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(-) Description

Title :  THE STRUCTURE OF A PUTATIVE 3-DEHYDROQUINATE DEHYDRATASE FROM STREPTOCOCCUS PYOGENES.
 
Authors :  M. E. Cuff, E. Duggan, S. Clancy, A. Joachimiak, Midwest Center For S Genomics (Mcsg)
Date :  21 Dec 06  (Deposition) - 23 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Type I 3-Dehydroquinate Dehydratase, Dhqase, Streptococcus Pyogenes, Dehydroshikimate, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, E. Duggan, S. Clancy, A. Joachimiak
The Structure Of A Putative 3-Dehydroquinate Dehydratase From Streptococcus Pyogenes.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
    Chains: A
    EC Number: 4.2.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AROD
    Organism Scientific: STREPTOCOCCUS PYOGENES SEROTYPE M1
    Organism Taxid: 301447
    Strain: M1 GAS
    Synonym: 3-DEHYDROQUINASE, TYPE I DHQASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MG1Ligand/IonMAGNESIUM ION
3MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 26)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION
3MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:89 , HOH A:505 , HOH A:533 , HOH A:552 , HOH A:707 , HOH A:711BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREGLN A:105 , LEU A:108 , LEU A:137 , HOH A:627 , HOH A:665 , HOH A:790BINDING SITE FOR RESIDUE EDO A 501
3AC3SOFTWARELEU A:108 , PHE A:110 , HOH A:536 , HOH A:639 , HOH A:774BINDING SITE FOR RESIDUE EDO A 502
4AC4SOFTWAREGLY A:179 , ARG A:186 , GLY A:208 , GLN A:209BINDING SITE FOR RESIDUE EDO A 503
5AC5SOFTWARETYR A:117 , PRO A:124 , ASN A:126 , HOH A:599 , HOH A:631 , HOH A:772BINDING SITE FOR RESIDUE EDO A 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OCZ)

(-) Exons   (0, 0)

(no "Exon" information available for 2OCZ)

(-) 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:218
 aligned with AROD_STRP1 | P63590 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:224
                             1                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           AROD_STRP1     - -MRIVAPVMPRHFDEAQAIDISKYEDVNLIEWRADFLPKDEIVAVAPAIFEKFAGKEIIFTLRTVQEGGNITLSSQEYVDIIKEINAIYNPDYIDFEYFTHKSVFQEMLDFPNLILSYHNFEETPENLMEAFSEMTKLAPRVVKIAVMPQSEQDVLDLMNYTRGFKTLNPEQEFATISMGKLGRLSRFAGDVIGSSWTYVSLDHVSGPGQVTLNDMKRIIEVLE 223
               SCOP domains d2ocza_ A: Type I 3-dehydroquinate dehydratase                                                                                                                                                                                   SCOP domains
               CATH domains 2oczA00 A:0-223 Aldolase class I                                                                                                                                                                                                 CATH domains
               Pfam domains ----DHquinase_I-2oczA01 A:4-220                                                                                                                                                                                              --- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhh.hhhhhh...eeeee.hhhhhhhhhhhhhhhhhhh...eeeee..hhhhh.....hhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh....eeeeeee......hhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh..eee...------...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ocz A   0 AmRIVAPVmPRHFDEAQAIDISKYEDVNLIEWRADFLPKDEIVAVAPAIFEKFAGKEIIFTLRTVQEGGNITLSSQEYVDIIKEINAIYNPDYIDFEYFTHKSVFQEmLDFPNLILSYHNFEETPENLmEAFSEmTKLAPRVVKIAVmPQSEQDVLDLmNYTRGFKTLNPEQEFATISmGKLGRLSRFAGDVIGSSWTYVSL------GQVTLNDmKRIIEVLE 223
                             |      |9        19        29        39        49        59        69        79        89        99       109       119       129    |  139       149       159       169       179       189       199 |     209     | 219    
                             |      8-MSE                                                                                            107-MSE              128-MSE |          147-MSE    158-MSE             178-MSE                201    208      |        
                             1-MSE                                                                                                                              134-MSE                                                                          215-MSE
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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  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (AROD_STRP1 | P63590)
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: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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