1kew: Difference between revisions

Revision as of 14:33, 21 February 2008

The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium with thymidine diphosphate bound

OverviewOverview

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.

About this StructureAbout this Structure

1KEW is a Single protein structure of sequence from Salmonella enterica subsp. enterica serovar typhimurium with , and as ligands. Active as dTDP-glucose 4,6-dehydratase, with EC number 4.2.1.46 Full crystallographic information is available from OCA.

ReferenceReference

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

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-[[Image:1kew.jpg|left|200px]]<br /><applet load="1kew" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1kew.jpg|left|200px]]<br /><applet load="1kew" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1kew, resolution 1.80&Aring;" />
 '''The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium with thymidine diphosphate bound'''<br />
 ==Overview==
-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-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.
 ==About this Structure==
-KEW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium] with TYD, NAD and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KEW OCA].
+KEW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium] with <scene name='pdbligand=TYD:'>TYD</scene>, <scene name='pdbligand=NAD:'>NAD</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEW OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Single protein]]
 [[Category: dTDP-glucose 4,6-dehydratase]]
-[[Category: Allard, S.T.M.]]
+[[Category: Allard, S T.M.]]
-[[Category: Allen, A.G.]]
+[[Category: Allen, A G.]]
 [[Category: Beis, K.]]
-[[Category: Giraud, M.F.]]
+[[Category: Giraud, M F.]]
 [[Category: Graninger, M.]]
-[[Category: Gross, J.W.]]
+[[Category: Gross, J W.]]
-[[Category: Hegeman, A.D.]]
+[[Category: Hegeman, A D.]]
 [[Category: Messner, P.]]
-[[Category: Naismith, J.H.]]
+[[Category: Naismith, J H.]]
 [[Category: Whitfield, C.]]
 [[Category: GOL]]
@@ Line 29: / Line 29: @@
 [[Category: rossmann fold]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:08:32 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:33:28 2008''