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(-) Description

Title :  CRYSTAL STRUCTURE OF K170M MUTANT OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA TYPHIMURIUM LT2 IN NON-COVALENT COMPLEX WITH DEHYDROQUINATE.
 
Authors :  G. Minasov, S. H. Light, L. Shuvalova, L. Papazisi, W. F. Anderson, Cent Structural Genomics Of Infectious Diseases (Csgid)
Date :  24 Jun 10  (Deposition) - 28 Jul 10  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Light, G. Minasov, L. Shuvalova, M. E. Duban, M. Caffrey, W. F. Anderson, A. Lavie
Insights Into The Mechanism Of Type I Dehydroquinate Dehydratases From Structures Of Reaction Intermediates.
J. Biol. Chem. V. 286 3531 2011
PubMed-ID: 21087925  |  Reference-DOI: 10.1074/JBC.M110.192831

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AROD, STM1358
    Mutation: YES
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2
    Synonym: 3-DEHYDROQUINASE, TYPE I DHQASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1DQA2Ligand/Ion1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:21 , GLU A:46 , ARG A:48 , ARG A:82 , HIS A:143 , MET A:170 , MET A:203 , MET A:205 , ARG A:213 , PHE A:225 , SER A:232 , ALA A:233 , GLN A:236BINDING SITE FOR RESIDUE DQA A 253
2AC2SOFTWARESER B:21 , GLU B:46 , ARG B:48 , ARG B:82 , HIS B:143 , MET B:170 , MET B:203 , MET B:205 , ARG B:213 , PHE B:225 , SER B:232 , ALA B:233 , GLN B:236BINDING SITE FOR RESIDUE DQA B 253

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IPS01028 Dehydroquinase class I active site.AROD_SALTY114-144
 		  2A:114-144
B:114-144

(-) Exons   (0, 0)

(no "Exon" information available for 3NNT)

(-) Sequences/Alignments

Asymmetric/Biological 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:257
 aligned with AROD_SALTY | P58687 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:257
                                  1                                                                                                                                                                                                                                                          
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       
           AROD_SALTY     - ------MKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQ 251
               SCOP domains d3nnta_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhh....eeee..hhhhh.....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: A:114-14----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nnt A  -5 YFQSNAMKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPMIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQ 251
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       


Chain B from PDB  Type:PROTEIN  Length:257
 aligned with AROD_SALTY | P58687 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:257
                                  1                                                                                                                                                                                                                                                          
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       
           AROD_SALTY     - ------MKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQ 251
               SCOP domains d3nntb_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------DHquinase_I-3nntB01 B:19-247                                                                                                                                                                                                         ---- Pfam domains (1)
           Pfam domains (2) ------------------------DHquinase_I-3nntB02 B:19-247                                                                                                                                                                                                         ---- Pfam domains (2)
         Sec.struct. author .eee....eeee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhh....eeee............hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: B:114-14----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nnt B  -5 YFQSNAMKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPMIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQ 251
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NNT)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AROD_SALTY | P58687)
molecular function
    GO:0003855    3-dehydroquinate dehydratase activity    Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0046279    3,4-dihydroxybenzoate biosynthetic process    The chemical reactions and pathways resulting in the formation of 3,4-dihydroxybenzoate.
    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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  AROD_SALTY | P58687
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 Related Entries

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

UniProtKB/Swiss-Prot
        AROD_SALTY | P58687: 3l2i 3lb0 3m7w 3o1n 3oex 3s42 4gfs 4guf 4gug 4guh 4gui 4guj 4iuo

(-) Related Entries Specified in the PDB File

3l2i CRYSTAL STRUCTURE OF THE 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA TYPHIMURIUM LT2.
3lb0 CRYSTAL STRUCTURE OF THE 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA TYPHIMURIUM LT2 WITH CITRATE BOUND TO THE ACTIVE SITE.
3m7w CRYSTAL STRUCTURE OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA TYPHIMURIUM LT2 IN COVALENT COMPLEX WITH DEHYDROQUINATE. RELATED ID: IDP90922 RELATED DB: TARGETDB