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PDBsum entry 7k4x
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PDB id:
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Hydrolase
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Title:
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Crystal structure of kemp eliminase hg3.7 in complex with the transition state analog 6-nitrobenzotriazole
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Structure:
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Endo-1,4-beta-xylanase. Chain: a, b. Synonym: xylanase,1,4-beta-d-xylan xylanohydrolase,taxi. Engineered: yes
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Source:
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Thermoascus aurantiacus. Organism_taxid: 5087. Gene: xyna. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008
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Resolution:
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1.60Å
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R-factor:
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0.197
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R-free:
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0.228
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Authors:
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R.A.P.Padua,R.Otten,A.Bunzel,V.Nguyen,W.Pitsawong,M.Patterson,S.Sui, S.L.Perry,A.E.Cohen,D.Hilvert,D.Kern
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Key ref:
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R.Otten
et al.
(2020).
How directed evolution reshapes the energy landscape in an enzyme to boost catalysis.
Science,
370,
1442-1446.
PubMed id:
DOI:
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Date:
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16-Sep-20
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Release date:
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02-Dec-20
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PROCHECK
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Headers
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References
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P23360
(XYNA_THEAU) -
Endo-1,4-beta-xylanase from Thermoascus aurantiacus
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Seq:
Struc:
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329 a.a.
302 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 17 residue positions (black
crosses)
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Enzyme class:
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E.C.3.2.1.8
- endo-1,4-beta-xylanase.
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Reaction:
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Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
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DOI no:
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Science
370:1442-1446
(2020)
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PubMed id:
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How directed evolution reshapes the energy landscape in an enzyme to boost catalysis.
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R.Otten,
R.A.P.Pádua,
H.A.Bunzel,
V.Nguyen,
W.Pitsawong,
M.Patterson,
S.Sui,
S.L.Perry,
A.E.Cohen,
D.Hilvert,
D.Kern.
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ABSTRACT
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The advent of biocatalysts designed computationally and optimized by laboratory
evolution provides an opportunity to explore molecular strategies for augmenting
catalytic function. Applying a suite of nuclear magnetic resonance,
crystallography, and stopped-flow techniques to an enzyme designed for an
elementary proton transfer reaction, we show how directed evolution gradually
altered the conformational ensemble of the protein scaffold to populate a
narrow, highly active conformational ensemble and accelerate this transformation
by nearly nine orders of magnitude. Mutations acquired during optimization
enabled global conformational changes, including high-energy backbone
rearrangements, that cooperatively organized the catalytic base and oxyanion
stabilizer, thus perfecting transition-state stabilization. The development of
protein catalysts for many chemical transformations could be facilitated by
explicitly sampling conformational substates during design and specifically
stabilizing productive substates over all unproductive conformations.
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