3WSV

Crystal structure of minor L-lactate dehydrogenase from Enterococcus mundtii in the ligands-unbound form

Summary for 3WSV

• Entry DOI: 10.2210/pdb3wsv/pdb
• Related: 3WSW
• Descriptor: L-lactate dehydrogenase, GLYCEROL (3 entities in total)
• Functional Keywords: dehydrogenase, oxidoreductase
• Biological source: Enterococcus mundtii
• Total number of polymer chains: 4
• Total formula weight: 142388.92

Authors

Matoba, Y.,Sugiyama, M. (deposition date: 2014-03-27, release date: 2014-09-10, Last modification date: 2023-11-08)

Primary citation

Matoba, Y.,Miyasako, M.,Matsuo, K.,Oda, K.,Noda, M.,Higashikawa, F.,Kumagai, T.,Sugiyama, M.
An alternative allosteric regulation mechanism of an acidophilic l-lactate dehydrogenase from Enterococcus mundtii 15-1A.
Febs Open Bio, 4:834-847, 2014

PubMed Abstract: A plant-derived Enterococcus mundtii 15-1A, that has been previously isolated from Brassica rapa L. subsp. nipposinica (L.H. Bailey) Hanelt var. linearifolia by our group, possesses two kinds of l-lactate dehydrogenase (l-LDH): LDH-1 and LDH-2. LDH-1 was activated under low concentration of fluctose-1,6-bisphosphate (FBP) at both pH 5.5 and 7.5. Although LDH-2 was also activated under the low concentration of FBP at pH 5.5, a high concentration of FBP is necessary to activate it at pH 7.5. The present study shows the crystal structures of the acidophilic LDH-2 in a complex with and without FBP and NADH. Although the tertiary structure of the ligands-bound LDH-2 is similar to that of the active form of other bacterial l-LDHs, the structure without the ligands is different from that of any other previously determined l-LDHs. Major structural alterations between the two structures of LDH-2 were observed at two regions in one subunit. At the N-terminal parts of the two regions, the ligands-bound form takes an α-helical structure, while the form without ligands displays more disordered and extended structures. A vacuum-ultraviolet circular dichroism analysis showed that the α-helix content of LDH-2 in solution is approximately 30% at pH 7.5, which is close to that in the crystal structure of the form without ligands. A D241N mutant of LDH-2, which was created by us to easily form an α-helix at one of the two parts, exhibited catalytic activity even in the absence of FBP at both pH 5.5 and 7.5.

PubMed: 25379380
DOI: 10.1016/j.fob.2014.08.006

Experimental method

X-RAY DIFFRACTION (2.38 Å)