1jpu: Difference between revisions

{{Structure

|PDB= 1jpu |SIZE=350|CAPTION= <scene name='initialview01'>1jpu</scene>, resolution 1.80&Aring;

|SITE=  

|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>

|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerol_dehydrogenase Glycerol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.6 1.1.1.6] </span>

|GENE= GLDA or GLD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])

|DOMAIN=

|RELATEDENTRY=[[1jq5|1JQ5]], [[1jqa|1JQA]]

|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jpu OCA], [http://www.ebi.ac.uk/pdbsum/1jpu PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1jpu RCSB]</span>

 

 

 

==Overview==

BACKGROUND: Bacillus stearothermophilus glycerol dehydrogenase (GlyDH) (glycerol:NAD(+) 2-oxidoreductase, EC 1.1.1.6) catalyzes the oxidation of glycerol to dihydroxyacetone (1,3-dihydroxypropanone) with concomitant reduction of NAD(+) to NADH. Analysis of the sequence of this enzyme indicates that it is a member of the so-called iron-containing alcohol dehydrogenase family. Despite this sequence similarity, GlyDH shows a strict dependence on zinc for activity. On the basis of this, we propose to rename this group the family III metal-dependent polyol dehydrogenases. To date, no structural data have been reported for any enzyme in this group. RESULTS: The crystal structure of B. stearothermophilus glycerol dehydrogenase has been determined at 1.7 A resolution to provide structural insights into the mechanistic features of this family. The enzyme has 370 amino acid residues, has a molecular mass of 39.5 kDa, and is a homooctamer in solution. CONCLUSIONS: Analysis of the crystal structures of the free enzyme and of the binary complexes with NAD(+) and glycerol show that the active site of GlyDH lies in the cleft between the enzyme's two domains, with the catalytic zinc ion playing a role in stabilizing an alkoxide intermediate. In addition, the specificity of this enzyme for a range of diols can be understood, as both hydroxyls of the glycerol form ligands to the enzyme-bound Zn(2+) ion at the active site. The structure further reveals a previously unsuspected similarity to dehydroquinate synthase, an enzyme whose more complex chemistry shares a common chemical step with that catalyzed by glycerol dehydrogenase, providing a striking example of divergent evolution. Finally, the structure suggests that the NAD(+) binding domain of GlyDH may be related to that of the classical Rossmann fold by switching the sequence order of the two mononucleotide binding folds that make up this domain.

 

==About this Structure==

1JPU is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JPU OCA].  

 

==Reference==

Glycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase., Ruzheinikov SN, Burke J, Sedelnikova S, Baker PJ, Taylor R, Bullough PA, Muir NM, Gore MG, Rice DW, Structure. 2001 Sep;9(9):789-802. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11566129 11566129]

[[Category: Glycerol dehydrogenase]]

[[Category: Single protein]]

[[Category: Baker, P J.]]

[[Category: Bullough, P A.]]

[[Category: Burke, J.]]

[[Category: Gore, M G.]]

[[Category: Muir, N M.]]

[[Category: Rice, D W.]]

[[Category: Ruzheinikov, S N.]]

[[Category: Sedelnikova, S.]]

[[Category: Taylor, R.]]

[[Category: oxidoreductase,nad]]