Characterization of the acetate binding pocket in the Methanosarcina thermophila acetate kinase.
Acetate kinase catalyzes the reversible magnesium-dependent synthesis of acetyl phosphate by transfer of the ATP gamma-phosphoryl group to acetate. Inspection of the crystal structure of the Methanosarcina thermophila enzyme containing only ADP revealed a solvent-accessible hydrophobic pocket formed by residues Val(93), Leu(122), Phe(179), and Pro(232) in the active site cleft, which identified a potential acetate binding site. The hypothesis that this was a binding site was further supported by alignment of all acetate kinase sequences available from databases, which showed strict conservation of all four residues, and the recent crystal structure of the M. thermophila enzyme with acetate bound in this pocket. Replacement of each residue in the pocket produced variants with K(m) values for acetate that were 7- to 26-fold greater than that of the wild type, and perturbations of this binding pocket also altered the specificity for longer-chain carboxylic acids and acetyl phosphate. The kinetic analyses of variants combined with structural modeling indicated that the pocket has roles in binding the methyl group of acetate, influencing substrate specificity, and orienting the carboxyl group. The kinetic analyses also indicated that binding of acetyl phosphate is more dependent on interactions of the phosphate group with an unidentified residue than on interactions between the methyl group and the hydrophobic pocket. The analyses also indicated that Phe(179) is essential for catalysis, possibly for domain closure. Alignments of acetate kinase, propionate kinase, and butyrate kinase sequences obtained from databases suggested that these enzymes have similar catalytic mechanisms and carboxylic acid substrate binding sites.
Ingram-Smith
Cheryl
C
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802-4500, USA.
Gorrell
Andrea
A
Lawrence
Sarah H
SH
Iyer
Prabha
P
Smith
Kerry
K
Ferry
James G
JG
D000084:Acetate Kinase / Q000737:chemistry* / Q000378:metabolism*; D000085:Acetates / Q000378:metabolism*; D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D000595:Amino Acid Sequence; D001665:Binding Sites / Q000502:physiology; D007700:Kinetics; D017020:Methanosarcina / Q000201:enzymology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017851:Phosphotransferases (Carboxyl Group Acceptor) / Q000737:chemistry / Q000378:metabolism; D011422:Propionates / Q000378:metabolism; D011487:Protein Conformation; D016415:Sequence Alignment
D000085:Acetates; D011422:Propionates; D000255:Adenosine Triphosphate; D017851:Phosphotransferases (Carboxyl Group Acceptor); D000084:Acetate Kinase; C019285:butyrate kinase