Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 81183.81 
• Atom Count: 5444 
• Residue Count: 718 
• Unique protein chains: 1

1H2B

Crystal Structure of the Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Aeropyrum pernix at 1.65A Resolution

• DOI: 10.2210/pdb1H2B/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
• Expression System: Escherichia coli DH5[alpha]


• Deposited: 2002-08-02 Released: 2003-08-28 
• Deposition Author(s): Guy, J.E., Isupov, M.N., Littlechild, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.203 
• R-Value Work: 0.168 

Literature

The structure of an alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.

Guy, J.E., Isupov, M.N., Littlechild, J.A.

(2003) J.Mol.Biol. 331: 1041-1051

• PubMed: 12927540 


• PubMed Abstract: 
  

The structure of the recombinant medium chain alcohol dehydrogenase (ADH) from the hyperthermophilic archaeon Aeropyrum pernix has been solved by the multiple anomalous dispersion technique using the signal from the naturally occurring zinc ions. The enzyme is a tetramer with 222 point group symmetry. The ADH monomer is formed from a catalytic and a cofactor-binding domain, with the overall fold similar to previously solved ADH structures. The 1.62 A resolution A.pernix ADH structure is that of the holo form, with the cofactor NADH bound into the cleft between the two domains. The electron density found in the active site has been interpreted to be octanoic acid, which has been shown to be an inhibitor of the enzyme. This inhibitor is positioned with its carbonyl oxygen atom forming the fourth ligand of the catalytic zinc ion. The structural zinc ion of each monomer is present at only partial occupancy and in its absence a disulfide bond is formed. The enhanced thermal stability of the A.pernix ADH is thought to arise primarily from increased ionic and hydrophobic interactions on the subunit interfaces.

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Related Citations: 

• Crystallization and Preliminary X-Ray Diffraction Studies of a Novel Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Aeropyrum Pernix.
  Guy, J.E.,Isupov, M.N.,Littlechild, J.A.
  (2003) Acta Crystallogr.,Sect.D 59: 174




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Organizational Affiliation: 

Schools of Chemistry and Biological Sciences, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ALCOHOL DEHYDROGENASE	A, B	359	Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)	Mutation(s): 0  Gene Names: adh EC: 1.1.1.1
Find proteins for Q9Y9P9 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Go to UniProtKB:  Q9Y9P9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NAJ	A, B	NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
OCA	A, B	OCTANOIC ACID (CAPRYLIC ACID) C8 H16 O2 WWZKQHOCKIZLMA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.203 
• R-Value Work: 0.168 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 100.661	α = 90.00
b = 103.186	β = 90.00
c = 67.521	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
SHELXS	phasing
MOLREP	phasing
DENZO	data reduction
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-08-02 
• Released Date: 2003-08-28 
• Deposition Author(s): Guy, J.E., Isupov, M.N., Littlechild, J.A.

Revision History 

• Version 1.0: 2003-08-28
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-02-28
  Type: Database references, Source and taxonomy
• Version 1.4: 2019-07-24
  Type: Data collection
• Version 1.5: 2019-10-09
  Type: Data collection, Database references, Other