1kep

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:57, 16 August 2023) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1kep.jpg|left|200px]]
 
-
{{Structure
+
==The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose bound==
-
|PDB= 1kep |SIZE=350|CAPTION= <scene name='initialview01'>1kep</scene>, resolution 1.80&Aring;
+
<StructureSection load='1kep' size='340' side='right'caption='[[1kep]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TDX:THYMIDINE-5&#39;-DIPHOSPHO-BETA-D-XYLOSE'>TDX</scene>
+
<table><tr><td colspan='2'>[[1kep]] 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=1KEP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KEP FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-glucose_4,6-dehydratase dTDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-
|GENE= rmlB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1307 Streptococcus suis])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TDX:THYMIDINE-5-DIPHOSPHO-BETA-D-XYLOSE'>TDX</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kep OCA], [https://pdbe.org/1kep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kep RCSB], [https://www.ebi.ac.uk/pdbsum/1kep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kep ProSAT]</span></td></tr>
-
|RELATEDENTRY=[[1ker|1KER]], [[1ket|1KET]], [[1keu|1KEU]], [[1kew|1KEW]], [[1g1a|1G1A]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kep OCA], [http://www.ebi.ac.uk/pdbsum/1kep PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kep RCSB]</span>
+
== 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/1kep_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=1kep 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.
-
'''The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose bound'''
+
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1kep" style="background-color:#fffaf0;"></div>
-
==Overview==
+
==See Also==
-
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.
+
*[[DTDP-glucose 4%2C6-dehydratase|DTDP-glucose 4%2C6-dehydratase]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
1KEP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEP OCA].
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
[[Category: Large Structures]]
-
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:[http://www.ncbi.nlm.nih.gov/pubmed/11796113 11796113]
+
-
[[Category: Single protein]]
+
[[Category: Streptococcus suis]]
[[Category: Streptococcus suis]]
-
[[Category: dTDP-glucose 4,6-dehydratase]]
+
[[Category: Allard STM]]
-
[[Category: Allard, S T.M.]]
+
[[Category: Allen AG]]
-
[[Category: Allen, A G.]]
+
[[Category: Beis K]]
-
[[Category: Beis, K.]]
+
[[Category: Giraud M-F]]
-
[[Category: Giraud, M F.]]
+
[[Category: Graninger M]]
-
[[Category: Graninger, M.]]
+
[[Category: Gross JW]]
-
[[Category: Gross, J W.]]
+
[[Category: Hegeman AD]]
-
[[Category: Hegeman, A D.]]
+
[[Category: Messner P]]
-
[[Category: Messner, P.]]
+
[[Category: Naismith JH]]
-
[[Category: Naismith, J H.]]
+
[[Category: Whitfield C]]
-
[[Category: Whitfield, C.]]
+
-
[[Category: rossmann fold]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:47:29 2008''
+

Current revision

The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose bound

PDB ID 1kep

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1kep"
Personal tools