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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ISC DOMAIN OF VIBB
 
Authors :  S. Liu, C. Zhang, B. Niu, N. Li, M. Liu, T. Wei, D. Zhu, S. Xu, L. Gu
Date :  05 Aug 11  (Deposition) - 29 Aug 12  (Release) - 01 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Isc Domain, Isochorismatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Liu, C. Zhang, N. Li, B. Niu, M. Liu, X. Liu, T. Wei, D. Zhu, Y. Huang, S. Xu, L. Gu
Structural Insight Into The Isc Domain Of Vibb From Vibrio Cholerae At Atomic Resolution: A Snapshot Just Before The Enzymatic Reaction
Acta Crystallogr. , Sect. D V. 68 1329 2012
PubMed-ID: 22993087  |  Reference-DOI: 10.1107/S090744491202848X

(-) Compounds

Molecule 1 - VIBRIOBACTIN-SPECIFIC ISOCHORISMATASE
    Chains: A
    EC Number: 3.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ISC DOMAIN, UNP RESIDUES 1-215
    Gene: VC_0771, VIBB
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Strain: EL TOR INABA N16961
    Synonym: 2,3 DIHYDRO-2,3 DIHYDROXYBENZOATE SYNTHASE, ISOCHORISMATE LYASE-ARCP

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 5)

Asymmetric Unit (5, 5)
No.NameCountTypeFull Name
1BOG1Ligand/IonB-OCTYLGLUCOSIDE
2CA1Ligand/IonCALCIUM ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1BOG2Ligand/IonB-OCTYLGLUCOSIDE
2CA-1Ligand/IonCALCIUM ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:40 , TYR A:43 , GLN A:77 , ARG A:86 , LEU A:89 , GLY A:96 , TYR A:121 , CA A:505 , HOH A:610 , HOH A:665 , HOH A:694 , HOH A:705 , HOH A:742 , HOH A:764BINDING SITE FOR RESIDUE BOG A 501
2AC2SOFTWAREHIS A:149 , LEU A:153 , ASP A:180 , TYR A:187 , ARG A:191BINDING SITE FOR RESIDUE PGE A 502
3AC3SOFTWARELEU A:116 , THR A:117 , TRP A:119 , LYS A:126 , SER A:127 , PRO A:128BINDING SITE FOR RESIDUE EDO A 503
4AC4SOFTWAREASP A:21 , HIS A:42 , HOH A:792BINDING SITE FOR RESIDUE PEG A 504
5AC5SOFTWARETYR A:147 , ILE A:150 , GLY A:151 , BOG A:501BINDING SITE FOR RESIDUE CA A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TB4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:49 -Pro A:50
2Val A:146 -Tyr A:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TB4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TB4)

(-) Exons   (0, 0)

(no "Exon" information available for 3TB4)

(-) 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:205
 aligned with VIBB_VIBCH | P0C6D3 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:205
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202     
           VIBB_VIBCH     3 IPKIASYPLPVSLPTNKVDWRIDASRAVLLIHDMQEYFVHYFDSQAEPIPSLIKHIQQLKAHAKQAGIPVVYTAQPANQDPAERALLSDFWGPGLSEETAIIAPLAPESGDVQLTKWRYSAFKKSPLLDWLRETGRDQLIITGVYAHIGILSTALDAFMFDIQPFVIGDGVADFSLSDHEFSLRYISGRTGAVKSTQQACLEIAA 207
               SCOP domains d3tb4a_ A: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................eeeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh.........hhhhh.....eeee..........hhhhhhhhhh..eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhhh.eeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tb4 A   3 IPKIASYPLPVSLPTNKVDWRIDASRAVLLIHDMQEYFVHYFDSQAEPIPSLIKHIQQLKAHAKQAGIPVVYTAQPANQDPAERALLSDFWGPGLSEETAIIAPLAPESGDVQLTKWRYSAFKKSPLLDWLRETGRDQLIITGVYAHIGILSTALDAFMFDIQPFVIGDGVADFSLSDHEFSLRYISGRTGAVKSTQQACLEIAA 207
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TB4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TB4)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (VIBB_VIBCH | P0C6D3)
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:0008908    isochorismatase activity    Catalysis of the reaction: H(2)O + isochorismate = 2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate.
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.
    GO:0019537    vibriobactin biosynthetic process    The chemical reactions and pathways resulting in the formation of vibriobactin, the major siderophore produced by Vibrio cholerae.

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  3tb4
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 Related Entries

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

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        VIBB_VIBCH | P0C6D3: 3tg2

(-) Related Entries Specified in the PDB File

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