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Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase

OverviewOverview

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 StructureAbout this Structure

1JPU is a Single protein structure of sequence from Geobacillus stearothermophilus with as ligand. Active as Glycerol dehydrogenase, with EC number 1.1.1.6 Full crystallographic information is available from OCA.

ReferenceReference

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:11566129

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-[[Image:1jpu.jpg|left|200px]]<br /><applet load="1jpu" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1jpu.jpg|left|200px]]<br /><applet load="1jpu" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1jpu, resolution 1.80&Aring;" />
 '''Crystal Structure of Bacillus Stearothermophilus Glycerol Dehydrogenase'''<br />
 ==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.
+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==
-JPU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JPU OCA].
+JPU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JPU OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Glycerol dehydrogenase]]
 [[Category: Single protein]]
-[[Category: Baker, P.J.]]
+[[Category: Baker, P J.]]
-[[Category: Bullough, P.A.]]
+[[Category: Bullough, P A.]]
 [[Category: Burke, J.]]
-[[Category: Gore, M.G.]]
+[[Category: Gore, M G.]]
-[[Category: Muir, N.M.]]
+[[Category: Muir, N M.]]
-[[Category: Rice, D.W.]]
+[[Category: Rice, D W.]]
-[[Category: Ruzheinikov, S.N.]]
+[[Category: Ruzheinikov, S N.]]
 [[Category: Sedelnikova, S.]]
 [[Category: Taylor, R.]]
@@ Line 28: / Line 28: @@
 [[Category: oxidoreductase]]
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