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(-) Description

Title :  CRYSTAL STRUCTURE OF O-SUCCINYLBENZOIC ACID SYNTHETASE FROM STAPHYLOCOCCUS AUREUS, LIGAND-FREE FORM
 
Authors :  Y. Patskovsky, R. Toro, V. Malashkevich, J. M. Sauder, S. Ozyurt, D. Smi M. Dickey, M. Maletic, A. Powell, T. Gheyi, S. R. Wasserman, J. Gerlt, S. K. Burley, S. C. Almo, New York Sgx Research Center For Struct Genomics (Nysgxrc)
Date :  17 Jan 07  (Deposition) - 30 Jan 07  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Enolase, O-Succinylbenzoic Acid Synthetase, Structural Genomics, Protein Structure Initiative, Psi, Nysgrc, New York Structural Genomics Research Consortium, New York Sgx Research Center For Structural Genomics, Nysgxrc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Odokonyero, A. Sakai, Y. Patskovsky, V. N. Malashkevich, A. A. Fedorov, J. B. Bonanno, E. V. Fedorov, R. Toro, R. Agarwal, C. Wang N. D. Ozerova, W. S. Yew, J. M. Sauder, S. Swaminathan, S. K. Burley, S. C. Almo, M. E. Glasner
Loss Of Quaternary Structure Is Associated With Rapid Sequence Divergence In The Osbs Family.
Proc. Natl. Acad. Sci. Usa V. 111 8535 2014
PubMed-ID: 24872444  |  Reference-DOI: 10.1073/PNAS.1318703111

(-) Compounds

Molecule 1 - O-SUCCINYLBENZOIC ACID SYNTHETASE
    Chains: A
    EC Number: 4.2.1.113
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MENC
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 93062
    Strain: COL
    Synonym: OSB SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2OKT)

(-) Sites  (0, 0)

(no "Site" information available for 2OKT)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OKT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OKT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OKT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OKT)

(-) Exons   (0, 0)

(no "Exon" information available for 2OKT)

(-) 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:342
 aligned with A0A0H2WWB5_S | A0A0H2WWB5 from UniProtKB/TrEMBL  Length:333

    Alignment length:342
                             1                                                                                                                                                                                                                                                                                                                                         333        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329   |     -  
         A0A0H2WWB5_S     - -MKLTALHFYKYSEPFKSQIVTPKVTLTHRDCLFIELIDDKGNAYFGECNAFQTDWYDHETIASVKHVIEQWFEDNRNKSFETYEAALKLVDSLENTPAARATIVMALYQMFHVLPSFSVAYGATASGLSNKQLESLKATKPTRIKLKWTPQIMHQIRVLRELDFHFQLVIDANESLDRQDFTQLQLLAREQVLYIEEPFKDISMLDEVADGTIPPIALDEKATSLLDIINLIELYNVKVVVLKPFRLGGIDKVQTAIDTLKSHGAKVVIGGMYEYGLSRYFTAMLARKGDYPGDVTPAGYYFEQDVVAHSGILKEGRLEFRPPLVDITQLQPY--------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2oktA01 A:0-115,A:322-333 Enolase-like, N-terminal domain                                                           2oktA02 A:116-321 Enolase superfamily                                                                                                                                                                         2oktA01     -------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeee....eeeee............hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhh......eeee.eeee...hhhhhhhhhhhh..eeeee...hhhhhhhhhh......eeeee.....hhhhhhhhhhhh...eeeee....hhhhhhhh.......eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh........................eee..eeee.....hhhhhee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2okt A   0 SLKLTALHFYKYSEPFKSQIVTPKVTLTHRDCLFIELIDDKGNAYFGECNAFQTDWYDHETIASVKHVIEQWFEDNRNKSFETYEAALKLVDSLENTPAARATIVMALYQMFHVLPSFSVAYGATASGLSNKQLESLKATKPTRIKLKWTPQIMHQIRVLRELDFHFQLVIDANESLDRQDFTQLQLLAREQVLYIEEPFKDISMLDEVADGTIPPIALDEKATSLLDIINLIELYNVKVVVLKPFRLGGIDKVQTAIDTLKSHGAKVVIGGMYEYGLSRYFTAMLARKGDYPGDVTPAGYYFEQDVVAHSGILKEGRLEFRPPLVDITQLQPYEGHHHHHH 341
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  


Chain A from PDB  Type:PROTEIN  Length:342
 aligned with Q53635_STAAU | Q53635 from UniProtKB/TrEMBL  Length:333

    Alignment length:342
                             1                                                                                                                                                                                                                                                                                                                                         333        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329   |     -  
         Q53635_STAAU     - -MKLTALHFYKYSEPFKSQIVTPKVTLTHRDCLFIELIDDKGNAYFGECNAFQTDWYDHETIASVKHVIEQWFEDNRNKSFETYEAALKLVDSLENTPAARATIVMALYQMFHVLPSFSVAYGATASGLSNKQLESLKATKPTRIKLKWTPQIMHQIRVLRELDFHFQLVIDANESLDRQDFTQLQLLAREQVLYIEEPFKDISMLDEVADGTIPPIALDEKATSLLDIINLIELYNVKVVVLKPFRLGGIDKVQTAIDTLKSHGAKVVIGGMYEYGLSRYFTAMLARKGDYPGDVTPAGYYFEQDVVAHSGILKEGRLEFRPPLVDITQLQPY--------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2oktA01 A:0-115,A:322-333 Enolase-like, N-terminal domain                                                           2oktA02 A:116-321 Enolase superfamily                                                                                                                                                                         2oktA01     -------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeee....eeeee............hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhh......eeee.eeee...hhhhhhhhhhhh..eeeee...hhhhhhhhhh......eeeee.....hhhhhhhhhhhh...eeeee....hhhhhhhh.......eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh........................eee..eeee.....hhhhhee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2okt A   0 SLKLTALHFYKYSEPFKSQIVTPKVTLTHRDCLFIELIDDKGNAYFGECNAFQTDWYDHETIASVKHVIEQWFEDNRNKSFETYEAALKLVDSLENTPAARATIVMALYQMFHVLPSFSVAYGATASGLSNKQLESLKATKPTRIKLKWTPQIMHQIRVLRELDFHFQLVIDANESLDRQDFTQLQLLAREQVLYIEEPFKDISMLDEVADGTIPPIALDEKATSLLDIINLIELYNVKVVVLKPFRLGGIDKVQTAIDTLKSHGAKVVIGGMYEYGLSRYFTAMLARKGDYPGDVTPAGYYFEQDVVAHSGILKEGRLEFRPPLVDITQLQPYEGHHHHHH 341
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339
   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  (0, 0)

(no "SCOP Domain" information available for 2OKT)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OKT)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q53635_STAAU | Q53635)
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:0016836    hydro-lyase activity    Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
    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.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009234    menaquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
    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   (A0A0H2WWB5_S | A0A0H2WWB5)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q53635_STAAU | Q53635: 2ola
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        Q53635_STAAU | Q53635: 3h70

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