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(-) Description

Title :  CRYSTAL STRUCTURE OF O-SUCCINYLBENZOATE SYNTHASE FROM BDELLOVIBRIO BACTERIOVORUS LIGANDED WITH MG
 
Authors :  A. A. Fedorov, E. V. Fedorov, A. Sakai, S. K. Burley, J. A. Gerlt, S. C. Alm York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  20 Feb 08  (Deposition) - 04 Mar 08  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Structural Genomics, Psi-2, Nysgxrc, Target 9462A, O-Succinylbenzoate Synthase, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Oxidoreductase (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-SUCCINYLBENZOATE SYNTHASE
    Atcc: 15356
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BD0547
    Organism Scientific: BDELLOVIBRIO BACTERIOVORUS HD100
    Organism Taxid: 264462
    Strain: HD100 / DSM 50701 / NCIB 9529

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:155 , GLU A:184 , ASP A:206BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREASP B:155 , GLU B:184 , ASP B:206BINDING SITE FOR RESIDUE MG B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CAW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CAW)

(-) Sequences/Alignments

Asymmetric 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:316
 aligned with Q6MQC7_BDEBA | Q6MQC7 from UniProtKB/TrEMBL  Length:330

    Alignment length:326
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322      
         Q6MQC7_BDEBA     3 KISYSPYTLKPVQSLNAATAATAREGVLLKVEWNDGLYGFADLHPWPELGDLSLEEQLSDLRMGRMTTQIEQSIWLARRDALLRKEKKHVFDGGEKIKNNYLLSHFQDLKPGFLDGLKNEGYNTVKVKMGRDLQKEADMLTHIAASGMRMRLDFNALGSWQTFEKFMVNLPLTVRPLIEYVEDPFPFDFHAWGEARKLAKIALDNQYDKVPWGKIASAPFDVIVIKPAKTDVDKAVAQCQKWNLKLAVTSYMDHPVGVVHAVGVAMELKDKYGDMILESGCLTHRLYQMDSFAAELSTQGPYLLKNKGTGVGFDKLLEALTWYQLK 328
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cawA01 A:3-          89,A:315-328 Enolase-like, N-terminal domain                     3cawA02 A:90-314 Enolase superfamily                                                                                                                                                                                             3cawA01        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...----------.eeeeeeeee.....eeeeee..hhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..............eee........hhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhh....hhh.eeeee.....hhhhhhhhh....eee..hhhhh...........eeee.....hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhh....hhhhh.ee..ee.........hhhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3caw A   3 KISYSPYTLKPV----------AREGVLLKVEWNDGLYGFADLHPWPELGDLSLEEQLSDLRMGRMTTQIEQSIWLARRDALLRKEKKHVFDGGEKIKNNYLLSHFQDLKPGFLDGLKNEGYNTVKVKMGRDLQKEADMLTHIAASGMRMRLDFNALGSWQTFEKFMVNLPLTVRPLIEYVEDPFPFDFHAWGEARKLAKIALDNQYDKVPWGKIASAPFDVIVIKPAKTDVDKAVAQCQKWNLKLAVTSYMDHPVGVVHAVGVAMELKDKYGDMILESGCLTHRLYQMDSFAAELSTQGPYLLKNKGTGVGFDKLLEALTWYQLK 328
                                    12 |       -  |     32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322      
                                      14         25                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:316
 aligned with Q6MQC7_BDEBA | Q6MQC7 from UniProtKB/TrEMBL  Length:330

    Alignment length:326
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322      
         Q6MQC7_BDEBA     3 KISYSPYTLKPVQSLNAATAATAREGVLLKVEWNDGLYGFADLHPWPELGDLSLEEQLSDLRMGRMTTQIEQSIWLARRDALLRKEKKHVFDGGEKIKNNYLLSHFQDLKPGFLDGLKNEGYNTVKVKMGRDLQKEADMLTHIAASGMRMRLDFNALGSWQTFEKFMVNLPLTVRPLIEYVEDPFPFDFHAWGEARKLAKIALDNQYDKVPWGKIASAPFDVIVIKPAKTDVDKAVAQCQKWNLKLAVTSYMDHPVGVVHAVGVAMELKDKYGDMILESGCLTHRLYQMDSFAAELSTQGPYLLKNKGTGVGFDKLLEALTWYQLK 328
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cawB01 B:3-          89,B:315-328 Enolase-like, N-terminal domain                     3cawB02 B:90-314 Enolase superfamily                                                                                                                                                                                             3cawB01        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...----------.eeeeeeeee.....eeeeee..hhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.............ee.........hhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhh...hhh.eeeee.....hhhhhhhhh....eee..hhhhhhhhhh......eeee.....hhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhh....hhhhh.ee..ee.........hhhhhhhh..eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3caw B   3 KISYSPYTLKPV----------AREGVLLKVEWNDGLYGFADLHPWPELGDLSLEEQLSDLRMGRMTTQIEQSIWLARRDALLRKEKKHVFDGGEKIKNNYLLSHFQDLKPGFLDGLKNEGYNTVKVKMGRDLQKEADMLTHIAASGMRMRLDFNALGSWQTFEKFMVNLPLTVRPLIEYVEDPFPFDFHAWGEARKLAKIALDNQYDKVPWGKIASAPFDVIVIKPAKTDVDKAVAQCQKWNLKLAVTSYMDHPVGVVHAVGVAMELKDKYGDMILESGCLTHRLYQMDSFAAELSTQGPYLLKNKGTGVGFDKLLEALTWYQLK 328
                                    12 |       -  |     32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322      
                                      14         25
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 3CAW)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q6MQC7_BDEBA | Q6MQC7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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