7QLQ

CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N151G, L259V COMPLEXED WITH FE, NAD, AND DIMETHOXYPHENYL ACETAMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.187 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structures and kinetic studies of a laboratory evolved aldehyde reductase explain the dramatic shift of its new substrate specificity.

Sridhar, S.Zavarise, A.Kiema, T.R.Dalwani, S.Eriksson, T.Hajee, Y.Reddy Enugala, T.Wierenga, R.K.Widersten, M.

(2023) IUCrJ 10: 437-447

  • DOI: https://doi.org/10.1107/S205225252300444X
  • Primary Citation of Related Structures:  
    7QLG, 7QLQ, 7QLS, 7QNH

  • PubMed Abstract: 

    The Fe 2+ -dependent E. coli enzyme FucO catalyzes the reversible interconversion of short-chain (S)-lactaldehyde and (S)-1,2-propanediol, using NADH and NAD + as cofactors, respectively. Laboratory-directed evolution experiments have been carried out previously using phenylacetaldehyde as the substrate for screening catalytic activity with bulky substrates, which are very poorly reduced by wild-type FucO. These experiments identified the N151G/L259V double mutant (dubbed DA1472) as the most active variant with this substrate via a two-step evolutionary pathway, in which each step consisted of one point mutation. Here the crystal structures of DA1472 and its parent D93 (L259V) are reported, showing that these amino acid substitutions provide more space in the active site, though they do not cause changes in the main-chain conformation. The catalytic activity of DA1472 with the physiological substrate (S)-lactaldehyde and a series of substituted phenylacetaldehyde derivatives were systematically quantified and compared with that of wild-type as well as with the corresponding point-mutation variants (N151G and L259V). There is a 9000-fold increase in activity, when expressed as k cat /K M values, for DA1472 compared with wild-type FucO for the phenylacetaldehyde substrate. The crystal structure of DA1472 complexed with a non-reactive analog of this substrate (3,4-dimethoxyphenylacetamide) suggests the mode of binding of the bulky group of the new substrate. These combined structure-function studies therefore explain the dramatic increase in catalytic activity of the DA1472 variant for bulky aldehyde substrates. The structure comparisons also suggest why the active site in which Fe 2+ is replaced by Zn 2+ is not able to support catalysis.


  • Organizational Affiliation

    Department of Chemistry - BMC, Uppsala University, SE-751 23 Uppsala, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lactaldehyde reductaseA [auth AAA],
B [auth BBB]
390Escherichia coli str. K-12 substr. MG1655Mutation(s): 2 
Gene Names: fucOZ4116ECs3659
EC: 1.1.1.77
UniProt
Find proteins for P0A9S1 (Escherichia coli (strain K12))
Explore P0A9S1 
Go to UniProtKB:  P0A9S1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9S1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APR (Subject of Investigation/LOI)
Query on APR

Download Ideal Coordinates CCD File 
D [auth AAA],
J [auth BBB]
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
E9I (Subject of Investigation/LOI)
Query on E9I

Download Ideal Coordinates CCD File 
C [auth AAA],
H [auth BBB]
2-(3,4-dimethoxyphenyl)ethanamide
C10 H13 N O3
CUWOZWFDSYIYHL-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
I [auth BBB]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)
Query on ACT

Download Ideal Coordinates CCD File 
E [auth AAA],
G [auth AAA]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
F [auth AAA],
K [auth BBB]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.291α = 90
b = 85.455β = 90
c = 137.226γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateSwedenOlle Engkvist Byggmastare Foundation - 194-0638

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references, Refinement description
  • Version 1.2: 2023-07-19
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description