1wm9: Difference between revisions

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-[[Image:1wm9.gif|left|200px]]
-<!--
+==Structure of GTP cyclohydrolase I from Thermus thermophilus HB8==
-The line below this paragraph, containing "STRUCTURE_1wm9", creates the "Structure Box" on the page.
+<StructureSection load='1wm9' size='340' side='right'caption='[[1wm9]], [[Resolution|resolution]] 2.20&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'>[[1wm9]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WM9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WM9 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]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1wm9|  PDB=1wm9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wm9 OCA], [https://pdbe.org/1wm9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wm9 RCSB], [https://www.ebi.ac.uk/pdbsum/1wm9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wm9 ProSAT], [https://www.topsan.org/Proteins/RSGI/1wm9 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5SH52_THET8 Q5SH52_THET8]
+== 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/wm/1wm9_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=1wm9 ConSurf].
+<div style="clear:both"></div>
-'''Structure of GTP cyclohydrolase I from Thermus thermophilus HB8'''
+==See Also==
+*[[Cyclohydrolase 3D structures|Cyclohydrolase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-GTP cyclohydrolase I (GTPCH1) catalyzes the conversion of GTP to dihydroneopterin 3'-triphosphate. We found that an 8-oxoguanine derivative of GTP (8-oxo-GTP) strongly bound to GTPCH1 from Thermus thermophilus HB8 (tGTPCH1) as a competitive inhibitor. The affinity of 8-oxo-GTP was three orders of magnitude greater than that of GTP. These results suggest that 8-oxo-GTP is a transition state analogue of GTPCH1. We have solved the X-ray crystal structures of tGTPCH1 complexed with 8-oxo-GTP and 8-oxo-dGTP at 2.0 and 1.8 A resolution, respectively, as well as the free form of the enzyme at 2.2 A resolution. In the structure of tGTPCH1 complexed with 8-oxo-GTP or 8-oxo-dGTP, the oxygen atoms at O8 of the 8-oxoguanine groups, together with residues Cys108, His111 and Cys179, are coordinated to the zinc ion. The water molecule between Ndelta1 of His177 and N7 of 8-oxoguanine is conserved in both structures. These structural data are in accordance with one of the proposed transition states. Superimpositioning of the structures indicates the imidazole ring of His110 is rotated, implying concomitant proton transfer to the ribose ring O4'. Based on these structural data we propose a novel reaction mechanism for GTPCH1.
+[[Category: Large Structures]]
+[[Category: Thermus thermophilus HB8]]
-==About this Structure==
+[[Category: Tanaka Y]]
-WM9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WM9 OCA].
-==Reference==
-Novel reaction mechanism of GTP cyclohydrolase I. High-resolution X-ray crystallography of Thermus thermophilus HB8 enzyme complexed with a transition state analogue, the 8-oxoguanine derivative., Tanaka Y, Nakagawa N, Kuramitsu S, Yokoyama S, Masui R, J Biochem. 2005 Sep;138(3):263-75. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16169877 16169877]
-[[Category: GTP cyclohydrolase I]]
-[[Category: Single protein]]
-[[Category: Thermus thermophilus]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
-[[Category: Tanaka, Y.]]
-[[Category: Beta barrel]]
-[[Category: Hydrolase]]
-[[Category: Pteridine]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-[[Category: Tetrahydrobiopterin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 13:52:09 2008''