1RJW

CRYSTAL STRUCTURE OF NAD(+)-DEPENDENT ALCOHOL DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS STRAIN LLD-R

DOI: 10.2210/pdb1RJW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-11-20 Released: 2004-05-11
Deposition Author(s): Ceccarelli, C., Bahnson, B.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.252
R-Value Work: 0.214
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure and Amide H/D Exchange of Binary Complexes of Alcohol Dehydrogenase from Bacillus stearothermophilus: Insight into Thermostability and Cofactor Binding

Ceccarelli, C., Liang, Z.X., Strickler, M., Prehna, G., Goldstein, B.M., Klinman, J.P., Bahnson, B.J.

(2004) Biochemistry 43: 5266-5277

PubMed: 15122892 Search on PubMed
DOI: 10.1021/bi049736p
Primary Citation of Related Structures:
1RJW

PubMed Abstract:

The crystal structure of NAD(+)-dependent alcohol dehydrogenase from Bacillus stearothermophilus strain LLD-R (htADH) was determined using X-ray diffraction data at a resolution of 2.35 A. The structure of homotetrameric htADH is highly homologous to those of bacterial and archaeal homotetrameric alcohol dehydrogenases (ADHs) and also to the mammalian dimeric ADHs. There is one catalytic zinc atom and one structural zinc atom per enzyme subunit. The enzyme was crystallized as a binary complex lacking the nicotinamide adenine dinucleotide (NAD(+)) cofactor but including a zinc-coordinated substrate analogue trifluoroethanol. The binary complex structure is in an open conformation similar to ADH structures without the bound cofactor. Features important for the thermostability of htADH are suggested by a comparison with a homologous mesophilic enzyme (55% identity), NAD(+)-dependent alcohol dehydrogenase from Escherichia coli. To gain insight into the conformational change triggered by NAD(+) binding, amide hydrogen-deuterium exchange of htADH, in the presence and absence of NAD(+), was studied by HPLC-coupled electrospray mass spectrometry. When the deuteron incorporation of the protein-derived peptides was analyzed, it was found that 9 of 21 peptides show some decrease in the level of deuteron incorporation upon NAD(+) binding, and another 4 peptides display slower exchange rates. With one exception (peptide number 8), none of the peptides that are altered by bound NAD(+) are in contact with the alcohol-substrate-binding pocket. Furthermore, peptides 5 and 8, which are located outside the NAD(+)-binding pocket, are notable by displaying changes upon NAD(+) binding. This suggests that the transition from the open to the closed conformation caused by cofactor binding has some long-range effects on the protein structure and dynamics.

Related Citations:

A few amino acid substitutions are responsible for the higher thermostability of a novel NAD(+)-dependent bacillar alcohol dehydrogenase
Cannio, R., Rossi, M., Bartolucci, S.
(1994) Eur J Biochem 222: 345

Organizational Affiliation:

Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase	A, B, C, D	339	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: ADH-HT EC: 1.1.1.1
Find proteins for P42328 (Geobacillus stearothermophilus) Explore P42328 Go to UniProtKB: P42328
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ETF Query on ETF Download Ideal Coordinates CCD File SDF format, chain G [A] SDF format, chain H [A] SDF format, chain K [B] SDF format, chain L [B] SDF format, chain M [B] SDF format, chain N [B] SDF format, chain Q [C] SDF format, chain R [C] SDF format, chain S [C] SDF format, chain V [D] SDF format, chain W [D] SDF format, chain X [D] SDF format, chain Y [D] MOL2 format, chain G [A] MOL2 format, chain H [A] MOL2 format, chain K [B] MOL2 format, chain L [B] MOL2 format, chain M [B] MOL2 format, chain N [B] MOL2 format, chain Q [C] MOL2 format, chain R [C] MOL2 format, chain S [C] MOL2 format, chain V [D] MOL2 format, chain W [D] MOL2 format, chain X [D] MOL2 format, chain Y [D]	A, B, C, D	TRIFLUOROETHANOL C₂ H₃ F₃ O RHQDFWAXVIIEBN-UHFFFAOYSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain F [A] SDF format, chain I [B] SDF format, chain J [B] SDF format, chain O [C] SDF format, chain P [C] SDF format, chain T [D] SDF format, chain U [D] MOL2 format, chain E [A] MOL2 format, chain F [A] MOL2 format, chain I [B] MOL2 format, chain J [B] MOL2 format, chain O [C] MOL2 format, chain P [C] MOL2 format, chain T [D] MOL2 format, chain U [D]	A, B, C, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction