2ZTU

T190A mutant of D-3-hydroxybutyrate dehydrogenase complexed with NAD+

Summary for 2ZTU

• Entry DOI: 10.2210/pdb2ztu/pdb
• Related: 1WMB 1X1T 2ZTL 2ZTM 2ZTV
• Descriptor: D(-)-3-hydroxybutyrate dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: short chain dehydrogenase/reductase, sdr family, nad, nadh, hbdh, oxidoreductase
• Biological source: Pseudomonas fragi
• Total number of polymer chains: 4
• Total formula weight: 108768.44

Authors

Nakashima, K.,Nakajima, Y.,Ito, K.,Yoshimoto, T. (deposition date: 2008-10-09, release date: 2009-08-25, Last modification date: 2023-11-01)

Primary citation

Nakashima, K.,Ito, K.,Nakajima, Y.,Yamazawa, R.,Miyakawa, S.,Yoshimoto, T.
Closed complex of the D-3-hydroxybutyrate dehydrogenase induced by an enantiomeric competitive inhibitor.
J.Biochem., 145:467-479, 2009

PubMed Abstract: D-3-Hydroxybutyrate dehydrogenase (HBDH) from Pseudomonas fragi showed a strict stereospecificity to the d-enantiomer of 3-hydroxybutyrate (d-3-HB) as a substrate. The l-enantiomer acts as a competitive inhibitor, with a K(i) value comparable to the K(m) value for d-3-HB. We have determined the crystal structures of the ternary complex of HBDH-NAD(+)-l-3-HB and the binary complex of HBDH-NAD(+). The former structure showed a so-called closed-form conformation, which is considered an active form for catalysis, while the latter stayed mostly in a open-form conformation. The determined structures along with the site-directed mutagenesis confirmed the substrate recognition mechanism that we proposed previously. The hydrogen bonding interaction between Gln196, located in the moving helix, and the carboxyl group of the substrate/inhibitor is important for the stable ternary complex formation. Finally, the crystal structures of the Thr190 mutants, T190S and T190A, indicate that the Thr190 is a key residue for the open-closed conformational change. T190S retained 37% of the activity. In T190A, however, the activity decreased to 0.1% that of the wild-type enzyme. Fixing the position of the hydroxyl group of Thr190 to form hydrogen bonds to the pyrophosphate moiety and the carboxamide of NAD(+) seems to be a significant factor for the open-closed conformational change.

PubMed: 19122202
DOI: 10.1093/jb/mvn186

Experimental method

X-RAY DIFFRACTION (2 Å)