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PDBsum entry 4guj
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PDB id:
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Lyase
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Title:
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1.50 angstrom crystal structure of the salmonella enterica 3- dehydroquinate dehydratase (arod) in complex with shikimate
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Structure:
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3-dehydroquinate dehydratase. Chain: a, b. Synonym: 3-dehydroquinase, type i dhqase. Engineered: yes
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Source:
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Salmonella enterica subsp. Enterica serovar typhimurium. Organism_taxid: 99287. Strain: lt2 / sgsc1412 / atcc 700720. Gene: arod, stm1358. Expressed in: escherichia coli. Expression_system_taxid: 511693.
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Resolution:
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1.50Å
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R-factor:
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0.157
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R-free:
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0.182
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Authors:
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S.H.Light,G.Minasov,M.-E.Duban,L.Shuvalova,K.Kwon,A.Lavie, W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid)
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Key ref:
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S.H.Light
et al.
(2014).
Crystal structures of type I dehydroquinate dehydratase in complex with quinate and shikimate suggest a novel mechanism of Schiff base formation.
Biochemistry,
53,
872-880.
PubMed id:
DOI:
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Date:
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29-Aug-12
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Release date:
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12-Sep-12
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PROCHECK
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Headers
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References
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P58687
(AROD_SALTY) -
3-dehydroquinate dehydratase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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Seq:
Struc:
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252 a.a.
251 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.4.2.1.10
- 3-dehydroquinate dehydratase.
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Pathway:
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Shikimate and Chorismate Biosynthesis
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Reaction:
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3-dehydroquinate = 3-dehydroshikimate + H2O
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3-dehydroquinate
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=
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3-dehydroshikimate
Bound ligand (Het Group name = )
corresponds exactly
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+
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H2O
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Biochemistry
53:872-880
(2014)
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PubMed id:
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Crystal structures of type I dehydroquinate dehydratase in complex with quinate and shikimate suggest a novel mechanism of Schiff base formation.
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S.H.Light,
A.Antanasijevic,
S.N.Krishna,
M.Caffrey,
W.F.Anderson,
A.Lavie.
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ABSTRACT
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A component of the shikimate biosynthetic pathway, dehydroquinate dehydratase
(DHQD) catalyzes the dehydration of 3-dehydroquniate (DHQ) to
3-dehydroshikimate. In the type I DHQD reaction mechanism a lysine forms a
Schiff base intermediate with DHQ. The Schiff base acts as an electron sink to
facilitate the catalytic dehydration. To address the mechanism of Schiff base
formation, we determined structures of the Salmonella enterica wild-type DHQD in
complex with the substrate analogue quinate and the product analogue shikimate.
In addition, we determined the structure of the K170M mutant (Lys170 being the
Schiff base forming residue) in complex with quinate. Combined with nuclear
magnetic resonance and isothermal titration calorimetry data that revealed
altered binding of the analogue to the K170M mutant, these structures suggest a
model of Schiff base formation characterized by the dynamic interplay of
opposing forces acting on either side of the substrate. On the side distant from
the substrate 3-carbonyl group, closure of the enzyme's β8-α8 loop is proposed
to guide DHQ into the proximity of the Schiff base-forming Lys170. On the
3-carbonyl side of the substrate, Lys170 sterically alters the position of DHQ's
reactive ketone, aligning it at an angle conducive for nucleophilic attack. This
study of a type I DHQD reveals the interplay between the enzyme and substrate
required for the correct orientation of a functional group constrained within a
cyclic substrate.
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