3ph3: Difference between revisions
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==Clostridium thermocellum Ribose-5-Phosphate Isomerase B with d-ribose== | |||
<StructureSection load='3ph3' size='340' side='right'caption='[[3ph3]], [[Resolution|resolution]] 2.07Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ph3]] 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=3PH3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PH3 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]] 2.07Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RB5:D-RIBOSE'>RB5</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=3ph3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ph3 OCA], [https://pdbe.org/3ph3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ph3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ph3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ph3 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A3DIL8_ACET2 A3DIL8_ACET2] | |||
<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 3ph3" 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/> | ||
< | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Acetivibrio thermocellus ATCC 27405]] | ||
[[Category: Ahn | [[Category: Large Structures]] | ||
[[Category: Jung | [[Category: Ahn YJ]] | ||
[[Category: Kang | [[Category: Jung J]] | ||
[[Category: Kim | [[Category: Kang LW]] | ||
[[Category: Oh | [[Category: Kim JK]] | ||
[[Category: Yeom | [[Category: Oh DK]] | ||
[[Category: Yeom SJ]] | |||
Latest revision as of 20:06, 1 November 2023
Clostridium thermocellum Ribose-5-Phosphate Isomerase B with d-riboseClostridium thermocellum Ribose-5-Phosphate Isomerase B with d-ribose
Structural highlights
FunctionPublication 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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