1b15: Difference between revisions

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Revision as of 18:51, 30 March 2008

File:1b15.gif

, resolution 2.2Å

Sites:

, , , , , , , , and

Ligands:

Activity:

Alcohol dehydrogenase, with EC number 1.1.1.1

Related:

1B14, 1B2L

Resources:

FirstGlance, OCA, PDBsum, RCSB

Coordinates:

save as pdb, mmCIF, xml

ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS TERNARY COMPLEX WITH NAD-ACETONE

OverviewOverview

Drosophila alcohol dehydrogenase (DADH) is an NAD+-dependent enzyme that catalyzes the oxidation of alcohols to aldehydes/ketones. DADH is the member of the short-chain dehydrogenases/reductases family (SDR) for which the largest amount of biochemical data has been gathered during the last three decades. The crystal structures of one binary form (NAD+) and three ternary complexes with NAD+.acetone, NAD+.3-pentanone and NAD+.cyclohexanone were solved at 2.4, 2.2, 1. 4 and 1.6 A resolution, respectively. From the molecular interactions observed, the reaction mechanism could be inferred. The structure of DADH undergoes a conformational change in order to bind the coenzyme. Furthermore, upon binding of the ketone, a region that was disordered in the apo form (186-191) gets stabilized and closes the active site cavity by creating either a small helix (NAD+. acetone, NAD+.3-pentanone) or an ordered loop (NAD+.cyclohexanone). The active site pocket comprises a hydrophobic bifurcated cavity which explains why the enzyme is more efficient in oxidizing secondary aliphatic alcohols (preferably R form) than primary ones. Difference Fourier maps showed that the ketone inhibitor molecule has undergone a covalent reaction with the coenzyme in all three ternary complexes. Due to the presence of the positively charged ring of the coenzyme (NAD+) and the residue Lys155, the amino acid Tyr151 is in its deprotonated (tyrosinate) state at physiological pH. Tyr151 can subtract a proton from the enolic form of the ketone and catalyze a nucleophilic attack of the Calphaatom to the C4 position of the coenzyme creating an NAD-ketone adduct. The binding of these NAD-ketone adducts to DADH accounts for the inactivation of the enzyme. The catalytic reaction proceeds in a similar way, involving the same amino acids as in the formation of the NAD-ketone adduct. The p Kavalue of 9-9.5 obtained by kinetic measurements on apo DADH can be assigned to a protonated Tyr151 which is converted to an unprotonated tyrosinate (p Ka7.6) by the influence of the positively charged nicotinamide ring in the binary enzyme-NAD+form. pH independence during the release of NADH from the binary complex enzyme-NADH can be explained by either a lack of electrostatic interaction between the coenzyme and Tyr151 or an apparent p Kavalue for this residue higher than 10.0.

About this StructureAbout this Structure

1B15 is a Single protein structure of sequence from Scaptodrosophila lebanonensis. Full crystallographic information is available from OCA.

ReferenceReference

The catalytic reaction and inhibition mechanism of Drosophila alcohol dehydrogenase: observation of an enzyme-bound NAD-ketone adduct at 1.4 A resolution by X-ray crystallography., Benach J, Atrian S, Gonzalez-Duarte R, Ladenstein R, J Mol Biol. 1999 Jun 4;289(2):335-55. PMID:10366509

Page seeded by OCA on Sun Mar 30 18:51:46 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 4: / Line 4: @@
 |PDB= 1b15 |SIZE=350|CAPTION= <scene name='initialview01'>1b15</scene>, resolution 2.2&Aring;
 |SITE= <scene name='pdbsite=ACA:Catalytic+Triad'>ACA</scene>, <scene name='pdbsite=ACB:Catalytic+Triad'>ACB</scene>, <scene name='pdbsite=CAA:Ca2++Binding+Residues'>CAA</scene>, <scene name='pdbsite=CAB:Ca2++Binding+Residues'>CAB</scene>, <scene name='pdbsite=NA1:Nad+Binding+Motif+In+Dadhs+G(A)Xgxxg'>NA1</scene>, <scene name='pdbsite=NA2:Nad+Binding+Motif+In+Sdrs+Gxxxgxg'>NA2</scene>, <scene name='pdbsite=NA3:Nad/Nadp+Selectivity+Amino+Acid'>NA3</scene>, <scene name='pdbsite=NB1:Nad+Binding+Motif+In+Dadhs+G(A)Xgxxg'>NB1</scene>, <scene name='pdbsite=NB2:Nad+Binding+Motif+In+Sdrs+Gxxxgxg'>NB2</scene> and <scene name='pdbsite=NB3:Nad/Nadp+Selectivity+Amino+Acid'>NB3</scene>
-|LIGAND= <scene name='pdbligand=NAE:NICOTINAMIDE ADENINE DINUCLEOTIDE ACETONE ADDUCT'>NAE</scene>
+|LIGAND= <scene name='pdbligand=NAE:NICOTINAMIDE+ADENINE+DINUCLEOTIDE+ACETONE+ADDUCT'>NAE</scene>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1]
+|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] </span>
 |GENE=
+|DOMAIN=
+|RELATEDENTRY=[[1b14|1B14]], [[1b2l|1B2L]]
+|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1b15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b15 OCA], [http://www.ebi.ac.uk/pdbsum/1b15 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1b15 RCSB]</span>
 }}
@@ Line 27: / Line 30: @@
 [[Category: Gonzalez-Duarte, R.]]
 [[Category: Ladenstein, R.]]
-[[Category: NAE]]
 [[Category: alcohol dehydrogenase]]
 [[Category: detoxification]]
@@ Line 37: / Line 39: @@
 [[Category: ternary complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:04:59 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:51:46 2008''