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(-) Description

Title :  DETERMINATION OF THE CRYSTAL STRUCTURE OF THE PYRAZINAMIDASE FROM M.TUBERCULOSIS : A STRUCTURE-FUNCTION ANALYSIS FOR PREDICTION RESISTANCE TO PYRAZINAMIDE.
 
Authors :  S. Petrella, N. Gelus-Ziental, C. Mayer, W. Sougakoff
Date :  12 Nov 10  (Deposition) - 12 Jan 11  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold, Nicotinamidase-Pyrazinamidase, Resistance To Pyrazinamide, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Petrella, N. Gelus-Ziental, A. Maudry, C. Laurans, R. Boudjelloul W. Sougakoff
Crystal Structure Of The Pyrazinamidase Of Mycobacterium Tuberculosis: Insights Into Natural And Acquired Resistance To Pyrazinamide.
Plos One V. 6 15785 2011
PubMed-ID: 21283666  |  Reference-DOI: 10.1371/JOURNAL.PONE.0015785

(-) Compounds

Molecule 1 - PYRAZINAMIDASE/NICOTINAMIDASE PNCA (PZASE)
    ChainsA
    EC Number3.5.1.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET29
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMT2103, PNCA, RV2043C
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid83332
    StrainH37RV
    SynonymPYRAZINAMIDASE, PYRAZINAMIDASE/NICOTINAMIDASE

 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
1FE21Ligand/IonFE (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:49 , HIS A:51 , HIS A:57 , HIS A:71 , HOH A:220 , HOH A:221BINDING SITE FOR RESIDUE FE2 A 188

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PL1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:38 -Ala A:39
2Ile A:133 -Ala A:134

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PL1)

(-) Exons   (0, 0)

(no "Exon" information available for 3PL1)

(-) 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:185
 aligned with PNCA_MYCTU | I6XD65 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     
           PNCA_MYCTU     1 MRALIIVDVQNDFCEGGSLAVTGGAALARAISDYLAEAADYHHVVATKDFHIDPGDHFSGTPDYSSSWPPHCVSGTPGADFHPSLDTSAIEAVFYKGAYTGAYSGFEGVDENGTPLLNWLRQRGVDEVDVVGIATDHCVRQTAEDAVRNGLATRVLVDLTAGVSADTTVAALEEMRTASVELVCS 185
               SCOP domains d3pl1a_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh........hhhhhhhhhh..........eeeeeee....hhhhh.................hhhhh...........eeeee.......hhhhh......hhhhhhhh....eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pl1 A   1 MRALIIVDVQNDFCEGGSLAVTGGAALARAISDYLAEAADYHHVVATKDFHIDPGDHFSGTPDYSSSWPPHCVSGTPGADFHPSLDTSAIEAVFYKGAYTGAYSGFEGVDENGTPLLNWLRQRGVDEVDVVGIATDHCVRQTAEDAVRNGLATRVLVDLTAGVSADTTVAALEEMRTASVELVCS 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     

Chain A from PDB  Type:PROTEIN  Length:185
 aligned with Q50575_MYCTX | Q50575 from UniProtKB/TrEMBL  Length:186

    Alignment length:185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     
         Q50575_MYCTX     1 MRALIIVDVQNDFCEGGSLAVTGGAALARAISDYLAEAADYHHVVATKDFHIDPGDHFSGTPDYSSSWPPHCVSGTPGADFHPSLDTSAIEAVFYKGAYTGAYSGFEGVDENGTPLLNWLRQRGVDEVDVVGIATDHCVRQTAEDAVRNGLATRVLVDLTAGVSADTTVAALEEMRTASVELVCS 185
               SCOP domains d3pl1a_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh........hhhhhhhhhh..........eeeeeee....hhhhh.................hhhhh...........eeeee.......hhhhh......hhhhhhhh....eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pl1 A   1 MRALIIVDVQNDFCEGGSLAVTGGAALARAISDYLAEAADYHHVVATKDFHIDPGDHFSGTPDYSSSWPPHCVSGTPGADFHPSLDTSAIEAVFYKGAYTGAYSGFEGVDENGTPLLNWLRQRGVDEVDVVGIATDHCVRQTAEDAVRNGLATRVLVDLTAGVSADTTVAALEEMRTASVELVCS 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     

   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

(-) CATH Domains  (0, 0 ; only for superseded entry 3GBC: 1,1)

(no "CATH Domain" information available for 3PL1, only for superseded entry 3GBC replaced by 3PL1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PL1)

(-) Gene Ontology  (11, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PNCA_MYCTU | I6XD65)
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.
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.

Chain A   (Q50575_MYCTX | Q50575)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016811    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008936    nicotinamidase activity    Catalysis of the reaction: nicotinamide + H2O = nicotinate + NH3.
biological process
    GO:0034355    NAD salvage    Any process that generates nicotinamide adenine dinucleotide (NAD) from derivatives of it, without de novo synthesis; salvage is usually from the degradation products nicotinic acid (Na) and nicotinamide (Nam).
    GO:0016999    antibiotic metabolic process    The chemical reactions and pathways involving an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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.
    GO:0006769    nicotinamide metabolic process    The chemical reactions and pathways involving nicotinamide, pyridine-3-carboxamide, the amide of nicotinic acid. It is a member of the B complex of vitamins and occurs widely in living organisms.

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 Related Entries

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