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(-) Description

Title :  THE STRUCTURE OF THE STAPHYLOCOCCUS AUREUS HAM1 PROTEIN
 
Authors :  C. Abergel, J. M. Claverie
Date :  16 May 13  (Deposition) - 29 May 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Ham, Inosine Triphosphate Pyrophosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Abergel
Molecular Replacement: Tricks And Treats.
Acta Crystallogr. , Sect. D V. 69 2167 2013
PubMed-ID: 24189227  |  Reference-DOI: 10.1107/S0907444913015291

(-) Compounds

Molecule 1 - NON-CANONICAL PURINE NTP PYROPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: IN HOUSE
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 46170
    Strain: N315
    Synonym: NON-STANDARD PURINE NTP PYROPHOSPHATASE, NUCLEOSIDE-TRIPHOS PHATE DIPHOSPHATASE, NUCLEOSIDE-TRIPHOSPHATE PYROPHOSPHATASE, NTPASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO45Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:8 , ASN A:9 , ASN A:10 , LYS A:13 , GLU A:40 , LYS A:52 , ASP A:67 , HOH A:2003 , HOH A:2004 , HOH A:2009 , HOH A:2010BINDING SITE FOR RESIDUE PO4 A 800
2AC2SOFTWAREGLU A:3 , LYS A:62 , THR A:108 , THR A:109 , ASP A:110 , HOH A:2131BINDING SITE FOR RESIDUE PO4 A 801
3AC3SOFTWARESER A:136 , LYS A:159 , HOH A:2084 , HOH A:2085 , HOH A:2107 , HOH A:2132 , HOH A:2133 , SER B:136 , LYS B:159BINDING SITE FOR RESIDUE PO4 A 802
4AC4SOFTWAREHOH A:2001 , HOH A:2058 , HOH A:2128BINDING SITE FOR RESIDUE PO4 A 804
5AC5SOFTWARESER B:8 , ASN B:9 , LYS B:13 , HOH B:2003BINDING SITE FOR RESIDUE PO4 B 803
6AC6SOFTWARETHR B:44 , PHE B:45 , GLU B:72 , LYS B:132BINDING SITE FOR RESIDUE GOL B 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BNQ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:79 -Pro A:80
2Glu B:79 -Pro B:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BNQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BNQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4BNQ)

(-) 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:194
 aligned with IXTPA_STAAN | P99094 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:194
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191    
          IXTPA_STAAN     2 KEIVIASNNQGKINDFKVIFPDYHVIGISELIPDFDVEETGSTFEENAILKSEAAAKALNKTVIADDSGLEVFALNGEPGIYSARYAGENKSDEANIEKLLNKLGNTTDRRAQFVCVISMSGPDMETKVFKGTVSGEIADGKYGENGFGYDPIFYVPKLDKTMAQLSKEQKGQISHRRNAINLLQAFLEGEKNV 195
               SCOP domains d4bnqa_ A: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...eeeehhhhh..........hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh...hhhhhhh.....hhhhhhhhhhhhh......eeeeeeeeeeee..eeeeeeeeeeeeee...........hhh.eeehhhhee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bnq A   2 KEIVIASNNQGKINDFKVIFPDYHVIGISELIPDFDVEETGSTFEENAILKSEAAAKALNKTVIADDSGLEVFALNGEPGIYSARYAGENKSDEANIEKLLNKLGNTTDRRAQFVCVISMSGPDMETKVFKGTVSGEIADGKYGENGFGYDPIFYVPKLDKTMAQLSKEQKGQISHRRNAINLLQAFLEGEKNV 195
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191    


Chain B from PDB  Type:PROTEIN  Length:193
 aligned with IXTPA_STAAN | P99094 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   
          IXTPA_STAAN     2 KEIVIASNNQGKINDFKVIFPDYHVIGISELIPDFDVEETGSTFEENAILKSEAAAKALNKTVIADDSGLEVFALNGEPGIYSARYAGENKSDEANIEKLLNKLGNTTDRRAQFVCVISMSGPDMETKVFKGTVSGEIADGKYGENGFGYDPIFYVPKLDKTMAQLSKEQKGQISHRRNAINLLQAFLEGEKN 194
               SCOP domains d4bnqb_ B: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhh...eeee.hhh...........hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh...hhhh........hhhhhhhhhhhhhh.....eeeeeeeeeeee..eeeeeeeeeeeeee...........hhh.eehhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bnq B   2 KEIVIASNNQGKINDFKVIFPDYHVIGISELIPDFDVEETGSTFEENAILKSEAAAKALNKTVIADDSGLEVFALNGEPGIYSARYAGENKSDEANIEKLLNKLGNTTDRRAQFVCVISMSGPDMETKVFKGTVSGEIADGKYGENGFGYDPIFYVPKLDKTMAQLSKEQKGQISHRRNAINLLQAFLEGEKN 194
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BNQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BNQ)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IXTPA_STAAN | P99094)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    GO:0047429    nucleoside-triphosphate diphosphatase activity    Catalysis of the reaction: H2O + a nucleoside triphosphate = diphosphate + a nucleotide.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0009143    nucleoside triphosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    GO:0006163    purine nucleotide metabolic process    The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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