3hee: Difference between revisions
New page: '''Unreleased structure''' The entry 3hee is ON HOLD Authors: Kang, L.W, Kim, J.K, Jung, J.H, Hong, M.K Description: Structural study of Clostridium thermocellum Ribose-5-Phosphate Iso... |
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==Structural study of Clostridium thermocellum Ribose-5-Phosphate Isomerase B and ribose-5-phosphate== | |||
<StructureSection load='3hee' size='340' side='right'caption='[[3hee]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3hee]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HEE FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></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=3hee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hee OCA], [https://pdbe.org/3hee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hee RCSB], [https://www.ebi.ac.uk/pdbsum/3hee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hee ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A3DIL8_ACET2 A3DIL8_ACET2] | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/he/3hee_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</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/main_output.php?pdb_ID=3hee ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Ribose-5-phosphate isomerase (Rpi) catalyzes the conversion of D: -ribose 5-phosphate (R5P) to D: -ribulose 5-phosphate, which is an important step in the non-oxidative pathway of the pentose phosphate pathway and the Calvin cycle of photosynthesis. Recently, Rpis have been used to produce valuable rare sugars for industrial purposes. Of the Rpis, D: -ribose-5-phosphate isomerase B from Clostridium thermocellum (CtRpi) has the fastest reactions kinetics. While Thermotoga maritime Rpi (TmRpi) has the same substrate specificity as CtRpi, the overall activity of CtRpi is approximately 200-fold higher than that of TmRpi. To understand the structural basis of these kinetic differences, we determined the crystal structures, at 2.1-A resolution or higher, of CtRpi alone and bound to its substrates, R5P, D: -ribose, and D: -allose. Structural comparisons of CtRpi and TmRpi showed overall conservation of their structures with two notable differences. First, the volume of the CtRpi substrate binding pocket (SBP) was 20% less than that of the TmRpi SBP. Second, the residues next to the sugar-ring opening catalytic residue (His98) were different. We switched the key residues, involved in SBP shaping or catalysis, between CtRpi and TmRpi by site-directed mutagenesis, and studied the enzyme kinetics of the mutants. We found that tight interactions between the two monomers, narrow SBP width, and the residues near the catalytic residue are all critical for the fast enzyme kinetics of CtRpi. | |||
Crystal structure of Clostridium thermocellum ribose-5-phosphate isomerase B reveals properties critical for fast enzyme kinetics.,Jung J, Kim JK, Yeom SJ, Ahn YJ, Oh DK, Kang LW Appl Microbiol Biotechnol. 2011 Apr;90(2):517-27. Epub 2011 Jan 21. PMID:21253719<ref>PMID:21253719</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3hee" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribose-5-phosphate isomerase 3D structures|Ribose-5-phosphate isomerase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Acetivibrio thermocellus ATCC 27405]] | |||
[[Category: Large Structures]] | |||
[[Category: Hong MK]] | |||
[[Category: Jung JH]] | |||
[[Category: Kang LW]] | |||
[[Category: Kim JK]] | |||
Latest revision as of 18:48, 1 November 2023
Structural study of Clostridium thermocellum Ribose-5-Phosphate Isomerase B and ribose-5-phosphateStructural study of Clostridium thermocellum Ribose-5-Phosphate Isomerase B and ribose-5-phosphate
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedRibose-5-phosphate isomerase (Rpi) catalyzes the conversion of D: -ribose 5-phosphate (R5P) to D: -ribulose 5-phosphate, which is an important step in the non-oxidative pathway of the pentose phosphate pathway and the Calvin cycle of photosynthesis. Recently, Rpis have been used to produce valuable rare sugars for industrial purposes. Of the Rpis, D: -ribose-5-phosphate isomerase B from Clostridium thermocellum (CtRpi) has the fastest reactions kinetics. While Thermotoga maritime Rpi (TmRpi) has the same substrate specificity as CtRpi, the overall activity of CtRpi is approximately 200-fold higher than that of TmRpi. To understand the structural basis of these kinetic differences, we determined the crystal structures, at 2.1-A resolution or higher, of CtRpi alone and bound to its substrates, R5P, D: -ribose, and D: -allose. Structural comparisons of CtRpi and TmRpi showed overall conservation of their structures with two notable differences. First, the volume of the CtRpi substrate binding pocket (SBP) was 20% less than that of the TmRpi SBP. Second, the residues next to the sugar-ring opening catalytic residue (His98) were different. We switched the key residues, involved in SBP shaping or catalysis, between CtRpi and TmRpi by site-directed mutagenesis, and studied the enzyme kinetics of the mutants. We found that tight interactions between the two monomers, narrow SBP width, and the residues near the catalytic residue are all critical for the fast enzyme kinetics of CtRpi. Crystal structure of Clostridium thermocellum ribose-5-phosphate isomerase B reveals properties critical for fast enzyme kinetics.,Jung J, Kim JK, Yeom SJ, Ahn YJ, Oh DK, Kang LW Appl Microbiol Biotechnol. 2011 Apr;90(2):517-27. Epub 2011 Jan 21. PMID:21253719[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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