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(-) Description

Title :  THE STRUCTURE OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE FROM SALMONELLA TYPHI
 
Authors :  A. K. Shrive, I. Polikarpov, L. Sawyer, J. R. Coggins, A. R. Hawkins
Date :  05 Apr 99  (Deposition) - 05 Apr 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydratase, Conversion Of 3-Dehydroquinate To Dehydroshikimate, 3Rd Enzyme In The Shikimate Pathway, Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. G. Gourley, A. K. Shrive, I. Polikarpov, T. Krell, J. R. Coggins, A. R. Hawkins, N. W. Isaacs, L. Sawyer
The Two Types Of 3-Dehydroquinase Have Distinct Structures But Catalyze The Same Overall Reaction.
Nat. Struct. Biol. V. 6 521 1999
PubMed-ID: 10360352  |  Reference-DOI: 10.1038/9287
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (3-DEHYDROQUINATE DEHYDRATASE)
    Chains: A, B
    EC Number: 4.2.1.10
    Organism Scientific: SALMONELLA TYPHI
    Organism Taxid: 601
    Other Details: THE PRODUCT 3-DEHYDROSHIKIMATE IS COVALENTLY ATTACHED TO THE ACTIVE SITE LYS 170 BY BOROHYDRIDE REDUCTION OF THE IMINE (SCHIFF BASE).
    Synonym: 3-DEHYDROQUINASE

 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
1DHS2Ligand/Ion3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:21 , GLU A:46 , ARG A:48 , ARG A:82 , HIS A:143 , LYS A:170 , MET A:203 , ARG A:213 , PHE A:225 , SER A:232 , ALA A:233 , GLN A:236 , HOH A:409 , HOH A:461BINDING SITE FOR RESIDUE DHS A 301
2AC2SOFTWARESER B:21 , GLU B:46 , ARG B:48 , ARG B:82 , HIS B:143 , LYS B:170 , MET B:203 , ARG B:213 , PHE B:225 , SER B:232 , ALA B:233 , GLN B:236 , HOH B:410 , HOH B:452BINDING SITE FOR RESIDUE DHS B 301
3ASRAUTHORLYS A:170 , HIS A:143 , ARG A:213LYS 170 FORMS THE IMINE INTERMEDIATE WITH THE AID OF HIS 143 ARG 213 INTERACTS WITH THE CARBOXYL GROUP OF THE 3-DEHYDROQUINATE SUBSTRATE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QFE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QFE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QFE)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IPS01028 Dehydroquinase class I active site.AROD_SALTI114-144
 		  2A:114-144
B:114-144

(-) Exons   (0, 0)

(no "Exon" information available for 1QFE)

(-) 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:252
 aligned with AROD_SALTI | P24670 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  
           AROD_SALTI     1 MKTVTVKNLIIGEGMPKIIVSLMGRDINSVKAEALAYREATFDILEWRVDHFMDIASTQSVLTAARVIRDAMPDIPLLFTFRSAKEGGEQTITTQHYLTLNRAAIDSGLVDMIDLELFTGDADVKATVDYAHAHNVYVVMSNHDFHQTPSAEEMVLRLRKMQALGADIPKIAVMPQSKHDVLTLLTATLEMQQHYADRPVITMSMAKEGVISRLAGEVFGSAATFGAVKQASAPGQIAVNDLRSVLMILHNA 252
               SCOP domains d1qfea_ A: Type I 3-dehydroquinate dehydratase                                                                                                                                                                                                               SCOP domains
               CATH domains 1qfeA00 A:1-252 Aldolase class I                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee..eee.....eeeeee....hhhhhhhhhhhhh....eeeeehhh......hhhhhhhhhhhhhh....eeeee...hhh.......hhhhhhhhhhhhhh....eeeeehhh.hhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhh.....eeeeee....hhhhh.hhhh...eeee............hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: A:114-14------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qfe A   1 MKTVTVKNLIIGEGMPKIIVSLMGRDINSVKAEALAYREATFDILEWRVDHFMDIASTQSVLTAARVIRDAMPDIPLLFTFRSAKEGGEQTITTQHYLTLNRAAIDSGLVDMIDLELFTGDADVKATVDYAHAHNVYVVMSNHDFHQTPSAEEMVSRLRKMQALGADIPKIAVMPQSKHDVLTLLTATLEMQQHYADRPVITMSMAKEGVISRLAGEVFGSAATFGAVKQASAPGQIAVNDLRSVLMILHNA 252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with AROD_SALTI | P24670 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  
           AROD_SALTI     1 MKTVTVKNLIIGEGMPKIIVSLMGRDINSVKAEALAYREATFDILEWRVDHFMDIASTQSVLTAARVIRDAMPDIPLLFTFRSAKEGGEQTITTQHYLTLNRAAIDSGLVDMIDLELFTGDADVKATVDYAHAHNVYVVMSNHDFHQTPSAEEMVLRLRKMQALGADIPKIAVMPQSKHDVLTLLTATLEMQQHYADRPVITMSMAKEGVISRLAGEVFGSAATFGAVKQASAPGQIAVNDLRSVLMILHNA 252
               SCOP domains d1qfeb_ B: Type I 3-dehydroquinate dehydratase                                                                                                                                                                                                               SCOP domains
               CATH domains 1qfeB00 B:1-252 Aldolase class I                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ------------------DHquinase_I-1qfeB01 B:19-247                                                                                                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) ------------------DHquinase_I-1qfeB02 B:19-247                                                                                                                                                                                                         ----- Pfam domains (2)
         Sec.struct. author ...eee..eee.....eeeeee....hhhhhhhhhhhhh....eeeeehhh......hhhhhhhhhhhhhh....eeeee...hhh.......hhhhhhhhhhhhhh....eeeeehhh.hhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhh.....eeeeee....hhhhh.hhhh...eeee............hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: B:114-14------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qfe B   1 MKTVTVKNLIIGEGMPKIIVSLMGRDINSVKAEALAYREATFDILEWRVDHFMDIASTQSVLTAARVIRDAMPDIPLLFTFRSAKEGGEQTITTQHYLTLNRAAIDSGLVDMIDLELFTGDADVKATVDYAHAHNVYVVMSNHDFHQTPSAEEMVSRLRKMQALGADIPKIAVMPQSKHDVLTLLTATLEMQQHYADRPVITMSMAKEGVISRLAGEVFGSAATFGAVKQASAPGQIAVNDLRSVLMILHNA 252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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  (1, 2)

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

(-) 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_SALTI | P24670)
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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 Related Entries

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        AROD_SALTI | P24670: 1gqn 1l9w 4clm 4cnn 4cno 4cnp 4uio

(-) Related Entries Specified in the PDB File

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