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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS EPOXIDE HYDROLASE B COMPLEXED WITH AN INHIBITOR
 
Authors :  B. K. Biswal, Tb Structural Genomics Consortium (Tbsgc)
Date :  07 Mar 08  (Deposition) - 01 Apr 08  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Hydrolase Fold, Inhibitor, Enzyme Mechanism, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. K. Biswal, C. Morisseau, G. Garen, M. M. Cherney, C. Garen, C. Niu, B. D. Hammock, M. N. James
The Molecular Structure Of Epoxide Hydrolase B From Mycobacterium Tuberculosis And Its Complex With A Urea-Base Inhibitor.
J. Mol. Biol. V. 381 897 2008
PubMed-ID: 18585390  |  Reference-DOI: 10.1016/J.JMB.2008.06.030

(-) Compounds

Molecule 1 - PROBABLE EPOXIDE HYDROLASE EPHB
    Atcc: 25618
    Chains: A
    EC Number: 3.3.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDEST17_RV1938
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: EPHB, MT1988, RV1938
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: EPOXIDE HYDRATASE, EPOXIDE HYDROLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2BSU1Ligand/Ion1,3-DIPHENYLUREA
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2BSU2Ligand/Ion1,3-DIPHENYLUREA
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2BSU1Ligand/Ion1,3-DIPHENYLUREA

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:37 , THR A:190 , TYR A:256 , TRP A:334 , GLN A:337BINDING SITE FOR RESIDUE ACT A 357
2AC2SOFTWAREARG A:63 , GLU A:81 , THR A:176BINDING SITE FOR RESIDUE ACT A 358
3AC3SOFTWAREHIS A:153 , ASP A:166 , ALA A:169 , TYR A:272 , ASP A:276 , HOH A:367BINDING SITE FOR RESIDUE ACT A 359
4AC4SOFTWAREPHE A:36 , ASP A:104 , TRP A:105 , ILE A:137 , TYR A:164 , LEU A:189 , TYR A:272 , HIS A:333 , TRP A:334BINDING SITE FOR RESIDUE BSU A 360

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:36 -Pro A:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZJF)

(-) 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:346
 aligned with EPHB_MYCTO | P95276 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:353
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353   
           EPHB_MYCTO     4 VHRILNCRGTRIHAVADSPPDQQGPLVVLLHGFPESWYSWRHQIPALAGAGYRVVAIDQRGYGRSSKYRVQKAYRIKELVGDVVGVLDSYGAEQAFVVGHDWGAPVAWTFAWLHPDRCAGVVGISVPFAGRGVIGLPGSPFGERRPSDYHLELAGPGRVWYQDYFAVQDGIITEIEEDLRGWLLGLTYTVSGEGMMAATKAAVDAGVDLESMDPIDVIRAGPLCMAEGARLKDAFVYPETMPAWFTEADLDFYTGEFERSGFGGPLSFYHNIDNDWHDLADQQGKPLTPPALFIGGQYDVGTIWGAQAIERAHEVMPNYRGTHMIADVGHWIQQEAPEETNRLLLDFLGGLRP 356
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeeeee........eeeee.....hhhhhh.hhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh...eeeeeee....hhhhh...........hhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-------..hhhhh......eee...hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zjf A   4 VHRILNCRGTRIHAVADSPPDQQGPLVVLLHGFPESWYSWRHQIPALAGAGYRVVAIDQRGYGRSSKYRVQKAYRIKELVGDVVGVLDSYGAEQAFVVGHDWGAPVAWTFAWLHPDRCAGVVGISVPFAGRGVIGLPGSPFGERRPSDYHLELAGPGRVWYQDYFAVQDGIITEIEEDLRGWLLGLTYTVSGEGMMAATKAAV-------SMDPIDVIRAGPLCMAEGARLKDAFVYPETMPAWFTEADLDFYTGEFERSGFGGPLSFYHNIDNDWHDLADQQGKPLTPPALFIGGQYDVGTIWGAQAIERAHEVMPNYRGTHMIADVGHWIQQEAPEETNRLLLDFLGGLRP 356
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203  |      -|      223       233       243       253       263       273       283       293       303       313       323       333       343       353   
                                                                                                                                                                                                                                    206     214
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZJF)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (EPHB_MYCTO | P95276)
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:0018742    epoxide hydrolase B activity    Catalysis of the hydrolysis of the ether in chloro- or hydroxyepoxypropane to produce chloropropane diol or glycerol. Acts on R enantiomers.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.

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 Related Entries

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UniProtKB/Swiss-Prot
        EPHB_MYCTO | P95276: 2e3j

(-) Related Entries Specified in the PDB File

2e3j CRYSTAL STRUCTURE OF EPOXIDE HYDROLASE B (RV1938) FROM MYCOBACTERIUM TUBERCULOSIS AT 2.1 ANGSTROM RESOLUTION