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PDBsum entry 1a5u
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structure of the bis(mg2+)-Atp-Oxalate complex of the rabbit muscle pyruvate kinase at 2.1 a resolution: ATP binding over a barrel.
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Authors
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T.M.Larsen,
M.M.Benning,
I.Rayment,
G.H.Reed.
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Ref.
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Biochemistry, 1998,
37,
6247-6255.
[DOI no: ]
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PubMed id
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Abstract
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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.
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