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(-) Description

Title :  CRYSTAL STRUCTURE OF THE QUINATE DEHYDROGENASE FROM CORYNEBACTERIUM GLUTAMICUM
 
Authors :  J. Schoepe, K. Niefind, D. Schomburg
Date :  20 Oct 06  (Deposition) - 14 Nov 06  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Quinate; Shikimate; Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Schoepe, K. Niefind, D. Schomburg
1. 6 A Structure Of An Nad(+)-Dependent Quinate Dehydrogenas From Corynebacterium Glutamicum
Acta Crystallogr. , Sect. D V. 64 803 2008
PubMed-ID: 18566515  |  Reference-DOI: 10.1107/S090744490801411X

(-) Compounds

Molecule 1 - SHIKIMATE DEHYDROGENASE
    ChainsA
    EC Number1.1.1.25
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPETNHIS
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCGL0424
    MutationYES
    Organism ScientificCORYNEBACTERIUM GLUTAMICUM ATCC 13032
    Organism Taxid196627
    StrainATCC13032
    SynonymSHIKIMATE 5-DEHYDROGENASE

 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
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:86 , ILE A:87 , THR A:88 , LYS A:92 , ASN A:113 , ASP A:129 , VAL A:157 , GLN A:277 , HOH A:355 , HOH A:506BINDING SITE FOR RESIDUE GOL A 9991

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:89 -Pro A:90
2Met A:250 -Pro A:251

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NLO)

(-) 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:281
 aligned with AROE_CORGL | Q9X5C9 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:281
                                    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       262       272       282 
           AROE_CORGL     3 DSILLGLIGQGLDLSRTPAMHEAEGLAQGRATVYRRIDTLGSRASGQDLKTLLDAALYLGFNGLNITHPYKQAVLPLLDEVSEQATQLGAVNTVVIDATGHTTGHNTDVSGFGRGMEEGLPNAKLDSVVQVGAGGVGNAVAYALVTHGVQKLQVADLDTSRAQALADVINNAVGREAVVGVDARGIEDVIAAADGVVNATPMGMPAHPGTAFDVSCLTKDHWVGDVVYMPIETELLKAARALGCETLDGTRMAIHQAVDAFRLFTGLEPDVSRMRETFLSL 283
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------Shikimate_dh_N-2nloA02 A:28-115                                                         ---------------------Shikimate_DH-2nloA01 A:137-266                                                                                                    ------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhh...eeee.......hhhhh.eehhhhhhhh...eeee.....eeeehhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhh.eeee..............hhhhh....eeee.......hhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nlo A  22 DSILLGLIGQGLDLSRTPAMHEAEGLAQGRATVYRRIDTLGSRASGQDLKTLLDAALYLGFNGLNITHPYKQAVLPLLDEVSEQATQLGAVNTVVIDATGHTTGHNTDVSGFGRGMEEGLPNAKLDSVVQVGAGGVGNAVAYALVTHGVQKLQVADLDTSRAQALADVINNAVGREAVVGVDARGIEDVIAAADGVVNATPMGMPAHPGTAFDVSCLTKDHWVGDVVYMPIETELLKAARALGCETLDGTRMAIHQAVDAFRLFTGLEPDVSRMRETFLSL 302
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301 

   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  (0, 0)

(no "SCOP Domain" information available for 2NLO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2NLO)

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (AROE_CORGL | Q9X5C9)
molecular function
    GO:0070403    NAD+ binding    Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0030266    quinate 3-dehydrogenase (NAD+) activity    Catalysis of the reaction: (-)-quinate + NAD+ = (-)-3-dehydroquinate + NADH + H+.
    GO:0004764    shikimate 3-dehydrogenase (NADP+) activity    Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
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.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0019632    shikimate metabolic process    The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AROE_CORGL | Q9X5C93jyo 3jyp 3jyq

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