1A49

BIS MG-ATP-K-OXALATE COMPLEX OF PYRUVATE KINASE

Summary for 1A49

• Entry DOI: 10.2210/pdb1a49/pdb
• Descriptor: PYRUVATE KINASE, POTASSIUM ION, OXALATE ION, ... (6 entities in total)
• Functional Keywords: transferase, pyruvate kinase, rabbit muscle, domain movement, potassium binding
• Biological source: Oryctolagus cuniculus (rabbit)
• Cellular location: Cytoplasm : P11974
• Total number of polymer chains: 8
• Total formula weight: 468390.85

Authors

Larsen, T.M.,Benning, M.M.,Rayment, I.,Reed, G.H. (deposition date: 1998-02-12, release date: 1999-04-20, Last modification date: 2024-05-22)

Primary citation

Larsen, T.M.,Benning, M.M.,Rayment, I.,Reed, G.H.
Structure of the bis(Mg2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 A resolution: ATP binding over a barrel.
Biochemistry, 37:6247-6255, 1998

PubMed Abstract: Pyruvate kinase from rabbit muscle has been cocrystallized as a complex with MgIIATP, oxalate, Mg2+, and either K+ or Na+. Crystals with either Na+ or K+ belong to the space group P2(1)2(1)2(1), and the asymmetric units contain two tetramers. The structures were solved by molecular replacement and refined to 2.1 (K+) and 2.35 A (Na+) resolution. The structures of the Na+ and K+ complexes are virtually isomorphous. Each of the eight subunits within the asymmetric unit contains MgIIoxalate as a bidentate complex linked to the protein through coordination of Mg2+ to the carboxylates of Glu 271 and Asp 295. Six of the subunits also contain an alpha,beta,gamma-tridentate complex of MgIIATP, and the active-site cleft, located between domains A and B, is closed in these subunits. In the remaining two subunits MgIIATP is missing, and the active-site cleft is open. Closure of the active-site cleft in the fully liganded subunits includes a rotation of 41 degrees of the B domain relative to the A domain. alpha-Carbons of residues in the B domain undergo movements of up to 17.8 A (Lys 124) in the cleft closure. Lys 206, Arg 119, and Asp 177 from the B domain move several angstroms from their positions in the open conformation to contact the MgIIATP complex in the active site. The gamma-phosphate of ATP coordinates to both magnesium ions and to the monovalent cation, K+ or Na+. A Mg2+-coordinated oxygen from the MgIIoxalate complex lies 3.0 A from Pgamma of ATP, and this oxygen is positioned for an in-line attack on the phosphorus. The side chains of Lys 269 and Arg 119 are positioned to provide leaving-group activation in the forward and reverse directions. There is no obvious candidate for the acid/base catalyst near the 2-si face of the prospective enolate of the normal substrate. A functional group linked through solvent and side-chain hydroxyls may function in a proton relay.

PubMed: 9572839
DOI: 10.1021/bi980243s

Experimental method

X-RAY DIFFRACTION (2.1 Å)