1rkd
From Proteopedia
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| - | [[Image:1rkd.gif|left|200px]] | + | [[Image:1rkd.gif|left|200px]] |
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| - | '''E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP''' | + | {{Structure |
| + | |PDB= 1rkd |SIZE=350|CAPTION= <scene name='initialview01'>1rkd</scene>, resolution 1.84Å | ||
| + | |SITE= <scene name='pdbsite=AB1:Residues+Making+Direct+H+Bonds+w.+Adp'>AB1</scene>, <scene name='pdbsite=AB2:Residues+Making+Water-Mediated+H+Bonds+w.+Adp'>AB2</scene>, <scene name='pdbsite=AB3:Residues+Within+Van+Der+Waals+Distance+Of+Adp'>AB3</scene>, <scene name='pdbsite=RB1:Residues+Making+Direct+H+Bonds+w.+Ribose'>RB1</scene>, <scene name='pdbsite=RB2:Residues+Making+Water-Mediated+H+Bonds+w.+Ribose'>RB2</scene> and <scene name='pdbsite=RB3:Residues+Within+Van+Der+Waals+Distance+Of+Ribose'>RB3</scene> | ||
| + | |LIGAND= <scene name='pdbligand=RIB:RIBOSE'>RIB</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene> and <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene> | ||
| + | |ACTIVITY= [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] | ||
| + | |GENE= RBSK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | }} | ||
| + | |||
| + | '''E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP''' | ||
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==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1RKD is a [ | + | 1RKD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKD OCA]. |
==Reference== | ==Reference== | ||
| - | 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:[http:// | + | 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:[http://www.ncbi.nlm.nih.gov/pubmed/9519409 9519409] |
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Ribokinase]] | [[Category: Ribokinase]] | ||
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[[Category: transferase]] | [[Category: transferase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:52:47 2008'' |
Revision as of 11:52, 20 March 2008
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| , resolution 1.84Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , and | ||||||
| Ligands: | , and | ||||||
| Gene: | RBSK (Escherichia coli) | ||||||
| Activity: | Ribokinase, with EC number 2.7.1.15 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP
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 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
1RKD is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Thu Mar 20 13:52:47 2008
Categories: Escherichia coli | Ribokinase | Single protein | Cameron, A D. | Jones, T A. | Mowbray, S L. | Sigrell, J A. | ADP | PO4 | RIB | Carbohydrate kinase | Nucleotide binding | Ribose | Transferase
