7U9N

S48A Horse Liver Alcohol Dehydrogenase in Complex with NADH and N-Cyclohexylformamide

PDB DOI: https://doi.org/10.2210/pdb7U9N/pdb

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

Deposited: 2022-03-11 Released: 2023-02-01
Deposition Author(s): Zheng, C., 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: 2.20 Å
R-Value Free: 0.259
R-Value Work: 0.213
R-Value Observed: 0.215

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: 163.78 kDa
Atom Count: 11,622
Modelled Residue Count: 1,496
Deposited Residue Count: 1,508
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, C, D	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	G [auth A], K [auth B], O [auth C], S [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D]
CXF (Subject of Investigation/LOI) Query on CXF Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	H [auth A], L [auth B], P [auth C], T [auth D]	CYCLOHEXYLFORMAMIDE C₇ H₁₃ N O SWGXDLRCJNEEGZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	E [auth A] F [auth A] I [auth B] J [auth B] M [auth C] E [auth A], F [auth A], I [auth B], J [auth B], M [auth C], N [auth C], Q [auth D], R [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D]