1ker: Difference between revisions
Jump to navigation
Jump to search
m Protected "1ker" [edit=sysop:move=sysop] |
No edit summary |
||
| (7 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
< | ==The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-D-glucose bound== | ||
<StructureSection load='1ker' size='340' side='right'caption='[[1ker]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1ker]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KER 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]] 2.2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAU:2DEOXY-THYMIDINE-5-DIPHOSPHO-ALPHA-D-GLUCOSE'>DAU</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1ker FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ker OCA], [https://pdbe.org/1ker PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ker RCSB], [https://www.ebi.ac.uk/pdbsum/1ker PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ker ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8GIP9_STRSU Q8GIP9_STRSU] | |||
== 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/ke/1ker_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=1ker ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
dTDP-D-glucose 4,6-dehydratase (RmlB) was first identified in the L-rhamnose biosynthetic pathway, where it catalyzes the conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose. The structures of RmlB from Salmonella enterica serovar Typhimurium in complex with substrate deoxythymidine 5'-diphospho-D-glucose (dTDP-D-glucose) and deoxythymidine 5'-diphosphate (dTDP), and RmlB from Streptococcus suis serotype 2 in complex with dTDP-D-glucose, dTDP, and deoxythymidine 5'-diphospho-D-pyrano-xylose (dTDP-xylose) have all been solved at resolutions between 1.8 A and 2.4 A. The structures show that the active sites are highly conserved. Importantly, the structures show that the active site tyrosine functions directly as the active site base, and an aspartic and glutamic acid pairing accomplishes the dehydration step of the enzyme mechanism. We conclude that the substrate is required to move within the active site to complete the catalytic cycle and that this movement is driven by the elimination of water. The results provide insight into members of the SDR superfamily. | |||
Toward a structural understanding of the dehydratase mechanism.,Allard ST, Beis K, Giraud MF, Hegeman AD, Gross JW, Wilmouth RC, Whitfield C, Graninger M, Messner P, Allen AG, Maskell DJ, Naismith JH Structure. 2002 Jan;10(1):81-92. PMID:11796113<ref>PMID:11796113</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1ker" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[DTDP-glucose 4%2C6-dehydratase|DTDP-glucose 4%2C6-dehydratase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[ | |||
== | |||
< | |||
[[Category: Streptococcus suis]] | [[Category: Streptococcus suis]] | ||
[[Category: Allard STM]] | |||
[[Category: Allard | [[Category: Allen AG]] | ||
[[Category: Allen | [[Category: Beis K]] | ||
[[Category: Beis | [[Category: Giraud M-F]] | ||
[[Category: Giraud | [[Category: Graninger M]] | ||
[[Category: Graninger | [[Category: Gross JW]] | ||
[[Category: Gross | [[Category: Hegeman AD]] | ||
[[Category: Hegeman | [[Category: Messner P]] | ||
[[Category: Messner | [[Category: Naismith JH]] | ||
[[Category: Naismith | [[Category: Whitfield C]] | ||
[[Category: Whitfield | |||
Latest revision as of 11:57, 16 August 2023
The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-D-glucose boundThe crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-D-glucose bound
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 PubMeddTDP-D-glucose 4,6-dehydratase (RmlB) was first identified in the L-rhamnose biosynthetic pathway, where it catalyzes the conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose. The structures of RmlB from Salmonella enterica serovar Typhimurium in complex with substrate deoxythymidine 5'-diphospho-D-glucose (dTDP-D-glucose) and deoxythymidine 5'-diphosphate (dTDP), and RmlB from Streptococcus suis serotype 2 in complex with dTDP-D-glucose, dTDP, and deoxythymidine 5'-diphospho-D-pyrano-xylose (dTDP-xylose) have all been solved at resolutions between 1.8 A and 2.4 A. The structures show that the active sites are highly conserved. Importantly, the structures show that the active site tyrosine functions directly as the active site base, and an aspartic and glutamic acid pairing accomplishes the dehydration step of the enzyme mechanism. We conclude that the substrate is required to move within the active site to complete the catalytic cycle and that this movement is driven by the elimination of water. The results provide insight into members of the SDR superfamily. Toward a structural understanding of the dehydratase mechanism.,Allard ST, Beis K, Giraud MF, Hegeman AD, Gross JW, Wilmouth RC, Whitfield C, Graninger M, Messner P, Allen AG, Maskell DJ, Naismith JH Structure. 2002 Jan;10(1):81-92. PMID:11796113[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
| ||||||||||||||||||