2zvr
From Proteopedia
(Difference between revisions)
| (One intermediate revision not shown.) | |||
| Line 1: | Line 1: | ||
==Crystal structure of a D-tagatose 3-epimerase-related protein from Thermotoga maritima== | ==Crystal structure of a D-tagatose 3-epimerase-related protein from Thermotoga maritima== | ||
| - | <StructureSection load='2zvr' size='340' side='right' caption='[[2zvr]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='2zvr' size='340' side='right'caption='[[2zvr]], [[Resolution|resolution]] 2.20Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2zvr]] is a 2 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[2zvr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZVR FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zvr OCA], [https://pdbe.org/2zvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zvr RCSB], [https://www.ebi.ac.uk/pdbsum/2zvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zvr ProSAT]</span></td></tr> |
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/IOLO_THEMA IOLO_THEMA] Catalyzes the reversible epimerization between 5-keto-L-gluconate (5-dehydro-L-gluconate) and D-tagaturonate, and thus probably functions in a myo-inositol degradation pathway together with IolG, IolM and IolN (PubMed:23441918). Is not active on the enantiomer 5-keto-D-gluconate (PubMed:23441918). Was also shown to be a nonphosphorylated sugar isomerase with broad substrate specificity in vitro (PubMed:28258150). Is able to catalyze the reversible C3-epimerization of L-ribulose to L-xylulose, D-ribulose to D-xylulose, D-psicose to D-fructose, and D-tagatose to D-sorbose, with a substrate preference for ketopentoses rather than ketohexoses (PubMed:28258150). Also catalyzes the aldose-ketose isomerization reaction from either D-erythrose or D-threose to D-erythrulose (PubMed:28258150). Exhibits no activity for C4-epimerization of D-tagatose to D-fructose (PubMed:28258150).<ref>PMID:23441918</ref> <ref>PMID:28258150</ref> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
| Line 17: | Line 19: | ||
</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=2zvr 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=2zvr ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | The crystal structure of a D-tagatose 3-epimerase-related protein (TM0416p) encoded by the hypothetical open reading frame TM0416 in the genome of the hyperthermophilic bacterium Thermotoga maritima was determined at a resolution of 2.2 A. The asymmetric unit contained two homologous subunits and a dimer was generated by twofold symmetry. The main-chain coordinates of the enzyme monomer proved to be similar to those of D-tagatose 3-epimerase from Pseudomonas cichorii and D-psicose 3-epimerase from Agrobacterium tumefaciens; however, TM0416p exhibited a unique solvent-accessible substrate-binding pocket that reflected the absence of an alpha-helix that covers the active-site cleft in the two aforementioned ketohexose 3-epimerases. In addition, the residues responsible for creating a hydrophobic environment around the substrate in TM0416p differ entirely from those in the other two enzymes. Collectively, these findings suggest that the substrate specificity of TM0416p is likely to differ substantially from those of other D-tagatose 3-epimerase family enzymes. | ||
| - | |||
| - | Structure of a D-tagatose 3-epimerase-related protein from the hyperthermophilic bacterium Thermotoga maritima.,Sakuraba H, Yoneda K, Satomura T, Kawakami R, Ohshima T Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Mar 1;65(Pt 3):199-203., Epub 2009 Feb 14. PMID:19255464<ref>PMID:19255464</ref> | ||
| - | |||
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 2zvr" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Large Structures]] |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
[[Category: Thermotoga maritima]] | [[Category: Thermotoga maritima]] | ||
| + | [[Category: Ohshima T]] | ||
| + | [[Category: Sakuraba H]] | ||
Current revision
Crystal structure of a D-tagatose 3-epimerase-related protein from Thermotoga maritima
| |||||||||||
