3IGY

Crystal structures of Leishmania mexicana phosphoglycerate mutase at high cobalt concentrations

3IGY の概要

• エントリーDOI: 10.2210/pdb3igy/pdb
• 関連するPDBエントリー: 1EJJ 1EQJ 3IGZ
• 分子名称: Cofactor-independent phosphoglycerate mutase, COBALT (II) ION, SODIUM ION, ... (6 entities in total)
• 機能のキーワード: glycolysis, mutase, cobalt, isomerase
• 由来する生物種: Leishmania mexicana
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 62388.40

構造登録者

Nowicki, M.W.,Kuaprasert, B.,McNae, I.W.,Morgan, H.P.,Harding, M.M.,Michels, P.A.,Fothergill-Gilmore, L.A.,Walkinshaw, M.D. (登録日: 2009-07-29, 公開日: 2009-10-27, 最終更新日: 2024-03-20)

主引用文献

Nowicki, M.W.,Kuaprasert, B.,McNae, I.W.,Morgan, H.P.,Harding, M.M.,Michels, P.A.,Fothergill-Gilmore, L.A.,Walkinshaw, M.D.
Crystal structures of Leishmania mexicana phosphoglycerate mutase suggest a one-metal mechanism and a new enzyme subclass
J.Mol.Biol., 394:535-543, 2009

PubMed Abstract: The structures of Leishmania mexicana cofactor-independent phosphoglycerate mutase (Lm iPGAM) crystallised with the substrate 3-phosphoglycerate at high and low cobalt concentrations have been solved at 2.00- and 1.90-A resolutions. Both structures are very similar and the active site contains both 3-phosphoglycerate and 2-phosphoglycerate at equal occupancies (50%). Lm iPGAM co-crystallised with the product 2-phosphoglycerate yields the same structure. Two Co(2+) are coordinated within the active site with different geometries and affinities. The cobalt at the M1 site has a distorted octahedral geometry and is present at 100% occupancy. The M2-site Co(2+) binds with distorted tetrahedral geometry, with only partial occupancy, and coordinates with Ser75, the residue involved in phosphotransfer. When the M2 site is occupied, the side chain of Ser75 adopts a position that is unfavourable for catalysis, indicating that this site may not be occupied under physiological conditions and that catalysis may occur via a one-metal mechanism. The geometry of the M2 site suggests that it is possible for Ser75 to be activated for phosphotransfer by H-bonding to nearby residues rather than by metal coordination. The 16 active-site residues of Lm iPGAM are conserved in the Mn-dependent iPGAM from Bacillus stearothermophilus (33% overall sequence identity). However, Lm iPGAM has an inserted tyrosine (Tyr210) that causes the M2 site to diminish in size, consistent with its reduced metal affinity. Tyr210 is present in trypanosomatid and plant iPGAMs, but not in the enzymes from other organisms, indicating that there are two subclasses of iPGAMs.

PubMed: 19781556
DOI: 10.1016/j.jmb.2009.09.041

実験手法

X-RAY DIFFRACTION (2.003 Å)