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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM SALMONELLA ENTERICA TYPHIMURIUM LT2 WITH MALONATE AND BORIC ACID AT THE ACTIVE SITE
 
Authors :  S. H. Light, G. Minasov, M. -E. Duban, A. S. Halavaty, S. N. Krishna, L. Sh K. Kwon, W. F. Anderson, Center For Structural Genomics Of Infec Diseases (Csgid)
Date :  18 May 11  (Deposition) - 01 Jun 11  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Light, G. Minasov, M. -E. Duban, A. S. Halavaty, S. N. Krishna, L. Shuvalova, K. Kwon, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of The 3-Dehydroquinate Dehydratase (Arod From Salmonella Enterica Typhimurium Lt2 With Malonate And Boric Acid At The Active Site
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: AROD, STM1358
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371
    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  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1BO31Ligand/IonBORIC ACID
2DMS6Ligand/IonDIMETHYL SULFOXIDE
3IMD1Ligand/IonIMIDAZOLE
4MLA2Ligand/IonMALONIC ACID
5NI1Ligand/IonNICKEL (II) ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:143 , LYS B:170 , ALA B:172 , MET B:203 , MET B:205 , ARG B:213 , PHE B:225 , ALA B:233 , GLN B:236 , HOH B:409BINDING SITE FOR RESIDUE MLA B 583
02AC2SOFTWARELYS A:207 , VAL A:210 , HOH A:348 , VAL B:218 , LEU B:249 , ALA B:252 , HOH B:308BINDING SITE FOR RESIDUE DMS B 591
03AC3SOFTWAREGLU A:217 , VAL A:218 , LEU A:249 , HOH A:277 , HOH A:300 , LYS B:207BINDING SITE FOR RESIDUE DMS A 592
04AC4SOFTWARESER B:83 , ALA B:84 , LEU B:92 , TYR B:97 , GLU B:116 , HOH B:378 , HOH B:398 , HOH B:455 , HOH B:474BINDING SITE FOR RESIDUE DMS B 593
05AC5SOFTWAREASN B:-1 , ALA B:0 , LYS B:85 , HIS B:143 , ASP B:144 , PHE B:145 , HIS B:146BINDING SITE FOR RESIDUE DMS B 594
06AC6SOFTWAREHIS A:134 , HOH A:547 , HIS B:-22 , HIS B:-20 , HIS B:134 , IMD B:253BINDING SITE FOR RESIDUE NI B 589
07AC7SOFTWAREGLN A:133 , HIS A:134 , HOH A:547 , HIS B:-20 , ASP B:106 , HIS B:134 , HOH B:466 , NI B:589BINDING SITE FOR RESIDUE IMD B 253
08AC8SOFTWAREHIS A:143 , LYS A:170 , ALA A:172 , MET A:203 , MET A:205 , ARG A:213 , PHE A:225 , ALA A:233 , GLN A:236 , BO3 A:253BINDING SITE FOR RESIDUE MLA A 586
09AC9SOFTWARESER A:83 , ALA A:84 , ALA A:91 , LEU A:92 , TYR A:97 , GLU A:116 , HOH A:520BINDING SITE FOR RESIDUE DMS A 590
10BC1SOFTWARELYS A:2 , HIS A:146 , GLN A:156 , GLU A:193 , ARG A:194 , TYR A:195 , ALA A:196BINDING SITE FOR RESIDUE DMS A 595
11BC2SOFTWARESER A:21 , GLU A:46 , ARG A:48 , ARG A:82 , LYS A:170 , HOH A:307 , HOH A:374 , HOH A:404 , MLA A:586BINDING SITE FOR RESIDUE BO3 A 253

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S42)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S42)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S42)

(-) 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 3S42)

(-) 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:260
 aligned with AROD_SALTY | P58687 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:260
                                    1                                                                                                                                                                                                                                                           
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252
           AROD_SALTY     - --------MKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
               SCOP domains d3s42a_ 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...hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: A:114-14------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s42 A  -7 NLYFQSNAMKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
                                     2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with AROD_SALTY | P58687 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:266
                                          1                                                                                                                                                                                                                                                           
                                     -    |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246      
           AROD_SALTY     - --------------MKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
               SCOP domains -------------d3s42b1 B:0-252 automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------DHquinase_I-3s42B01 B:19-247                                                                                                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) --------------------------------DHquinase_I-3s42B02 B:19-247                                                                                                                                                                                                         ----- Pfam domains (2)
         Sec.struct. author ........eeee....eeee..eee.....eeeeee...hhhhhhhhhhhhhh....eeeee.hhh....hhhhhhhhhhhhhhhh....eeee..hhhhh.....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
                 3s42 B -23 MHHHHHNLYFQSNAMKTVTVRDLVVGEGAPKIIVSLMGKTITDVKSEALAYREADFDILEWRVDHFANVTTAESVLEAAGAIREIITDKPLLFTFRSAKEGGEQALTTGQYIDLNRAAVDSGLVDMIDLELFTGDDEVKATVGYAHQHNVAVIMSNHDFHKTPAAEEIVQRLRKMQELGADIPKIAVMPQTKADVLTLLTATVEMQERYADRPIITMSMSKTGVISRLAGEVFGSAATFGAVKKASAPGQISVADLRTVLTILHQA 252
                                 || -4         6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246      
                               -18|                                                                                                                                                                                                                                                                   
                                 -7
   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 3S42)

(-) 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 3nnt 3o1n 3oex 4gfs 4guf 4gug 4guh 4gui 4guj 4iuo

(-) Related Entries Specified in the PDB File

3l2i STRUCTURE OF UNLIGANDED ENZYME
3lb0 STRUCTURE OF ENZYME WITH CITRATE BOUND AT ACTIVE SITE
3m7w STRUCTURE OF ENZYME IN COVALENT COMPLEX WITH SUBSTRATE RELATED ID: IDP90922 RELATED DB: TARGETDB
3nnt STRUCTURE OF THE K170M MUTANT IN NON-COVALENT COMPLEX WITH SUBSTRATE
3oex STRUCTURE OF ENZYME WITH CHLORIDE BOUND AT ACTIVE SITE