title: The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase.
abstract: The essential photosynthetic enzyme phosphoribulokinase (PRK) is responsible for the conversion of ribulose 5-phosphate (Ru5P) to ribulose 1,5-bisphosphate, the substrate for the CO2 fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). We have determined the structure of the octameric bacterial form of PRK to a resolution of 2.5 A. The protein is folded into a seven-member mixed beta-sheet surrounded by alpha-helices, giving the overall appearance of the nucleotide monophosphate family of kinases. Homology with the nucleotide monophosphate kinases suggests a number of amino acid residues that are likely to be important in catalysis and suggests the roles of some amino acid residues that have been mutated prior to the determination of the structure. Further, sequence identity across eukaryotic and prokaryotic species and a calculation of the buried surface area suggests the identity within the octamer of a dimer conserved throughout evolution. The width of the groove leading to the active site is consistent with an oriented molecule of thioredoxin controlling the oxidation state of two cysteines that regulate activity in the eukaryotic enzymes. Although neither Asp 42 nor Asp 169 can be definitively assigned as the catalytic base, the crystal structure suggests the location of a ribulose 5-phosphate binding site and suggests a role for several of the conserved basic residues.
authors.affiliation: Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
authors.forename: D H
authors.initials: DH
authors.lastname: Harrison
authors.forename: J A
authors.initials: JA
authors.lastname: Runquist
authors.forename: A
authors.initials: A
authors.lastname: Holub
authors.forename: H M
authors.initials: HM
authors.lastname: Miziorko
mesh_terms: D000263:Adenylate Kinase / Q000737:chemistry; D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D003545:Cysteine; D019143:Evolution, Molecular; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D012242:Rhodobacter sphaeroides / Q000201:enzymology*; D013045:Species Specificity
chemical_list: D017853:Phosphotransferases (Alcohol Group Acceptor); C022390:phosphoribulokinase; D000263:Adenylate Kinase; D003545:Cysteine