3WJA

The crystal structure of human cytosolic NADP(+)-dependent malic enzyme in apo form

Summary for 3WJA

• Entry DOI: 10.2210/pdb3wja/pdb
• Descriptor: NADP-dependent malic enzyme (2 entities in total)
• Functional Keywords: nadp(+)-binding rossmann-fold domains, oxidoreductase activity, metal ion binding, oxidoreductase
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: P48163
• Total number of polymer chains: 2
• Total formula weight: 130589.10

Authors

Li, S.-Y.,Chen, M.-C.,Yang, P.-C.,Chan, N.-L.,Liu, J.-H.,Hung, H.-C. (deposition date: 2013-10-08, release date: 2014-08-13, Last modification date: 2023-11-08)

Primary citation

Hsieh, J.Y.,Li, S.Y.,Chen, M.C.,Yang, P.C.,Chen, H.Y.,Chan, N.L.,Liu, J.H.,Hung, H.C.
Structural characteristics of the nonallosteric human cytosolic malic enzyme.
Biochim.Biophys.Acta, 1844:1773-1783, 2014

PubMed Abstract: Human cytosolic NADP(+)-dependent malic enzyme (c-NADP-ME) is neither a cooperative nor an allosteric enzyme, whereas mitochondrial NAD(P)(+)-dependent malic enzyme (m-NAD(P)-ME) is allosterically activated by fumarate. This study examines the molecular basis for the different allosteric properties and quaternary structural stability of m-NAD(P)-ME and c-NADP-ME. Multiple residues corresponding to the fumarate-binding site were mutated in human c-NADP-ME to correspond to those found in human m-NAD(P)-ME. Additionally, the crystal structure of the apo (ligand-free) human c-NADP-ME conformation was determined. Kinetic studies indicated no significant difference between the wild-type and mutant enzymes in Km,NADP, Km,malate, and kcat. A chimeric enzyme, [51-105]_c-NADP-ME, was designed to include the putative fumarate-binding site of m-NAD(P)-ME at the dimer interface of c-NADP-ME; however, this chimera remained nonallosteric. In addition to fumarate activation, the quaternary structural stability of c-NADP-ME and m-NAD(P)-ME is quite different; c-NADP-ME is a stable tetramer, whereas m-NAD(P)-ME exists in equilibrium between a dimer and a tetramer. The quaternary structures for the S57K/N59E/E73K/S102D and S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G mutants of c-NADP-ME are tetrameric, whereas the K57S/E59N/K73E/D102S m-NAD(P)-ME quadruple mutant is primarily monomeric with some dimer formation. These results strongly suggest that the structural features near the fumarate-binding site and the dimer interface are highly related to the quaternary structural stability of c-NADP-ME and m-NAD(P)-ME. In this study, we attempt to delineate the structural features governing the fumarate-induced allosteric activation of malic enzyme.

PubMed: 24998673
DOI: 10.1016/j.bbapap.2014.06.019

Experimental method

X-RAY DIFFRACTION (2.548 Å)