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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE 2 DEHYDROQUINASE IN COMPLEX WITH(1R,4R,5R)-1,4,5-TRIHYDROXY-3-((1S)-1-HYDROXY-2-PHENYL)ETHYLCYCLOHEX-2-EN-1-CARBOXYLIC ACID
 
Authors :  J. M. Otero, A. L. Llamas-Saiz, H. Lamb, A. R. Hawkins, B. Blanco, A. Sede C. Gonzalez-Bello, M. J. Van Raaij
Date :  17 Dec 13  (Deposition) - 16 Apr 14  (Release) - 07 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Bacterial Proteins, Lyase, Inhibitor, Protein Binding, Shikimis Acid Pathway, Substrate Specificity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Blanco, A. Sedes, A. Peon, J. M. Otero, M. J. Van Raaij, P. Thompson, A. R. Hawkins, C. Gonzalez-Bello
Exploring The Water-Binding Pocket Of The Type Ii Dehydroquinase Enzyme In The Structure-Based Design Of Inhibitors.
J. Med. Chem. V. 57 3494 2014
PubMed-ID: 24689821  |  Reference-DOI: 10.1021/JM500175Z

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
    Atcc: 27294
    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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2W4N1Ligand/Ion(1R,4R,5R)-1,4,5-TRIHYDROXY-3-[(1S)-1-HYDROXY-2-PHENYL]ETHYLCYCLOHEX-2-ENE-1-CARBOXYLICACID
Biological Unit 1 (2, 36)
No.NameCountTypeFull Name
1SO424Ligand/IonSULFATE ION
2W4N12Ligand/Ion(1R,4R,5R)-1,4,5-TRIHYDROXY-3-[(1S)-1-HYDROXY-2-PHENYL]ETHYLCYCLOHEX-2-ENE-1-CARBOXYLICACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:18 , 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 W4N A1143
2AC2SOFTWARESER A:54BINDING SITE FOR RESIDUE SO4 A1144
3AC3SOFTWAREARG A:87 , PHE A:111 , ARG A:113 , HIS A:114 , SER A:115 , TYR A:116 , PRO A:119BINDING SITE FOR RESIDUE SO4 A1145

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 4CIX)

(-) 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:133
 aligned with AROQ_MYCTO | P9WPX6 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
           AROQ_MYCTO     4 LIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAE 143
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..-------..hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DEHYDROQUINASE_II --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cix A   3 LIVNVINGPNLGRLGR-------GTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAE 142
                                    12     |   -   |    32        42        52        62        72        82        92       102       112       122       132       142
                                          18      26                                                                                                                    


Chain A from PDB  Type:PROTEIN  Length:133
 aligned with AROQ_MYCTU | P9WPX7 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
           AROQ_MYCTU     4 LIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAE 143
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..-------..hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----DEHYDROQUINASE_II --------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cix A   3 LIVNVINGPNLGRLGR-------GTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAE 142
                                    12     |   -   |    32        42        52        62        72        82        92       102       112       122       132       142
                                          18      26
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4CIX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 2xb8 2y71 2y76 2y77 3n59 3n76 3n7a 3n86 3n87 3n8k 3n8n 4b6o 4b6p 4b6q 4civ 4ciw 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 4b6q 4civ 4ciw 4ciy 4ckw 4ckx 4cky 4ckz 4cl0 4ki7 4kij 4kiu 4kiw 4v0s

(-) Related Entries Specified in the PDB File

4civ CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE 2 DEHYDROQUINASE IN COMPLEX WITH (1R,4S,5R)-1,4,5- TRIHYDROXY-3-HYDROXYMETHYLCYCLOHEX-2-ENE-1-CARBOXYLIC ACID
4ciw CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE 2 DEHYDROQUINASE IN COMPLEX WITH A CYCLOHEXENCARBOXYLIC ACID INHIBITOR
4ciy CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE 2 DEHYDROQUINASE IN COMPLEX WITH (1R,4R,5R)-1,4,5- TRIHYDROXY-3-((1R)-1-HYDROXY-2-PHENYL)ETHYLCYCLOHEX-2 -EN-1-CARBOXYLIC ACID