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(-) Description

Title :  QUINATE DEHYDROGENASE FROM CORYNEBACTERIUM GLUTAMICUM IN COMPLEX WITH SHIKIMATE AND NADH
 
Authors :  A. Hoeppner, D. Schomburg, K. Niefind
Date :  22 Sep 09  (Deposition) - 27 Oct 10  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.16
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Quinate Dehyrogenase, Ternary Complex, Shikimate, Nadh, Amino-Acid Biosynthesis, Aromatic Amino Acid Biosynthesis, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hoppner, D. Schomburg, K. Niefind
Enzyme-Substrate Complexes Of The Quinate/Shikimate Dehydrogenase From Corynebacterium Glutamicum Enable New Insights In Substrate And Cofactor Binding, Specificity, An Discrimination.
Biol. Chem. V. 394 1505 2013
PubMed-ID: 23929881  |  Reference-DOI: 10.1515/HSZ-2013-0170

(-) Compounds

Molecule 1 - QUINATE/SHIKIMATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.24, 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNHIS
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: QDH
    Gene: AROE, CG0504, CGL0424
    Organism Common: BREVIBACTERIUM FLAVUM
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 196627
    Strain: ATCC13032
    Synonym: NAD(+)-DEPENDENT QUINATE DEHYDROGENASE, QDH, CGLQDH

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SKM1Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SKM2Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:133 , GLY A:136 , GLY A:137 , VAL A:138 , ASP A:158 , LEU A:159 , ARG A:163 , ALA A:201 , THR A:202 , PRO A:203 , MET A:206 , ALA A:213 , VAL A:228 , VAL A:229 , GLY A:251 , ALA A:255 , HOH A:388 , HOH A:447 , HOH A:588 , HOH A:590 , HOH A:636 , HOH A:667BINDING SITE FOR RESIDUE NAD A 377
2AC2SOFTWARELEU A:9 , SER A:17 , THR A:19 , ASN A:67 , THR A:69 , LYS A:73 , ASN A:94 , ASP A:110 , GLN A:258 , HOH A:459 , HOH A:619BINDING SITE FOR RESIDUE SKM A 378

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:70 -Pro A:71
2Met A:231 -Pro A:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JYQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3JYQ)

(-) 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:282
 aligned with AROE_CORGL | Q9X5C9 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:282
                                    11        21        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  
           AROE_CORGL     2 NDSILLGLIGQGLDLSRTPAMHEAEGLAQGRATVYRRIDTLGSRASGQDLKTLLDAALYLGFNGLNITHPYKQAVLPLLDEVSEQATQLGAVNTVVIDATGHTTGHNTDVSGFGRGMEEGLPNAKLDSVVQVGAGGVGNAVAYALVTHGVQKLQVADLDTSRAQALADVINNAVGREAVVGVDARGIEDVIAAADGVVNATPMGMPAHPGTAFDVSCLTKDHWVGDVVYMPIETELLKAARALGCETLDGTRMAIHQAVDAFRLFTGLEPDVSRMRETFLSL 283
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------Shikimate_dh_N-3jyqA02 A:9-96                                                           ---------------------Shikimate_DH-3jyqA01 A:118-247                                                                                                    ------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhhh..eeee.......hhhhh.eehhhhhhhh...eeee.....eeeehhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhh.eeee..............hhhhh....eeee.......hhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jyq A   2 NDSILLGLIGQGLDLSRTPAMHEAEGLAQGRATVYRRIDTLGSRASGQDLKTLLDAALYLGFNGLNITHPYKQAVLPLLDEVSEQATQLGAVNTVVIDATGHTTGHNTDVSGFGRGMEEGLPNAKLDSVVQVGAGGVGNAVAYALVTHGVQKLQVADLDTSRAQALADVINNAVGREAVVGVDARGIEDVIAAADGVVNATPMGMPAHPGTAFDVSCLTKDHWVGDVVYMPIETELLKAARALGCETLDGTRMAIHQAVDAFRLFTGLEPDVSRMRETFLSL 283
                                    11        21        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
   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 3JYQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Shikimate_dh_N] (15)

(-) 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 | Q9X5C9: 2nlo 3jyo 3jyp

(-) Related Entries Specified in the PDB File

2nlo THE SAME PROTEIN WITH GLYCEROL BOUND TO THE ACTIVE SITE.
3jyo THE SAME PROTEIN IN COMPLEX WITH NAD.
3jyp THE SAME PROTEIN IN COMPLEX WITH QUINATE AND NADH.