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(-) Description

Title :  STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (2R)-2-( 4-METHOXYBENZYL)-3-DEHYDROQUINIC ACID
 
Authors :  J. M. Otero, L. Tizon, A. L. Llamas-Saiz, G. C. Fox, C. Gonzalez-Bello, M. J. Van Raaij
Date :  08 Apr 10  (Deposition) - 15 Sep 10  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Lyase, Amino Acid Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Peon, J. M. Otero, L. Tizon, V. F. V. Prazeres, A. L. Llamas-Saiz, G. C. Fox, M. J. Van Raaij, H. Lamb, A. R. Hawkins, F. Gago, L. Castedo, C. Gonzalez-Bello
Understanding The Key Factors That Control The Inhibition Of Type Ii Dehydroquinase By (2R)-2- Benzyl-3-Dehydroquinic Acids.
Chemmedchem V. 5 1726 2010
PubMed-ID: 20815012  |  Reference-DOI: 10.1002/CMDC.201000281
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
    Chains: A
    EC Number: 4.2.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK233-2
    Expression System Strain: SK3430
    Expression System Taxid: 562
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: TYPE II DHQASE, 3-DEHYDROQUINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3XNW1Ligand/Ion(1R,2R,4S,5R)-1,4,5-TRIHYDROXY-2-(4-METHOXYBENZYL)-3-OXOCYCLOHEXANECARBOXYLIC ACID
Biological Unit 1 (3, 108)
No.NameCountTypeFull Name
1SO484Ligand/IonSULFATE ION
2TRS12Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3XNW12Ligand/Ion(1R,2R,4S,5R)-1,4,5-TRIHYDROXY-2-(4-METHOXYBENZYL)-3-OXOCYCLOHEXANECARBOXYLIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:12 , LEU A:13 , LEU A:16 , 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:112 , HOH A:2025BINDING SITE FOR RESIDUE XNW A1144
2AC2SOFTWARESER A:54 , ALA A:56 , HOH A:2047BINDING SITE FOR RESIDUE SO4 A1145
3AC3SOFTWAREHIS A:114 , SER A:115 , TYR A:116 , SO4 A:1148BINDING SITE FOR RESIDUE SO4 A1146
4AC4SOFTWAREARG A:50 , TRP A:61 , GLN A:64 , HOH A:2020BINDING SITE FOR RESIDUE SO4 A1147
5AC5SOFTWAREHIS A:106 , ARG A:113 , HIS A:114 , SER A:115 , PRO A:119 , SO4 A:1146 , HOH A:2037BINDING SITE FOR RESIDUE SO4 A1148
6AC6SOFTWAREARG A:15 , ARG A:18 , HIS A:63 , ASP A:67 , HOH A:2048BINDING SITE FOR RESIDUE SO4 A1149
7AC7SOFTWAREARG A:87 , PHE A:111 , ARG A:113 , PRO A:119 , HOH A:2049BINDING SITE FOR RESIDUE SO4 A1150
8AC8SOFTWAREVAL A:48 , ARG A:50BINDING SITE FOR RESIDUE SO4 A1151
9AC9SOFTWARETYR A:24 , LEU A:128 , GLY A:129 , ILE A:130 , GLN A:131 , HIS A:143BINDING SITE FOR RESIDUE TRS A1152

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XB8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XB8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XB8)

(-) 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 2XB8)

(-) 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:141
 aligned with AROQ_MYCTO | P9WPX6 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:141
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143 
           AROQ_MYCTO     4 LIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEH 144
               SCOP domains d2xb8a_ A: Type II 3-dehydroquinate dehydratase                                                                                               SCOP domains
               CATH domains 2xb8A00 A:3-143  [code=3.40.50.9100, no name defined]                                                                                         CATH domains
               Pfam domains DHquinase_II-2xb8A01 A:3-142                                                                                                                - Pfam domains
         Sec.struct. author .eeeeee..hhhh....hhhhhh..hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DEHYDROQUINASE_II ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xb8 A   3 LIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEH 143
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142 


Chain A from PDB  Type:PROTEIN  Length:141
 aligned with AROQ_MYCTU | P9WPX7 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:141
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143 
           AROQ_MYCTU     4 LIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEH 144
               SCOP domains d2xb8a_ A: Type II 3-dehydroquinate dehydratase                                                                                               SCOP domains
               CATH domains 2xb8A00 A:3-143  [code=3.40.50.9100, no name defined]                                                                                         CATH domains
               Pfam domains DHquinase_II-2xb8A01 A:3-142                                                                                                                - Pfam domains
         Sec.struct. author .eeeeee..hhhh....hhhhhh..hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----DEHYDROQUINASE_II ---------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xb8 A   3 LIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEH 143
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142
   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  (1, 1)

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

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        AROQ_MYCTO | P9WPX6: 1h05 1h0r 1h0s 2dhq 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 4v0s
        AROQ_MYCTU | P9WPX7: 1h05 1h0r 1h0s 2dhq 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 4v0s

(-) Related Entries Specified in the PDB File

1h05 3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH SULPHATE
1h0r TYPE II DEHYDROQUINASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH 2,3-ANNHYDRO- QUINIC ACID
1h0s 3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH 3-HYDROXYIMINO -QUNIC ACID
2dhq 3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS
2xb9 STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (2R)-2-(4-METHOXYBENZYL)-3- DEHYDROQUINIC ACID