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==Overview== | ==Overview== | ||
BACKGROUND: D-ribose must be phosphorylated at O5' before it can be used, in either anabolism or catabolism. This reaction is catalysed by, ribokinase and requires the presence of ATP and magnesium. Ribokinase is a, member of a family of carbohydrate kinases of previously unknown, structure. RESULTS: The crystal structure of ribokinase from Escherichia, coli in complex with ribose and dinucleotide was determined at 1.84 A, resolution by multiple isomorphous replacement. There is one 33 kDa, monomer of ribokinase in the asymmetric unit but the protein forms a dimer, around a crystallographic twofold axis. Each subunit consists of a central, alpha/beta unit, with a new type of nucleotide-binding fold, and a, distinct beta sheet that forms a lid over the ribose-binding site. Contact, between ... | BACKGROUND: D-ribose must be phosphorylated at O5' before it can be used, in either anabolism or catabolism. This reaction is catalysed by, ribokinase and requires the presence of ATP and magnesium. Ribokinase is a, member of a family of carbohydrate kinases of previously unknown, structure. RESULTS: The crystal structure of ribokinase from Escherichia, coli in complex with ribose and dinucleotide was determined at 1.84 A, resolution by multiple isomorphous replacement. There is one 33 kDa, monomer of ribokinase in the asymmetric unit but the protein forms a dimer, around a crystallographic twofold axis. Each subunit consists of a central, alpha/beta unit, with a new type of nucleotide-binding fold, and a, distinct beta sheet that forms a lid over the ribose-binding site. Contact, between subunits involves orthogonal packing of beta sheets, in a novel, dimer interaction that we call a beta clasp. CONCLUSIONS: Inspection of, the complex indicates that ribokinase utilises both a catalytic base for, activation of the ribose in nucleophilic attack and an anion hole that, stabilises the transition state during phosphoryl transfer. The structure, suggests an ordered reaction mechanism, similar to those proposed for, other carbohydrate kinases that probably involves conformational changes., We propose that the beta-clasp structure acts as a lid, closing and, opening upon binding and release of ribose. From these observations, an, understanding of the structure and catalytic mechanism of related sugar, kinases can be obtained. | ||
==About this Structure== | ==About this Structure== | ||
1RKD is a | 1RKD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with RIB, PO4 and ADP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Ribokinase Ribokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.15 2.7.1.15] Structure known Active Sites: AB1, AB2, AB3, RB1, RB2 and RB3. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RKD OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: transferase]] | [[Category: transferase]] | ||
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Revision as of 15:53, 5 November 2007
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E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP
OverviewOverview
BACKGROUND: D-ribose must be phosphorylated at O5' before it can be used, in either anabolism or catabolism. This reaction is catalysed by, ribokinase and requires the presence of ATP and magnesium. Ribokinase is a, member of a family of carbohydrate kinases of previously unknown, structure. RESULTS: The crystal structure of ribokinase from Escherichia, coli in complex with ribose and dinucleotide was determined at 1.84 A, resolution by multiple isomorphous replacement. There is one 33 kDa, monomer of ribokinase in the asymmetric unit but the protein forms a dimer, around a crystallographic twofold axis. Each subunit consists of a central, alpha/beta unit, with a new type of nucleotide-binding fold, and a, distinct beta sheet that forms a lid over the ribose-binding site. Contact, between subunits involves orthogonal packing of beta sheets, in a novel, dimer interaction that we call a beta clasp. CONCLUSIONS: Inspection of, the complex indicates that ribokinase utilises both a catalytic base for, activation of the ribose in nucleophilic attack and an anion hole that, stabilises the transition state during phosphoryl transfer. The structure, suggests an ordered reaction mechanism, similar to those proposed for, other carbohydrate kinases that probably involves conformational changes., We propose that the beta-clasp structure acts as a lid, closing and, opening upon binding and release of ribose. From these observations, an, understanding of the structure and catalytic mechanism of related sugar, kinases can be obtained.
About this StructureAbout this Structure
1RKD is a Single protein structure of sequence from Escherichia coli with RIB, PO4 and ADP as ligands. Active as Ribokinase, with EC number 2.7.1.15 Structure known Active Sites: AB1, AB2, AB3, RB1, RB2 and RB3. Full crystallographic information is available from OCA.
ReferenceReference
Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures., Sigrell JA, Cameron AD, Jones TA, Mowbray SL, Structure. 1998 Feb 15;6(2):183-93. PMID:9519409
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