PDBsum entry: 2cvz

Oxidoreductase

PDB id: 2cvz

Contents

Protein chains

288 a.a. *

Ligands

NDP ×3

Waters ×856

* Residue conservation analysis

PDB id:

2cvz

Name:

Oxidoreductase

Title:

Structure of hydroxyisobutyrate dehydrogenase from thermus thermophilus hb8

Structure:

3-hydroxyisobutyrate dehydrogenase. Chain: a, b, c, d. Synonym: dehydrogenase. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.80Å R-factor: 0.182 R-free: 0.200

Authors:

N.K.Lokanath,N.Kunishima,M.Miyano,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

N.K.Lokanath et al. (2005). Crystal structure of novel NADP-dependent 3-hydroxyisobutyrate dehydrogenase from Thermus thermophilus HB8. J Mol Biol, 352, 905-917. PubMed id: 16126223 DOI: 10.1016/j.jmb.2005.07.068

Date:

14-Jun-05 Release date: 28-Jun-05

Supersedes:

1j3v

Protein chains

Q5SLQ6  (Q5SLQ6_THET8) -  3-hydroxyisobutyrate dehydrogenase

Seq: 289 a.a.

Struc: 288 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (3 terms)
• Biochemical function: binding (7 terms)

DOI no: 10.1016/j.jmb.2005.07.068

J Mol Biol 352:905-917 (2005)

PubMed id: 16126223

Crystal structure of novel NADP-dependent 3-hydroxyisobutyrate dehydrogenase from Thermus thermophilus HB8.

N.K.Lokanath, N.Ohshima, K.Takio, I.Shiromizu, C.Kuroishi, N.Okazaki, S.Kuramitsu, S.Yokoyama, M.Miyano, N.Kunishima.

ABSTRACT

3-Hydroxyisobutyrate, a central metabolite in the valine catabolic pathway, is reversibly oxidized to methylmalonate semialdehyde by a specific dehydrogenase belonging to the 3-hydroxyacid dehydrogenase family. To gain insight into the function of this enzyme at the atomic level, we have determined the first crystal structures of the 3-hydroxyisobutyrate dehydrogenase from Thermus thermophilus HB8: holo enzyme and sulfate ion complex. The crystal structures reveal a unique tetrameric oligomerization and a bound cofactor NADP+. This bacterial enzyme may adopt a novel cofactor-dependence on NADP, whereas NAD is preferred in eukaryotic enzymes. The protomer folds into two distinct domains with open/closed interdomain conformations. The cofactor NADP+ with syn nicotinamide and the sulfate ion are bound to distinct sites located at the interdomain cleft of the protomer through an induced-fit domain closure upon cofactor binding. From the structural comparison with the crystal structure of 6-phosphogluconate dehydrogenase, another member of the 3-hydroxyacid dehydrogenase family, it is suggested that the observed sulfate ion and the substrate 3-hydroxyisobutyrate share the same binding pocket. The observed oligomeric state might be important for the catalytic function through forming the active site involving two adjacent subunits, which seems to be conserved in the 3-hydroxyacid dehydrogenases. A kinetic study confirms that this enzyme has strict substrate specificity for 3-hydroxyisobutyrate and serine, but it cannot distinguish the chirality of the substrates. Lys165 is likely the catalytic residue of the enzyme.

Selected figure(s)

Figure 1.
Figure 1. Catabolic pathway of valine. The step catalyzed by HIBADH is boxed.

Figure 5.
Figure 5. Comparison of binding ligands between HIBADH and 6PGDH in stereo views. (a) NADP+/sulfate binding in the sulfate ion complex form of HIBADH. NADP+ and important residues are depicted as ball-and-stick models and labeled. Residues of the domains I and II of a protomer are colored yellow and green, respectively. Residues from the other subunit are shown in light blue. (b) Close-up view of the sulfate binding adjacent to the nicotinamide ring of NADP+ molecule. Important hydrogen bonds are indicated by broken lines. (c) Close-up view of the cofactor/substrate binding in 6PGDH with the presentation equivalent to (b). The active NADP+ analogue nicotinamide-8-bromo-adenine dinucleotide phosphate (Nbr8ADP+), the substrate 6-phosphogluconate (6PG) and the catalytic general base Lys183 are shown. This picture is produced from a superposition of the cofactor molecule in the Nbr8ADP+-6PGDH complex (PDB, 1PGN) to the 6PG-6PGDH complex structure (PDB, 1PGP).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 352, 905-917) copyright 2005.

Figures were selected by an automated process.