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| - | ==CRYSTAL STRUCTURE OF THE H99N MUTANT OF RIBOSE-5-PHOSPHATE ISOMERASE B FROM E. COLI SOAKED WITH RIBOSE 5-PHOSPHATE== | + | |
| - | <StructureSection load='2vvr' size='340' side='right' caption='[[2vvr]], [[Resolution|resolution]] 2.10Å' scene=''> | + | ==Crystal structure of the H99N mutant of ribose-5-phosphate isomerase B from E. coli soaked with ribose 5-phosphate== |
| | + | <StructureSection load='2vvr' size='340' side='right'caption='[[2vvr]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2vvr]] is a 6 chain structure with 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=2VVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VVR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2vvr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VVR FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1nn4|1nn4]], [[2vvq|2vvq]], [[2vvp|2vvp]], [[2vvo|2vvo]]</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose-5-phosphate_isomerase Ribose-5-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.6 5.3.1.6] </span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vvr OCA], [https://pdbe.org/2vvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vvr RCSB], [https://www.ebi.ac.uk/pdbsum/2vvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vvr ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vvr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vvr RCSB], [http://www.ebi.ac.uk/pdbsum/2vvr PDBsum]</span></td></tr>
| + | </table> |
| - | <table> | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RPIB_ECOLI RPIB_ECOLI] In addition to its activity on D-ribose 5-phosphate it probably also has activity on D-allose 6-phosphate.<ref>PMID:8576032</ref> <ref>PMID:4909663</ref> <ref>PMID:1104357</ref> <ref>PMID:9401019</ref> <ref>PMID:18640127</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vv/2vvr_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vv/2vvr_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| - | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vvr ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 2vvr" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Ribose-5-phosphate isomerase|Ribose-5-phosphate isomerase]] | + | *[[Ribose-5-phosphate isomerase 3D structures|Ribose-5-phosphate isomerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Escherichia coli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Ribose-5-phosphate isomerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Mowbray, S L.]] | + | [[Category: Mowbray SL]] |
| - | [[Category: Roos, A K.]] | + | [[Category: Roos AK]] |
| - | [[Category: Carbohydrate metabolism]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Pentose phosphate pathway]]
| + | |
| - | [[Category: Rpib]]
| + | |
| Structural highlights
Function
RPIB_ECOLI In addition to its activity on D-ribose 5-phosphate it probably also has activity on D-allose 6-phosphate.[1] [2] [3] [4] [5]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Interconversion of D-ribose-5-phosphate (R5P) and D-ribulose-5-phosphate is an important step in the pentose phosphate pathway. Two unrelated enzymes with R5P isomerase activity were first identified in Escherichia coli, RpiA and RpiB. In this organism, the essential 5-carbon sugars were thought to be processed by RpiA, while the primary role of RpiB was suggested to instead be interconversion of the rare 6-carbon sugars D-allose-6-phosphate (All6P) and D-allulose-6-phosphate. In Mycobacterium tuberculosis, where only an RpiB is found, the 5-carbon sugars are believed to be the enzyme's primary substrates. Here, we present kinetic studies examining the All6P isomerase activity of the RpiBs from these two organisms and show that only the E. coli enzyme can catalyze the reaction efficiently. All6P instead acts as an inhibitor of the M. tuberculosis enzyme in its action on R5P. X-ray studies of the M. tuberculosis enzyme co-crystallized with All6P and 5-deoxy-5-phospho-D-ribonohydroxamate (an inhibitor designed to mimic the 6-carbon sugar) and comparison with the E. coli enzyme's structure allowed us to identify differences in the active sites that explain the kinetic results. Two other structures, that of a mutant E. coli RpiB in which histidine 99 was changed to asparagine and that of wild-type M. tuberculosis enzyme, both co-crystallized with the substrate ribose-5-phosphate, shed additional light on the reaction mechanism of RpiBs generally.
D-ribose-5-phosphate isomerase B from Escherichia coli is also a functional D-allose-6-phosphate isomerase, while the Mycobacterium tuberculosis enzyme is not.,Roos AK, Mariano S, Kowalinski E, Salmon L, Mowbray SL J Mol Biol. 2008 Oct 10;382(3):667-79. Epub 2008 Jul 9. PMID:18640127[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Sorensen KI, Hove-Jensen B. Ribose catabolism of Escherichia coli: characterization of the rpiB gene encoding ribose phosphate isomerase B and of the rpiR gene, which is involved in regulation of rpiB expression. J Bacteriol. 1996 Feb;178(4):1003-11. PMID:8576032
- ↑ David J, Wiesmeyer H. Regulation of ribose metabolism in Escherichia coli. II. Evidence for two ribose-5-phosphate isomerase activities. Biochim Biophys Acta. 1970 Apr 14;208(1):56-67. PMID:4909663
- ↑ Essenberg MK, Cooper RA. Two ribose-5-phosphate isomerases from Escherichia coli K12: partial characterisation of the enzymes and consideration of their possible physiological roles. Eur J Biochem. 1975 Jul 1;55(2):323-32. PMID:1104357
- ↑ Kim C, Song S, Park C. The D-allose operon of Escherichia coli K-12. J Bacteriol. 1997 Dec;179(24):7631-7. PMID:9401019
- ↑ Roos AK, Mariano S, Kowalinski E, Salmon L, Mowbray SL. D-ribose-5-phosphate isomerase B from Escherichia coli is also a functional D-allose-6-phosphate isomerase, while the Mycobacterium tuberculosis enzyme is not. J Mol Biol. 2008 Oct 10;382(3):667-79. Epub 2008 Jul 9. PMID:18640127 doi:10.1016/j.jmb.2008.06.090
- ↑ Roos AK, Mariano S, Kowalinski E, Salmon L, Mowbray SL. D-ribose-5-phosphate isomerase B from Escherichia coli is also a functional D-allose-6-phosphate isomerase, while the Mycobacterium tuberculosis enzyme is not. J Mol Biol. 2008 Oct 10;382(3):667-79. Epub 2008 Jul 9. PMID:18640127 doi:10.1016/j.jmb.2008.06.090
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