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(-) Description

Title :  STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE INHIBITED BY (2R)-2-(BENZOTHIOPHEN-5-YL) METHYL-3-DEHYDROQUINIC ACID
 
Authors :  J. M. Otero, A. L. Llamas-Saiz, E. Lence, L. Tizon, A. Peon, V. F. V. Praze H. Lamb, A. R. Hawkins, C. Gonzalez-Bello, M. J. Van Raaij
Date :  14 Aug 12  (Deposition) - 19 Dec 12  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Lence, L. Tizon, J. M. Otero, A. Peon, V. F. V. Prazeres, A. L. Llamas-Saiz, M. J. Van Raaij, H. Lamb, A. R. Hawkins, C. Gonzalez-Bello
Mechanistic Basis Of The Inhibition Of Type Ii Dehydroquinase By (2S)- And (2R)-2-Benzyl-3-Dehydroquinic Acids.
Acs Chem. Biol. V. 8 568 2013
PubMed-ID: 23198883  |  Reference-DOI: 10.1021/CB300493S

(-) 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: K-12
    Expression System Taxid: 83333
    Expression System Variant: SK3430
    Expression System Vector Type: PLASMID
    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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1BZ51Ligand/Ion(1R,2R,4S,5R)-2-(BENZO[B]THIOPHEN-5-YL)METHYL-1,4,5-TRIHYDROXY-3-OXOCYCLOHEXANE-1-CARBOXYLIC ACID
2SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 96)
No.NameCountTypeFull Name
1BZ512Ligand/Ion(1R,2R,4S,5R)-2-(BENZO[B]THIOPHEN-5-YL)METHYL-1,4,5-TRIHYDROXY-3-OXOCYCLOHEXANE-1-CARBOXYLIC ACID
2SO484Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:12 , ARG A:15 , 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:2007BINDING SITE FOR RESIDUE BZ5 A1145
2AC2SOFTWARESER A:54 , HOH A:2052 , HOH A:2124BINDING SITE FOR RESIDUE SO4 A1146
3AC3SOFTWAREARG A:50 , TRP A:61 , GLN A:64BINDING SITE FOR RESIDUE SO4 A1147
4AC4SOFTWAREARG A:87 , GLU A:109 , PHE A:111 , ARG A:113 , PRO A:119 , HOH A:2106 , HOH A:2125BINDING SITE FOR RESIDUE SO4 A1148
5AC5SOFTWAREARG A:15 , ARG A:18 , HIS A:63 , HOH A:2050 , HOH A:2060 , HOH A:2061 , HOH A:2126BINDING SITE FOR RESIDUE SO4 A1149
6AC6SOFTWAREARG A:50 , GLN A:51 , HOH A:2043BINDING SITE FOR RESIDUE SO4 A1150
7AC7SOFTWARELYS A:46 , ARG A:50 , HOH A:2034BINDING SITE FOR RESIDUE SO4 A1151
8AC8SOFTWAREGLN A:57 , HOH A:2053 , HOH A:2128BINDING SITE FOR RESIDUE SO4 A1152

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B6Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B6Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B6Q)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IIPS01029 Dehydroquinase class II signature.AROQ_MYCTO9-26  1A:8-18
AROQ_MYCTU9-26  1A:8-18
Biological Unit 1 (1, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IIPS01029 Dehydroquinase class II signature.AROQ_MYCTO9-26  12A:8-18
AROQ_MYCTU9-26  12A:8-18

(-) Exons   (0, 0)

(no "Exon" information available for 4B6Q)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:135
 aligned with AROQ_MYCTO | P9WPX6 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:142
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  
           AROQ_MYCTO     4 LIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 145
               SCOP domains d4b6qa_ A: Type        II 3-dehydroquinate dehydratase                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..-------..hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----DEHYDROQUINASE_II ----------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6q A   3 LIVNVINGPNLGRLGR-------GTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 144
                                    12     |   -   |    32        42        52        62        72        82        92       102       112       122       132       142  
                                          18      26                                                                                                                      


Chain A from PDB  Type:PROTEIN  Length:135
 aligned with AROQ_MYCTU | P9WPX7 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:142
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  
           AROQ_MYCTU     4 LIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 145
               SCOP domains d4b6qa_ A: Type        II 3-dehydroquinate dehydratase                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..-------..hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DEHYDROQUINASE_II ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6q A   3 LIVNVINGPNLGRLGR-------GTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHV 144
                                    12     |   -   |    32        42        52        62        72        82        92       102       112       122       132       142  
                                          18      26
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4B6Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B6Q)

(-) Gene Ontology  (7, 12)

Asymmetric Unit(hide GO term definitions)
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.

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.

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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 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 3n76 3n7a 3n86 3n87 3n8k 3n8n 4b6o 4b6p 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
2xb8 STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (2R)-2 -(4-METHOXYBENZYL)-3-DEHYDROQUINIC ACID
2y71 STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE COMPLEXED WITH (1R,4S,5R)-1,4,5- TRIHYDROXY-3-((5-METHYLBENZO(B)THIOPHEN-2-YL)METHOXY) CYCLOHEX-2-ENECARBOXYLATE
2y76 STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE COMPLEXED WITH (1R,4S,5R)-3-(BENZO(B) THIOPHEN-5-YLMETHOXY)-2-(BENZO(B)THIOPHEN-5-YLMETHYL )-1,4,5-TRIHYDROXYCYCLOHEX-2-ENECARBOXYLATE
2y77 STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE COMPLEXED WITH (1R,4S,5R)-3-(BENZO(B) THIOPHEN-2-YLMETHOXY)-1,4,5-TRIHYDROXY-2-(THIOPHEN-2 -YLMETHYL)CYCLOHEX-2-ENECARBOXYLATE
4b6p STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINASE INHIBITED BY (2S)-2-PERFLUOROBENZYL-3- DEHYDROQUINIC ACID