1Q1N

APO AND HOLO STRUCTURES OF AN NADP(H)-DEPENDENT CINNAMYL ALCOHOL DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE

DOI: 10.2210/pdb1Q1N/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2003-07-22 Released: 2004-08-03
Deposition Author(s): Valencia, E., Larroy, C., Ochoa, W.F., Pares, X., Fita, I., Biosca, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.283
R-Value Work: 0.240
R-Value Observed: 0.244

wwPDB Validation 3D Report Full Report

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

Literature

Apo and Holo Structures of an NADP(H)-dependent Cinnamyl Alcohol Dehydrogenase from Saccharomyces cerevisiae

Valencia, E., Larroy, C., Ochoa, W.F., Pares, X., Fita, I., Biosca, J.A.

(2004) J Mol Biol 341: 1049-1062

PubMed: 15289102 Search on PubMed
DOI: 10.1016/j.jmb.2004.06.037
Primary Citation of Related Structures:
1PIW, 1Q1N, 1PS0

PubMed Abstract:

The crystal structure of Saccharomyces cerevisiae ScAdh6p has been solved using the anomalous signal from the two zinc atoms found per subunit, and it constitutes the first structure determined from a member of the cinnamyl alcohol dehydrogenase family. ScAdh6p subunits exhibit the general fold of the medium-chain dehydrogenases/reductases (MDR) but with distinct specific characteristics. In the three crystal structures solved (two trigonal and one monoclinic), ScAdh6p molecules appear to be structural heterodimers composed of one subunit in the apo and the second subunit in the holo conformation. Between the two conformations, the relative disposition of domains remains unchanged, while two loops, Cys250-Asn260 and Ile277-Lys292, experience large movements. The apo-apo structure is disfavoured because of steric impairment involving the loop Ile277-Lys292, while in the holo-holo conformation some of the hydrogen bonds between subunits would break apart. These suggest that the first NADPH molecule would bind to the enzyme much more tightly than the second. In addition, fluorimetric analysis of NADPH binding demonstrates that only one cofactor molecule binds per dimer. Therefore, ScAdh6p appears to function according to a half-of-the-sites reactivity mechanism, resulting from a pre-existing (prior to cofactor binding) tendency for the structural asymmetry in the dimer. The specificity of ScAdh6p towards NADPH is mainly due to the tripod-like interactions of the terminal phosphate group with Ser210, Arg211 and Lys215. The size and the shape of the substrate-binding pocket correlate well with the substrate specificity of ScAdh6p towards cinnamaldehyde and other aromatic compounds. The structural relationships of ScAdh6p with other MDR structures are analysed.

Related Citations:

Crystallization and preliminary X-ray analysis of NADP(H)-dependent alcohol dehydrogenases from Saccharomyces cerevisiae and Rana perezi
Valencia, E., Rosell, A., Larroy, C., Farres, J., Biosca, J.A., Fita, I., Pares, X., Ochoa, W.F.
(2003) Acta Crystallogr D Biol Crystallogr 59: 334

Organizational Affiliation:

Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Jordi-Girona 18-26, 08034 Barcelona, Spain.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical zinc-type alcohol dehydrogenase-like protein in PRE5-FET4 intergenic region	A	360	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: YMR318C (ADH6) EC: 1.1.1.2
Find proteins for Q04894 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04894 Go to UniProtKB: Q04894
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [A] SDF format, chain C [A] MOL2 format, chain B [A] MOL2 format, chain C [A]	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction