1h5r: Difference between revisions

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-{{Seed}}
-[[Image:1h5r.png|left|200px]]
-<!--
+==Thymidylyltransferase complexed with Thimidine and Glucose-1-phospate==
-The line below this paragraph, containing "STRUCTURE_1h5r", creates the "Structure Box" on the page.
+<StructureSection load='1h5r' size='340' side='right'caption='[[1h5r]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1h5r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H5R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H5R FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G1P:ALPHA-D-GLUCOSE-1-PHOSPHATE'>G1P</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene></td></tr>
-{{STRUCTURE_1h5r|  PDB=1h5r  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1h5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h5r OCA], [https://pdbe.org/1h5r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h5r RCSB], [https://www.ebi.ac.uk/pdbsum/1h5r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h5r ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RMLA1_ECOLI RMLA1_ECOLI] Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis.
+== 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/h5/1h5r_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=1h5r ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Glucose-1-phosphate thymidylyltransferase is the first enzyme in the biosynthesis of dTDP-l-rhamnose, the precursor of l-rhamnose, an essential component of surface antigens, such as the O-lipopolysaccharide, mediating virulence and adhesion to host tissues in many microorganisms. The enzyme catalyses the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis. To shed more light on the catalytic properties of glucose-1-phosphate thymidylyltransferase from Escherichia coli, specifically distinguishing between ping pong and sequential ordered bi bi reaction mechanisms, the enzyme kinetic properties have been analysed in the presence of different substrates and inhibitors. Moreover, three different complexes of glucose-1-phosphate thymidylyltransferase (co-crystallized with dTDP, with dTMP and glucose-1-phosphate, with d-thymidine and glucose-1-phosphate) have been analysed by X-ray crystallography, in the 1.9-2.3 A resolution range (R-factors of 17.3-17.5 %). The homotetrameric enzyme shows strongly conserved substrate/inhibitor binding modes in a surface cavity next to the topological switch-point of a quasi-Rossmann fold. Inspection of the subunit tertiary structure reveals relationships to other enzymes involved in the biosynthesis of nucleotide-sugars, including distant proteins such as the molybdenum cofactor biosynthesis protein MobA. The precise location of the substrate relative to putative reactive residues in the catalytic center suggests that, in keeping with the results of the kinetic measurements, both catalysed reactions, i.e. dTDP-glucose biosynthesis and pyrophosphorolysis, follow a sequential ordered bi bi catalytic mechanism.
-===THYMIDYLYLTRANSFERASE COMPLEXED WITH THIMIDINE AND GLUCOSE-1-PHOSPATE===
+Kinetic and crystallographic analyses support a sequential-ordered bi bi catalytic mechanism for Escherichia coli glucose-1-phosphate thymidylyltransferase.,Zuccotti S, Zanardi D, Rosano C, Sturla L, Tonetti M, Bolognesi M J Mol Biol. 2001 Nov 2;313(4):831-43. PMID:11697907<ref>PMID:11697907</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1h5r" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11697907}}, adds the Publication Abstract to the page
+*[[Glucose-1-phosphate thymidylyltransferase 3D structures|Glucose-1-phosphate thymidylyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11697907 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11697907}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli]]
-H5R is a [[Protein complex]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H5R OCA].
+[[Category: Large Structures]]
+[[Category: Bolognesi M]]
-==Reference==
+[[Category: Rosano C]]
-Kinetic and crystallographic analyses support a sequential-ordered bi bi catalytic mechanism for Escherichia coli glucose-1-phosphate thymidylyltransferase., Zuccotti S, Zanardi D, Rosano C, Sturla L, Tonetti M, Bolognesi M, J Mol Biol. 2001 Nov 2;313(4):831-43. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11697907 11697907]
+[[Category: Zuccotti S]]
-[[Category: Glucose-1-phosphate thymidylyltransferase]]
-[[Category: Protein complex]]
-[[Category: Bolognesi, M.]]
-[[Category: Rosano, C.]]
-[[Category: Zuccotti, S.]]
-[[Category: Nucleotide sugar methabolism]]
-[[Category: Pyrophosphatase]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 06:40:20 2008''