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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH COMPOUND 5
 
Authors :  M. V. B. Dias, W. C Snee, K. M. Bromfield, R. Payne, S. K. Palaninathan, A N. I. Howard, C Abell, J. C. Sacchettini, T. L. Blundell
Date :  26 May 10  (Deposition) - 11 May 11  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Dehydroquinate Dehydratase, Arod, Shikimate Pathway, Drug Discovery, Mycobacterium Tuberculosis, Lyase, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. V. Dias, W. C. Snee, K. M. Bromfield, R. J. Payne, S. K. Palaninathan, A. Ciulli, N. I. Howard, C. Abell, J. C. Sacchettini, T. L. Blundell
Structural Investigation Of Inhibitor Designs Targeting 3-Dehydroquinate Dehydratase From The Shikimate Pathway Of Mycobacterium Tuberculosis.
Biochem. J. V. 436 729 2011
PubMed-ID: 21410435  |  Reference-DOI: 10.1042/BJ20110002

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
    Chains: A
    EC Number: 4.2.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28(A)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AROD, AROQ, MT2612, MTCY159.19, RV2537C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: 3-DEHYDROQUINASE, TYPE II DHQASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CA21Ligand/Ion(1S,3R,4R,5S)-1,3,4-TRIHYDROXY-5-(3-PHENOXYPROPYL)CYCLOHEXANECARBOXYLIC ACID
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1CA212Ligand/Ion(1S,3R,4R,5S)-1,3,4-TRIHYDROXY-5-(3-PHENOXYPROPYL)CYCLOHEXANECARBOXYLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:12 , ARG A:15 , ARG A:19 , TYR A:24 , ASN A:75 , GLY A:77 , GLY A:78 , HIS A:81 , ASP A:88 , HIS A:101 , ILE A:102 , SER A:103 , ARG A:112BINDING SITE FOR RESIDUE CA2 A 147

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N76)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N76)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N76)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IIPS01029 Dehydroquinase class II signature.AROQ_MYCTO9-26  1A:8-25
AROQ_MYCTU9-26  1A:8-25
Biological Unit 1 (1, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IIPS01029 Dehydroquinase class II signature.AROQ_MYCTO9-26  12A:8-25
AROQ_MYCTU9-26  12A:8-25

(-) Exons   (0, 0)

(no "Exon" information available for 3N76)

(-) Sequences/Alignments

Asymmetric 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
(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:143
 aligned with AROQ_MYCTO | P9WPX6 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:143
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142   
           AROQ_MYCTO     3 ELIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 145
               SCOP domains d3n76a_ A: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -DHquinase_II-3n76A01 A:3-142                                                                                                                -- Pfam domains
         Sec.struct. author ..eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhh....eeeee.......hhhhhh..hhhhh.eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------DEHYDROQUINASE_II ----------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n76 A   2 ELIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141   


Chain A from PDB  Type:PROTEIN  Length:143
 aligned with AROQ_MYCTU | P9WPX7 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:143
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142   
           AROQ_MYCTU     3 ELIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 145
               SCOP domains d3n76a_ A: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -DHquinase_II-3n76A01 A:3-142                                                                                                                -- Pfam domains
         Sec.struct. author ..eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhh....eeeee.......hhhhhh..hhhhh.eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------DEHYDROQUINASE_II ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n76 A   2 ELIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
   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 3N76)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: DHquinase_II] (16)

(-) Gene Ontology  (7, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (AROQ_MYCTO | P9WPX6)
molecular function
    GO:0003855    3-dehydroquinate dehydratase activity    Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
    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.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009423    chorismate biosynthetic process    The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.

Chain A   (AROQ_MYCTU | P9WPX7)
molecular function
    GO:0003855    3-dehydroquinate dehydratase activity    Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
    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.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009423    chorismate biosynthetic process    The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  3n76
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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 3n7a 3n86 3n87 3n8k 3n8n 4b6o 4b6p 4b6q 4civ 4ciw 4cix 4ciy 4ckw 4ckx 4cky 4ckz 4cl0 4ki7 4kij 4kiu 4kiw 4v0s
        AROQ_MYCTU | P9WPX7: 1h05 1h0r 1h0s 2dhq 2xb8 2y71 2y76 2y77 3n59 3n7a 3n86 3n87 3n8k 3n8n 4b6o 4b6p 4b6q 4civ 4ciw 4cix 4ciy 4ckw 4ckx 4cky 4ckz 4cl0 4ki7 4kij 4kiu 4kiw 4v0s

(-) Related Entries Specified in the PDB File

3n7a 3n86 3n87 3n8n