4GKV

Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD

PDB DOI: https://doi.org/10.2210/pdb4GKV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12, Escherichia coli
Expression System: Escherichia coli BL21, Escherichia coli
Mutation(s): No

Deposited: 2012-08-13 Released: 2013-07-10
Deposition Author(s): Sims, P.A., Thomas, L.M., Harper, A.R., Miner, W.A., Ajufo, H.O., Branscrum, K.M., Kao, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.184
R-Value Work: 0.138
R-Value Observed: 0.140

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Literature

Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD.

Thomas, L.M., Harper, A.R., Miner, W.A., Ajufo, H.O., Branscum, K.M., Kao, L., Sims, P.A.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 730-732

PubMed: 23832197 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309113015170
Primary Citation of Related Structures:
4GKV

PubMed Abstract:
The crystal structure of AdhP, a recombinantly expressed alcohol dehydrogenase from Escherichia coli K-12 (substrain MG1655), was determined to 2.01 Å resolution. The structure, which was solved using molecular replacement, also included the structural and catalytic zinc ions and the cofactor nicotinamide adenine dinucleotide (NAD). The crystals belonged to space group P21, with unit-cell parameters a = 68.18, b = 118.92, c = 97.87 Å, β = 106.41°. The final R factor and Rfree were 0.138 and 0.184, respectively. The structure of the active site of AdhP suggested a number of residues that may participate in a proton relay, and the overall structure of AdhP, including the coordination to structural and active-site zinc ions, is similar to those of other tetrameric alcohol dehydrogenase enzymes.

Organizational Affiliation

Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019-5251, USA.

Macromolecule Content

Total Structure Weight: 146.03 kDa
Atom Count: 11,944
Modelled Residue Count: 1,354
Deposited Residue Count: 1,354
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase, propanol-preferring	A, B, C, D	336	Escherichia coli K-12	Mutation(s): 0 Gene Names: adhP, yddN, b1478, JW1474 EC: 1.1.1.1
UniProt
Find proteins for P39451 (Escherichia coli (strain K12)) Explore P39451 Go to UniProtKB: P39451
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39451
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cleaved peptide fragment corresponding to the C-terminal His tag	E [auth P]	10	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D]	F [auth A], I [auth B], M [auth C], Q [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C]	L [auth B], P [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain P [auth C] Interactions & Density Focus chain L [auth B] Focus chain P [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D]	G [auth A] H [auth A] J [auth B] K [auth B] N [auth C] G [auth A], H [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.184
R-Value Work: 0.138
R-Value Observed: 0.140
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.16	α = 90
b = 118.92	β = 106.41
c = 97.87	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-07-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-10
Type: Initial release
Version 1.1: 2013-07-17
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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4GKV

Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD

Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2