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(-) Description

Title :  H. PYLORI TYPE II DHQASE IN COMPLEX WITH CITRATE
 
Authors :  D. A. Robinson, A. J. Lapthorn
Date :  24 Oct 05  (Deposition) - 22 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  3-Dehydroquinase, Shikimate Pathway, Aromatic Amino Acid Biosynthesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Robinson, K. A. Stewart, N. C. Price, P. A. Chalk, J. R. Coggins, A. J. Lapthorn
Crystal Structures Of Helicobacter Pylori Type Ii Dehydroquinase Inhibitor Complexes: New Directions For Inhibitor Design.
J. Med. Chem. V. 49 1282 2006
PubMed-ID: 16480265  |  Reference-DOI: 10.1021/JM0505361
(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: PET21A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Synonym: 3-DEHYDROQUINASE, DHQASE, TYPE II DEHYDROQUINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:17 , TYR A:22 , ASN A:76 , GLY A:78 , ALA A:79 , HIS A:82 , HIS A:102 , LEU A:103 , THR A:104 , ILE A:106 , ARG A:109 , ARG A:113 , HOH A:2001BINDING SITE FOR RESIDUE CIT A1159

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C4V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2C4V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C4V)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IIPS01029 Dehydroquinase class II signature.AROQ_HELPY6-23  1A:6-23
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IIPS01029 Dehydroquinase class II signature.AROQ_HELPY6-23  2A:6-23

(-) Exons   (0, 0)

(no "Exon" information available for 2C4V)

(-) 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:158
 aligned with AROQ_HELPY | Q48255 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           AROQ_HELPY     1 MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFFQTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKAFQEAQKNN 158
               SCOP domains d2c4va_ A: automated matches                                                                                                                                   SCOP domains
               CATH domains 2c4vA00 A:1-158  [code=3.40.50.9100, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhhh...eeeee.......hhhhh.........eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DEHYDROQUINASE_II --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c4v A   1 MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFFQTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKAFQEAQKNN 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
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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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C4V)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (AROQ_HELPY | Q48255)
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_HELPY | Q48255: 1j2y 2c4w 2c57 2wks 2xb9 2xd9 2xda 4b6r 4b6s

(-) Related Entries Specified in the PDB File

1j2y CRYSTAL STRUCTURE OF THE TYPE II 3- DEHYDROQUINASE
2c4w TYPE II DEHYDROQUINASE FROM H. PYLORI IN COMPLEX WITH AH9095
2c57 H.PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH FA1