4EEX | pdb_00004eex

Crystal Structure of Lactococcus lactis Alcohol Dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb4EEX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lactococcus lactis subsp. lactis KF147
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-28 Released: 2012-09-26
Deposition Author(s): Liu, X., Bastian, S., Snow, C.D., Brustad, E.M., Saleski, T., Xu, J.H., Meinhold, P., Arnold, F.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.235 (Depositor), 0.231 (DCC)
R-Value Work:
0.178 (Depositor), 0.177 (DCC)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure-guided engineering of Lactococcus lactis alcohol dehydrogenase LlAdhA for improved conversion of isobutyraldehyde to isobutanol.

Liu, X., Bastian, S., Snow, C.D., Brustad, E.M., Saleski, T.E., Xu, J.H., Meinhold, P., Arnold, F.H.

(2012) J Biotechnol 164: 188-195

PubMed: 22974724 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbiotec.2012.08.008
Primary Citation Related Structures:
4EEX, 4EEZ

PubMed Abstract:
We have determined the X-ray crystal structures of the NADH-dependent alcohol dehydrogenase LlAdhA from Lactococcus lactis and its laboratory-evolved variant LlAdhA(RE1) at 1.9Å and 2.5Å resolution, respectively. LlAdhA(RE1), which contains three amino acid mutations (Y50F, I212T, and L264V), was engineered to increase the microbial production of isobutanol (2-methylpropan-1-ol) from isobutyraldehyde (2-methylpropanal). Structural comparison of LlAdhA and LlAdhA(RE1) indicates that the enhanced activity on isobutyraldehyde stems from increases in the protein's active site size, hydrophobicity, and substrate access. Further structure-guided mutagenesis generated a quadruple mutant (Y50F/N110S/I212T/L264V), whose KM for isobutyraldehyde is ∼17-fold lower and catalytic efficiency (kcat/KM) is ∼160-fold higher than wild-type LlAdhA. Combining detailed structural information and directed evolution, we have achieved significant improvements in non-native alcohol dehydrogenase activity that will facilitate the production of next-generation fuels such as isobutanol from renewable resources.

Organizational Affiliation

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.

Macromolecule Content

Total Structure Weight: 74.23 kDa
Atom Count: 5,200
Modeled Residue Count: 680
Deposited Residue Count: 696
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase 1	A, B	348	Lactococcus lactis subsp. lactis KF147	Mutation(s): 0 Gene Names: adhA, LLKF_1981 EC: 1.1.1.1
UniProt
Find proteins for Q9CEN0 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CEN0 Go to UniProtKB: Q9CEN0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CEN0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.235 (Depositor), 0.231 (DCC)
R-Value Work: 0.178 (Depositor), 0.177 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.464	α = 90
b = 126.456	β = 90
c = 94.352	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2012-11-21
Changes: Database references
Version 1.2: 2018-01-24
Changes: Advisory, Structure summary
Version 1.3: 2024-02-28
Changes: Advisory, Data collection, Database references, Derived calculations