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Structure-Function Studies of Enzymes from Ribose Metabolism
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology.
2004 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In the pentose phosphate pathway, carbohydrates such as glucose and ribose are degraded with production of reductive power and energy. Another important function is to produce essential pentoses, such as ribose 5-phosphate, which later can be used in biosynthesis of nucleic acids and cofactors.

This thesis presents structural and functional studies on three enzymes involved in ribose metabolism in Escherichia coli.

Ribokinase is an enzyme that phosphorylates ribose in the presence of ATP and magnesium, as the first step of exogenous ribose metabolism. Two important aspects of ribokinase function, not previously known, have been elucidated. Ribokinase was shown to be activated by monovalent cations, specifically potassium. Structural analysis of the monovalent ion binding site indicates that the ion has a structural rather than catalytic role; a mode of activation involving a conformational change has been suggested. Product inhibition studies suggest that ATP is the first substrate to bind the enzyme. Independent Kd measurements with the ATP analogue AMP-PCP support this. The results presented here will have implications for several enzymes in the protein family to which ribokinase belongs, in particular the medically interesting enzyme adenosine kinase.

Ribose 5-phosphate isomerases convert ribose 5-phosphate into ribulose 5-phosphate or vice versa. Structural studies on the two genetically distinct isomerases in E. coli have shown them to be fundamentally different in many aspects, including active site architecture. However, a kinetic study has demonstrated both enzymes to be efficient in terms of catalysis. Sequence searches of completed genomes show ribose 5-phosphate isomerase B to be the sole isomerase in many bacteria, although ribose 5-phosphate isomerase A is a nearly universal enzyme. All genomes contain at least one of the two enzymes. These results confirm that both enzymes must be independently capable of supporting ribose metabolism, a fact that had not previously been established.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2004. , p. 45
Series
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ; 939
Keywords [en]
Molecular biology, activation, isomerase, kinase, potassium, product inhibition, ribose, ribose 5-phosphate, x-ray crystallography, enzyme kinetics, fluorescence spectroscopy, protein structure
Keywords [sv]
Molekylärbiologi
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-3999ISBN: 91-554-5875-0 (print)OAI: oai:DiVA.org:uu-3999DiVA, id: diva2:164074
Public defence
2004-03-05, B41, BMC, Husargatan 3, Uppsala, 13:00
Opponent
Supervisors
Available from: 2004-02-12 Created: 2004-02-12Bibliographically approved
List of papers
1. Activation of Ribokinase by Monovalent Cations
Open this publication in new window or tab >>Activation of Ribokinase by Monovalent Cations
2002 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 315, no 3, p. 409-419Article in journal (Refereed) Published
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-91364 (URN)10.1006/jmbi.2001.5248 (DOI)
Available from: 2004-02-12 Created: 2004-02-12 Last updated: 2017-12-14Bibliographically approved
2. Structure of Escherichia coli Ribose 5-phosphate Isomerase: A Ubiquitous Enzyme of the Pentose Phosphate Pathway and the Calvin Cycle
Open this publication in new window or tab >>Structure of Escherichia coli Ribose 5-phosphate Isomerase: A Ubiquitous Enzyme of the Pentose Phosphate Pathway and the Calvin Cycle
Show others...
2003 In: Structure, Vol. 11, no 1, p. 31-42Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-91365 (URN)
Available from: 2004-02-12 Created: 2004-02-12Bibliographically approved
3. The 2.2 Å Resolution Structure of RpiB/AlsB from Escherichia coli Illutrates a New Approach to the Ribose 5-phosphate Isomerase Reaction
Open this publication in new window or tab >>The 2.2 Å Resolution Structure of RpiB/AlsB from Escherichia coli Illutrates a New Approach to the Ribose 5-phosphate Isomerase Reaction
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2003 In: Journal of Molecular Biology, Vol. 332, no 5, p. 1083-1094Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-91366 (URN)
Available from: 2004-02-12 Created: 2004-02-12Bibliographically approved
4. Specificity and Activity of Escherichia coli Ribokinase
Open this publication in new window or tab >>Specificity and Activity of Escherichia coli Ribokinase
Manuscript (Other academic)
Identifiers
urn:nbn:se:uu:diva-91367 (URN)
Available from: 2004-02-12 Created: 2004-02-12 Last updated: 2016-05-09Bibliographically approved
5. Mycobacterium tuberculosis Ribose 5-phosphate Isomerase has a Known Fold, but a Novel Active Site
Open this publication in new window or tab >>Mycobacterium tuberculosis Ribose 5-phosphate Isomerase has a Known Fold, but a Novel Active Site
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2004 In: Journal of Molecular Biology, Vol. 335, no 3, p. 799-809Article in journal (Refereed) Published
Identifiers
urn:nbn:se:uu:diva-91368 (URN)
Available from: 2004-02-12 Created: 2004-02-12Bibliographically approved

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