PDBsum entry 1wmb

Oxidoreductase

PDB id: 1wmb

Contents

Protein chains

260 a.a. *

Ligands

CAC ×2

Metals

_MG ×2

Waters ×428

* Residue conservation analysis

PDB id:

1wmb

Name:

Oxidoreductase

Title:

Crystal structure of NAD dependent d-3-hydroxybutylate dehydrogenase

Structure:

D(-)-3-hydroxybutyrate dehydrogenase. Chain: a, b. Engineered: yes

Source:

Pseudomonas fragi. Organism_taxid: 296. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.00Å R-factor: 0.216 R-free: 0.247

Authors:

K.Ito,Y.Nakajima,E.Ichihara,K.Ogawa,T.Yoshimoto

Key ref:

K.Ito et al. (2006). D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi: molecular cloning of the enzyme gene and crystal structure of the enzyme. J Mol Biol, 355, 722-733. PubMed id: 16325199 DOI: 10.1016/j.jmb.2005.10.072

Date:

06-Jul-04 Release date: 06-Sep-05

Protein chains

Q5KST5  (Q5KST5_PSEFR) -  D(-)-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi

Seq: 260 a.a.

Struc: 260 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.30 - 3-hydroxybutyrate dehydrogenase.
• Reaction: (R)-3-hydroxybutanoate + NAD⁺ = acetoacetate + NADH + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2005.10.072

J Mol Biol 355:722-733 (2006)

PubMed id: 16325199

D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi: molecular cloning of the enzyme gene and crystal structure of the enzyme.

K.Ito, Y.Nakajima, E.Ichihara, K.Ogawa, N.Katayama, K.Nakashima, T.Yoshimoto.

ABSTRACT

The gene coding for d-3-hydroxybutyrate dehydrogenase (HBDH) was cloned from Pseudomonas fragi. The nucleotide sequence contained a 780 bp open reading frame encoding a 260 amino acid residue protein. The recombinant enzyme was efficiently expressed in Escherichia coli cells harboring pHBDH11 and was purified to homogeneity as judged by SDS-PAGE. The enzyme showed a strict stereospecificity to the D-enantiomer (3R-configuration) of 3-hydroxybutyrate as a substrate. Crystals of the ligand-free HBDH and of the enzyme-NAD+ complex were obtained using the hanging-drop, vapor-diffusion method. The crystal structure of the HBDH was solved by the multiwavelength anomalous diffraction method using the SeMet-substituted enzyme and was refined to 2.0 A resolution. The overall structure of P.fragi HBDH, including the catalytic tetrad of Asn114, Ser142, Tyr155, and Lys159, shows obvious relationships with other members of the short-chain dehydrogenase/reductase (SDR) family. A cacodylate anion was observed in both the ligand-free enzyme and the enzyme-NAD+ complex, and was located near the catalytic tetrad. It was shown that the cacodylate inhibited the NAD+-dependent D-3-hydroxybutyrate dehydrogenation competitively, with a Ki value of 5.6 mM. From the interactions between cacodylate and the enzyme, it is predicted that substrate specificity is achieved through the recognition of the 3-methyl and carboxyl groups of the substrate.

Selected figure(s)

Figure 4.
Figure 4. The stereo diagram of SDRs superimposed onto ligand-free HBDH. The C^a trace of HBDH is shown by the orange line, and 2hsd, 1ae1, 1k2w, 1gco, 1hxh, and 1ahh by red, blue, cyan, blue-violet, magenta, and green lines, respectively.

Figure 5.
Figure 5. Drawing of the NAD^+ binding site in HBDH. (a) The wire frame shows the F[o] -F[c] omit map for NAD^+ and cacodylate anion contoured at 2s levels. The stick models show residues interacting with NAD^+ or cacodylate anion. (b) The scheme diagram shows hydrogen-bonding interaction with NAD^+.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 355, 722-733) copyright 2006.

Figures were selected by an automated process.