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(-) Description

Title :  THE CRYSTAL STRUCTURE OF PYRAZINAMIDASE/NICOTINAMIDASE FROM STREPTOCOCCUS MUTANS UA159
 
Authors :  X. -D. Su, X. Liu, H. Zhang
Date :  17 May 11  (Deposition) - 16 May 12  (Release) - 16 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pyrazinamidase/Nicotinamidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Liu, H. Zhang, X. J. Wang, L. F. Li, X. -D. Su
Get Phases From Arsenic Anomalous Scattering: De Novo Sad Phasing Of Two Protein Structures Crystallized In Cacodylat Buffer
Plos One V. 6 24227 2011
PubMed-ID: 21912678  |  Reference-DOI: 10.1371/JOURNAL.PONE.0024227

(-) Compounds

Molecule 1 - PUTATIVE PYRAZINAMIDASE/NICOTINAMIDASE
    Chains: A, B, C, D
    EC Number: 3.5.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMIDE
    Gene: PNCA
    Organism Scientific: STREPTOCOCCUS MUTANS
    Organism Taxid: 1309
    Strain: UA159

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CAD4Ligand/IonCACODYLIC ACID
2ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:53 , HIS A:55 , GLU A:64 , HIS A:71 , HOH A:299 , HOH A:401BINDING SITE FOR RESIDUE ZN A 184
2AC2SOFTWAREASP A:9 , PHE A:14 , VAL A:131 , LEU A:132 , ILE A:135 , CYS A:136 , HOH A:401BINDING SITE FOR RESIDUE CAD A 185
3AC3SOFTWAREASP B:53 , HIS B:55 , GLU B:64 , HIS B:71 , HOH B:216BINDING SITE FOR RESIDUE ZN B 184
4AC4SOFTWAREASP B:9 , PHE B:14 , VAL B:131 , LEU B:132 , ILE B:135 , CYS B:136BINDING SITE FOR RESIDUE CAD B 185
5AC5SOFTWAREASP C:53 , HIS C:55 , GLU C:64 , HIS C:71 , HOH C:207BINDING SITE FOR RESIDUE ZN C 184
6AC6SOFTWAREASP C:9 , PHE C:14 , VAL C:131 , LEU C:132 , ILE C:135 , CYS C:136BINDING SITE FOR RESIDUE CAD C 185
7AC7SOFTWAREASP D:53 , HIS D:55 , GLU D:64 , HIS D:71 , HOH D:204BINDING SITE FOR RESIDUE ZN D 184
8AC8SOFTWAREASP D:9 , PHE D:14 , VAL D:131 , LEU D:132 , ILE D:135 , CYS D:136BINDING SITE FOR RESIDUE CAD D 185

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S2S)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:131 -Leu A:132
2Val B:131 -Leu B:132
3Val C:131 -Leu C:132
4Val D:131 -Leu D:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S2S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S2S)

(-) Exons   (0, 0)

(no "Exon" information available for 3S2S)

(-) 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:182
 aligned with Q8DSG2_STRMU | Q8DSG2 from UniProtKB/TrEMBL  Length:183

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
         Q8DSG2_STRMU     2 SKALISIDYTYDFVADDGKLTAGKPAQAISKAIAQVTQKAYDNGDYIFFTIDGHDEGDDFHPETKLFPPHNIKGTSGRDLYGALADFYQKHENDKRVFWMDKRHYSAFSGTDLDIRLRERRVDTVVLTGVLTDICVLHTAIDAYNLGYQIEVVQSAVASLSQENHQFALNHLQNVLGATIIE 183
               SCOP domains d3s2sa_ A: automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhh........hhhhh...hhhhhhhhh.....eeeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s2s A   2 SKALISIDYTYDFVADDGKLTAGKPAQAISKAIAQVTQKAYDNGDYIFFTIDGHDEGDDFHPETKLFPPHNIKGTSGRDLYGALADFYQKHENDKRVFWMDKRHYSAFSGTDLDIRLRERRVDTVVLTGVLTDICVLHTAIDAYNLGYQIEVVQSAVASLSQENHQFALNHLQNVLGATIIE 183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  


Chain B from PDB  Type:PROTEIN  Length:182
 aligned with Q8DSG2_STRMU | Q8DSG2 from UniProtKB/TrEMBL  Length:183

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
         Q8DSG2_STRMU     2 SKALISIDYTYDFVADDGKLTAGKPAQAISKAIAQVTQKAYDNGDYIFFTIDGHDEGDDFHPETKLFPPHNIKGTSGRDLYGALADFYQKHENDKRVFWMDKRHYSAFSGTDLDIRLRERRVDTVVLTGVLTDICVLHTAIDAYNLGYQIEVVQSAVASLSQENHQFALNHLQNVLGATIIE 183
               SCOP domains d3s2sb_ B: automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhh........hhhhh...hhhhhhhhh.....eeeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s2s B   2 SKALISIDYTYDFVADDGKLTAGKPAQAISKAIAQVTQKAYDNGDYIFFTIDGHDEGDDFHPETKLFPPHNIKGTSGRDLYGALADFYQKHENDKRVFWMDKRHYSAFSGTDLDIRLRERRVDTVVLTGVLTDICVLHTAIDAYNLGYQIEVVQSAVASLSQENHQFALNHLQNVLGATIIE 183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  


Chain C from PDB  Type:PROTEIN  Length:182
 aligned with Q8DSG2_STRMU | Q8DSG2 from UniProtKB/TrEMBL  Length:183

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
         Q8DSG2_STRMU     2 SKALISIDYTYDFVADDGKLTAGKPAQAISKAIAQVTQKAYDNGDYIFFTIDGHDEGDDFHPETKLFPPHNIKGTSGRDLYGALADFYQKHENDKRVFWMDKRHYSAFSGTDLDIRLRERRVDTVVLTGVLTDICVLHTAIDAYNLGYQIEVVQSAVASLSQENHQFALNHLQNVLGATIIE 183
               SCOP domains d3s2sc_ C: automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhh........hhhhh..hhhhhhhhhhh....eeeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s2s C   2 SKALISIDYTYDFVADDGKLTAGKPAQAISKAIAQVTQKAYDNGDYIFFTIDGHDEGDDFHPETKLFPPHNIKGTSGRDLYGALADFYQKHENDKRVFWMDKRHYSAFSGTDLDIRLRERRVDTVVLTGVLTDICVLHTAIDAYNLGYQIEVVQSAVASLSQENHQFALNHLQNVLGATIIE 183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  


Chain D from PDB  Type:PROTEIN  Length:181
 aligned with Q8DSG2_STRMU | Q8DSG2 from UniProtKB/TrEMBL  Length:183

    Alignment length:181
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
         Q8DSG2_STRMU     2 SKALISIDYTYDFVADDGKLTAGKPAQAISKAIAQVTQKAYDNGDYIFFTIDGHDEGDDFHPETKLFPPHNIKGTSGRDLYGALADFYQKHENDKRVFWMDKRHYSAFSGTDLDIRLRERRVDTVVLTGVLTDICVLHTAIDAYNLGYQIEVVQSAVASLSQENHQFALNHLQNVLGATII 182
               SCOP domains d3s2sd_ D: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhh........hhhhh...hhhhhhhhhh....eeeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhhhh.eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s2s D   2 SKALISIDYTYDFVADDGKLTAGKPAQAISKAIAQVTQKAYDNGDYIFFTIDGHDEGDDFHPETKLFPPHNIKGTSGRDLYGALADFYQKHENDKRVFWMDKRHYSAFSGTDLDIRLRERRVDTVVLTGVLTDICVLHTAIDAYNLGYQIEVVQSAVASLSQENHQFALNHLQNVLGATII 182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S2S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S2S)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8DSG2_STRMU | Q8DSG2)
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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