8EIX

Cobalt(II)-substituted S48A Horse Liver Alcohol Dehydrogenase in Complex with NADH and N-Cyclohexylformamide

PDB DOI: https://doi.org/10.2210/pdb8EIX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Equus caballus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-09-15 Released: 2023-02-01
Deposition Author(s): Zheng, C., Mathews, I.I., Boxer, S.G.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.244
R-Value Work: 0.206
R-Value Observed: 0.208

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Enhanced active-site electric field accelerates enzyme catalysis.

Zheng, C., Ji, Z., Mathews, I.I., Boxer, S.G.

(2023) Nat Chem 15: 1715-1721

PubMed: 37563323 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41557-023-01287-x
Primary Citation of Related Structures:
7U9N, 7UQ9, 7UTW, 8EIW, 8EIX, 8EIY

PubMed Abstract:
The design and improvement of enzymes based on physical principles remain challenging. Here we demonstrate that the principle of electrostatic catalysis can be leveraged to substantially improve a natural enzyme's activity. We enhanced the active-site electric field in horse liver alcohol dehydrogenase by replacing the serine hydrogen-bond donor with threonine and replacing the catalytic Zn ²⁺ with Co ²⁺. Based on the electric field enhancement, we make a quantitative prediction of rate acceleration-50-fold faster than the wild-type enzyme-which was in close agreement with experimental measurements. The effects of the hydrogen bonding and metal coordination, two distinct chemical forces, are described by a unified physical quantity-electric field, which is quantitative, and shown here to be additive and predictive. These results suggest a new design paradigm for both biological and non-biological catalysts.

Organizational Affiliation

Department of Chemistry, Stanford University, Stanford, CA, USA.

Macromolecule Content

Total Structure Weight: 81.88 kDa
Atom Count: 5,705
Modelled Residue Count: 748
Deposited Residue Count: 754
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase E chain	A, B	377	Equus caballus	Mutation(s): 1 EC: 1.1.1.1
UniProt
Find proteins for P00327 (Equus caballus) Explore P00327 Go to UniProtKB: P00327
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00327
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
CXF (Subject of Investigation/LOI) Query on CXF Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	CYCLOHEXYLFORMAMIDE C₇ H₁₃ N O SWGXDLRCJNEEGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
CXF	BindingDB: 8EIX	Ki: min: 2300, max: 5200 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.244
R-Value Work: 0.206
R-Value Observed: 0.208
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.27	α = 72.32
b = 57.56	β = 74.88
c = 68.25	γ = 71.6

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-02-01

Deposition Author(s):

Zheng, C.

Mathews, I.I.

Boxer, S.G.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118044
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133894