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PDBsum entry 5w3k
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PDB id:
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Isomerase
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Title:
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Crystal structure of staphylococcus aureus ketol-acid reductoisomerase in complex NADPH, mg2+ and cpd
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Structure:
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Ketol-acid reductoisomerase (NADP(+)). Chain: a, b. Synonym: kari,acetohydroxy-acid isomeroreductase,ahir,alpha-keto- beta-hydroxylacyl reductoisomerase. Engineered: yes
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Source:
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Staphylococcus aureus. Organism_taxid: 1280. Gene: ilvc, bmf23_13825, bo217_1422, ers072840_02559. Expressed in: escherichia coli. Expression_system_taxid: 511693.
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Resolution:
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1.59Å
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R-factor:
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0.161
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R-free:
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0.187
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Authors:
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K.M.Patel,D.Teran,S.Zheng,A.Kandale,M.Schembri,R.P.Mcgeary,G.Schenk, L.W.Guddat
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Key ref:
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K.M.Patel
et al.
(2017).
Crystal Structures of Staphylococcus aureus Ketol-Acid Reductoisomerase in Complex with Two Transition State Analogues that Have Biocidal Activity.
Chemistry,
23,
18289-18295.
PubMed id:
DOI:
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Date:
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08-Jun-17
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Release date:
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25-Oct-17
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PROCHECK
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Headers
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References
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Q2FWK4
(ILVC_STAA8) -
Ketol-acid reductoisomerase (NADP(+)) from Staphylococcus aureus (strain NCTC 8325 / PS 47)
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Seq:
Struc:
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334 a.a.
326 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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Enzyme class:
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E.C.1.1.1.86
- ketol-acid reductoisomerase (NADP(+)).
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Pathway:
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Isoleucine and Valine Biosynthesis
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Reaction:
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1.
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(2R)-2,3-dihydroxy-3-methylbutanoate + NADP+ = (2S)-2-acetolactate + NADPH + H+
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2.
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(2R,3R)-2,3-dihydroxy-3-methylpentanoate + NADP+ = (S)-2-ethyl-2- hydroxy-3-oxobutanoate + NADPH + H+
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(2R)-2,3-dihydroxy-3-methylbutanoate
Bound ligand (Het Group name = )
matches with 50.00% similarity
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NADP(+)
Bound ligand (Het Group name = )
corresponds exactly
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=
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(2S)-2-acetolactate
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NADPH
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H(+)
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(2R,3R)-2,3-dihydroxy-3-methylpentanoate
Bound ligand (Het Group name = )
matches with 46.15% similarity
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NADP(+)
Bound ligand (Het Group name = )
corresponds exactly
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=
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(S)-2-ethyl-2- hydroxy-3-oxobutanoate
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NADPH
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H(+)
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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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Chemistry
23:18289-18295
(2017)
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PubMed id:
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Crystal Structures of Staphylococcus aureus Ketol-Acid Reductoisomerase in Complex with Two Transition State Analogues that Have Biocidal Activity.
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K.M.Patel,
D.Teran,
S.Zheng,
A.Kandale,
M.Garcia,
Y.Lv,
M.A.Schembri,
R.P.McGeary,
G.Schenk,
L.W.Guddat.
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ABSTRACT
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Ketol-acid reductoisomerase (KARI) is an NAD(P)H and Mg2+-dependent
enzyme of the branched-chain amino acid (BCAA) biosynthesis pathway. Here, the
first crystal structures of Staphylococcus aureus (Sa) KARI in complex with two
transition state analogues, cyclopropane-1,1-dicarboxylate (CPD) and
N-isopropyloxalyl hydroxamate (IpOHA) are reported. These compounds bind
competitively and in multi-dentate manner to KARI with Kivalues of
2.73 μm and 7.9 nm, respectively; however, IpOHA binds slowly to the
enzyme. Interestingly, intact IpOHA is present in only ≈25 % of binding
sites, whereas its deoxygenated form is present in the remaining sites. This
deoxy form of IpOHA binds rapidly to Sa KARI, but with much weaker affinity
(Ki=21 μm). Thus, our data pinpoint the origin of the slow binding
mechanism of IpOHA. Furthermore, we propose that CPD mimics the early stage of
the catalytic reaction (preceding the reduction step), whereas IpOHA mimics the
late stage (after the reduction took place). These structural insights will
guide strategies to design potent and rapidly binding derivatives of these
compounds for the development of novel biocides.
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