5Z2X

Structure of Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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Ligand Structure Quality Assessment 


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Literature

Structural Insight into Enantioselective Inversion of an Alcohol Dehydrogenase Reveals a "Polar Gate" in Stereorecognition of Diaryl Ketones.

Zhou, J.Y.Wang, Y.Xu, G.C.Wu, L.Han, R.Z.Schwaneberg, U.Rao, Y.J.Zhao, Y.L.Zhou, J.H.Ni, Y.

(2018) J Am Chem Soc 140: 12645-12654

  • DOI: 10.1021/jacs.8b08640
  • Primary Citation of Related Structures:  
    5Z2X, 5ZEC, 5ZED

  • PubMed Abstract: 
  • Diaryl ketones are important building blocks for synthesizing pharmaceuticals and are generally regarded as "difficult-to-reduce" ketones due to the large steric hindrance of their two bulky aromatic side chains. Alcohol dehydrogenase from Kluyveromyces polyspora ( KpADH) has been identified as a robust biocatalyst due to its high conversion of diaryl ketone substrate (4-chlorophenyl)(pyridine-2-yl)ketone (CPMK) with a moderate R-selectivity of 82% ee ...

    Diaryl ketones are important building blocks for synthesizing pharmaceuticals and are generally regarded as "difficult-to-reduce" ketones due to the large steric hindrance of their two bulky aromatic side chains. Alcohol dehydrogenase from Kluyveromyces polyspora ( KpADH) has been identified as a robust biocatalyst due to its high conversion of diaryl ketone substrate (4-chlorophenyl)(pyridine-2-yl)ketone (CPMK) with a moderate R-selectivity of 82% ee. To modulate the stereoselectivity of KpADH, a "polarity scanning" strategy was proposed, in which six key residues inside and at the entrance of the substrate binding pocket were identified. After iterative combinatorial mutagenesis, variants Mu-R2 and Mu-S5 with enhanced (99.2% ee, R) and inverted (97.8% ee, S) stereoselectivity were obtained. The crystal structures of KpADH and two mutants in complex with NADPH were resolved to elucidate the evolution of enantioselective inversion. Based on MD simulation, Mu-R2-CPMK ProR and Mu-S5-CPMK ProS were more favorable in the formation of prereaction states. Interestingly, a quadrilateral plane formed by α-carbons of four residues (N136, V161, C237, and G214) was identified at the entrance of the substrate binding pocket of Mu-S5; this plane acts as a "polar gate" for substrates. Due to the discrepancy in charge characteristics between chlorophenyl and pyridine substituents, the pro- S orientation of CPMK is defined when it passes through the "polar gate" in Mu-S5, whereas the similar plane in wild-type is blocked by several aromatic residues. Our result paves the way for engineering stereocomplementary ADH toward bulky diaryl ketones and provides structural insight into the mechanism of stereoselective inversion.


    Organizational Affiliation

    Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , 214122 Jiangsu , China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alcohol dehydrogenaseA, B342Vanderwaltozyma polyspora DSM 70294Mutation(s): 0 
Gene Names: Kpol_529p27
EC: 1.1.1.2
UniProt
Find proteins for A7TM80 (Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294 / BCRC 21397 / CBS 2163 / NBRC 10782 / NRRL Y-8283 / UCD 57-17))
Explore A7TM80 
Go to UniProtKB:  A7TM80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7TM80
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B],
M [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
N [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.652α = 90
b = 102.652β = 90
c = 134.08γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
PHENIXphasing
PHENIXmodel building
PDB_EXTRACTdata extraction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China grant numberChina21506073
National Natural Science Foundation of China grant numberChina21776112
Natural Science Foundation of Jiangsu ProvinceChinaBK20150003
Natural Science Foundation of Jiangsu ProvinceChinaBK20171135

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release