Du, S. -H. Kim
Date :  09 May 01  (Deposition) - 12 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Pyrazinamidase, Pyrazinamide, Nicotinamidase, Tuberculosis, Pza Resistance, Drug Resistance, Metal Ion Catalysis, Cysteine Hydrolase, Hydrolase, Amidase, Covalent Catalysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Du, W. Wang, R. Kim, H. Yakota, H. Nguyen, S. H. Kim
Crystal Structure And Mechanism Of Catalysis Of A Pyrazinamidase From Pyrococcus Horikoshii.
Biochemistry V. 40 14166 2001
PubMed-ID: 11714269  |  Reference-DOI: 10.1021/BI0115479
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 180AA LONG HYPOTHETICAL PYRAZINAMIDASE/NICOTINAMIDASE
    Chains: A
    EC Number: 3.5.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: B834(DE3)/SJS1244
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH 999
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:52 , HIS A:54 , HIS A:71 , HOH A:203 , HOH A:214 , HOH A:223BINDING SITE FOR RESIDUE ZN A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IM5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:128 -Ala A:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IM5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IM5)

(-) Exons   (0, 0)

(no "Exon" information available for 1IM5)

(-) 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:179
 aligned with O58727_PYRHO | O58727 from UniProtKB/TrEMBL  Length:180

    Alignment length:179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171         
         O58727_PYRHO     2 PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATRDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKEAYSGFEGTDLAKILRGNGVKRVYICGVATEYCVRATALDALKHGFEVYLLRDAVKGIKPEDEERALEEMKSRGIKIVQF 180
               SCOP domains d1im5a_ A: Pyrazinamidase/nicotinamidase                                                                                                                                            SCOP domains
               CATH domains 1im5A00 A:2-180  [code=3.40.50.850, no name defined]                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhh........hhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhh..........hhhhh.........eeeee...............hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1im5 A   2 PEEALIVVDMQRDFMPGGALPVPEGDKIIPKVNEYIRKFKEKGALIVATRDWHPENHISFRERGGPWPRHCVQNTPGAEFVVDLPEDAVIISKATEPDKEAYSGFEGTDLAKILRGNGVKRVYICGVATEYCVRATALDALKHGFEVYLLRDAVKGIKPEDEERALEEMKSRGIKIVQF 180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IM5)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O58727_PYRHO | O58727)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

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

UniProtKB/TrEMBL
        O58727_PYRHO | O58727: 1ilw

(-) Related Entries Specified in the PDB File

1ilw 1ILW IS THE CRYSTAL STRUCTURE OF PYRAZINAMIDASE/ NICOTINAMIDASE OF PYROCOCCUS HORIKOSHII