Unliganded structure of human bisphosphoglycerate mutase reveals side-chain movements induced by ligand binding

Abstract

PDB Reference: bisphosphoglycerate mutase, 3nfy.Erythrocyte-specific bisphosphoglycerate mutase is a trifunctional enzyme which modulates the levels of 2,3-bisphosphoglycerate (2,3-BPG) in red blood cells by virtue of its synthase and phosphatase activities. Low levels of erythrocyte 2,3-BPG increase the affinity of haemoglobin for oxygen, thus limiting the release of oxygen into tissues. 2,3-BPG levels in stored blood decline rapidly owing to the phosphatase activity of bisphosphoglycerate mutase, which is enhanced by a fall in pH. Here, the 1.94 Å resolution X-ray structure of bisphosphoglycerate mutase is presented, focusing on the dynamic nature of key ligand-binding residues and their interaction with the inhibitor citrate. Residues at the binding pocket are complete. In addition, the movement of key residues in the presence and absence of ligand is described and alternative conformations are explored. The conformation in which the ligand citrate would bind at the substrate-binding pocket is proposed, with discussion and representations of its orientation. The characterization of bisphosphoglycerate mutase-citrate interactions will provide a framework for the design of specific inhibitors of the phosphatase activity of this enzyme, which may limit the decline of 2,3-BPG in stored blood.

Molecular insight into 2-phosphoglycolate activation of the phosphatase activity of bisphosphoglycerate mutase

“…Structural studies of BPGM in complex with 2-PG in the absence and presence of 3-PGA (BPGMÁ3-PGAÁ2-PG and BPGMÁ2-PG complexes) showed not only bound 3-PGA and/ or 2-PG at the two active sites but also bound 2-PG at a novel binding site at the dimer interface; the first such report of the latter binding. As previously noted (Patterson et al, 2010) and observed in our crystallographic studies, Arg100, Arg116 and Arg117 and the C-terminal residues are very dynamic, which appears to be a structural determinant for catalysis. In monomer A of both the binary and ternary complexes, these residues are well ordered, resulting in a closed active-site conformation that is similar to that in previously published BPGM structures in complex with 2,3-BPG or 3-PGA (Wang et al, 2006).…”

“…BPGM has two active sites in the C-terminal portion of an / domain of each monomer. The overall dimeric structure is identical to the previously published liganded and unliganded BPGM structures (PDB entries 1t8p, 2h4x, 2h4z, 2hhj and 3nfy; Wang et al, 2004Wang et al, , 2006Patterson et al, 2010).…”

Bisphosphoglycerate Mutase Deficiency Protects against Cerebral Malaria and Severe Malaria-Induced Anemia

“…See also Figure S1. Patterson et al, 2010;Wang et al, 2004). However, L166 is invariant among vertebrates, and the L166P substitution is non-conservative, suggesting possible structural or functional effects on BPGM (Figure 2A).…”

“…To examine protein stability, stably-transfected HEK293 cells expressing either wild-type BPGM L166 or the mutant BPGM P166 variant were treated with cycloheximide (100ug/mL; Sigma-Aldrich) for 2, 4, 6, 8, 12h, at which point cell lysates were prepared and analyzed by immunoblotting (anti-Flag antibody, 1:7000; Sigma-Aldrich, F1804-1MG). The L166 and P166 protein variants were modeled using the unliganded structure of human BPGM (PDB: 3NFY) using PyMOL (Patterson et al, 2010).…”

NLDB: a database for 3D protein–ligand interactions in enzymatic reactions

“…Bisphosphoglycerate mutase (BPGM; EC: 5.4.2.4) is an erythrocyte-specific enzyme, and its main function is to regulate the oxygen affinity of hemoglobin by controlling the synthesis of 2.3-bisphosphoglycerate (DG2; C3 H8 O10 P2), which is an allosteric effector of hemoglobin, via a phosphoryl transfer reaction [ 15 , 20 ]. The deficiency of BPGM (BPGMD) increases the hemoglobin oxygen affinity, leading to a decrease in the DG2 concentration, and is characterized by hemolytic anemia [ 3 ].…”