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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE D88N MUTANT INHIBITED BY A 3-DEHYDROQUINIC ACID DERIVATIVE
 
Authors :  J. M. Otero, A. L. Llamas-Saiz, C. Santiago, H. Lamb, A. R. Hawkins, M. Ma A. Peon, C. Gonzalez-Bello, M. J. Van Raaij
Date :  18 Sep 14  (Deposition) - 13 Jan 16  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Binding Sites, Type 2 Dehydroquinase, Lyase, Inhibitor, Protein Binding, Shikimis Acid Pathway, Substrate Specificity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Maneiro, J. M. Otero, A. Peon, M. J. Van Raaij, H. Lamb, A. R. Hawkings, C. Gonzalez-Bello
Investigation Of The Dehydratation Mechanism Catalyzed By The Type Ii Dehydroquinase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
    Atcc: 27294
    Chains: A, B
    EC Number: 4.2.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Plasmid: PKK233-2
    Expression System Taxid: 83333
    Expression System Variant: SK3430
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: 3-DEHYDROQUINASE, TYPE II DHQASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
12HN3Ligand/Ion(1R,2S,4S,5R)-2-(2,3,4,5,6-PENTAFLUOROPHENYL)METHYL-1,4,5-TRIHYDROXY-3-OXOCYCLOHEXANE-1-CARBOXYLIC ACID
27HN1Ligand/Ion3,4-DIHYDROXY-2-[(2,3,4,5,6-PENTAFLUOROPHENYL)METHYL]BENZOIC ACID
3CL2Ligand/IonCHLORIDE ION
4NA1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:11 , ASN A:12 , LEU A:13 , ARG A:15 , LEU A:16 , ARG A:19 , TYR A:24 , ASN A:75 , GLY A:77 , GLY A:78 , HIS A:101 , ILE A:102 , SER A:103 , HOH A:2060BINDING SITE FOR RESIDUE 2HN A1147
2AC2SOFTWAREASN A:6 , ILE A:8 , VAL A:48 , ARG A:50 , TRP A:61 , GLN A:64 , ALA A:65 , HOH A:2048 , HOH A:2088 , HOH A:2089 , HIS B:29 , ASP B:30BINDING SITE FOR RESIDUE 2HN A1148
3AC3SOFTWAREASP A:60 , HIS A:63 , ASP A:67 , ARG A:87 , ASN A:88 , ALA A:91 , HOH A:2047 , HOH A:2065 , ALA B:34 , GLU B:37 , ARG B:38BINDING SITE FOR RESIDUE 7HN A1149
4AC4SOFTWAREGLU A:42 , PRO B:11 , ASN B:12 , LEU B:13 , LEU B:16 , ARG B:19 , TYR B:24 , ASN B:75 , GLY B:77 , GLY B:78 , HIS B:101 , ILE B:102 , SER B:103 , ARG B:108 , HOH B:2046BINDING SITE FOR RESIDUE 2HN B1145
5AC5SOFTWAREGLN A:131 , ARG A:138BINDING SITE FOR RESIDUE CL A1150
6AC6SOFTWAREGLN B:131 , ARG B:138BINDING SITE FOR RESIDUE CL B1146
7AC7SOFTWAREGLU A:39 , GLU A:42 , GLU B:20 , HOH B:2011BINDING SITE FOR RESIDUE NA A1151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4V0S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4V0S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V0S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V0S)

(-) Exons   (0, 0)

(no "Exon" information available for 4V0S)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhhhhheeeeeee..hhhhhhhhhhhhhhhh..eeeehhhhh..hhhhhhhhhh....eeeee.........hhhhh.eeee...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v0s A   1 SELIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRNACAELSAPLIEVHISNVHAHSYLSPIATGVIVGLGIQGYLLALRYLAEHVGT 146
                                    10        20        30        40        50        60        70        80        90       100      |116       126       136       146
                                                                                                                                    107|                                
                                                                                                                                     114                                


Chain B from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh..eeeehhhhh..hhhhhhhhhh....eeeee..hhhhhh.......hhhhh.eeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v0s B   2 ELIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRNACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
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  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 4V0S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V0S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4V0S)

(-) Gene Ontology  (7, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        AROQ_MYCTO | P9WPX6: 1h05 1h0r 1h0s 2dhq 2xb8 2y71 2y76 2y77 3n59 3n76 3n7a 3n86 3n87 3n8k 3n8n 4b6o 4b6p 4b6q 4civ 4ciw 4cix 4ciy 4ckw 4ckx 4cky 4ckz 4cl0 4ki7 4kij 4kiu 4kiw
        AROQ_MYCTU | P9WPX7: 1h05 1h0r 1h0s 2dhq 2xb8 2y71 2y76 2y77 3n59 3n76 3n7a 3n86 3n87 3n8k 3n8n 4b6o 4b6p 4b6q 4civ 4ciw 4cix 4ciy 4ckw 4ckx 4cky 4ckz 4cl0 4ki7 4kij 4kiu 4kiw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4V0S)