1wm9: Difference between revisions

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New page: left|200px<br /><applet load="1wm9" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wm9, resolution 2.2Å" /> '''Structure of GTP cycl...
 
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[[Image:1wm9.gif|left|200px]]<br /><applet load="1wm9" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1wm9, resolution 2.2&Aring;" />
'''Structure of GTP cyclohydrolase I from Thermus thermophilus HB8'''<br />


==Overview==
==Structure of GTP cyclohydrolase I from Thermus thermophilus HB8==
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.
<StructureSection load='1wm9' size='340' side='right'caption='[[1wm9]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>


==About this Structure==
==See Also==
1WM9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/GTP_cyclohydrolase_I GTP cyclohydrolase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.16 3.5.4.16] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WM9 OCA].
*[[Cyclohydrolase 3D structures|Cyclohydrolase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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 (Tokyo). 2005 Sep;138(3):263-75. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16169877 16169877]
[[Category: Large Structures]]
[[Category: GTP cyclohydrolase I]]
[[Category: Thermus thermophilus HB8]]
[[Category: Single protein]]
[[Category: Tanaka Y]]
[[Category: Thermus thermophilus]]
[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
[[Category: Tanaka, Y.]]
[[Category: ZN]]
[[Category: beta barrel]]
[[Category: hydrolase]]
[[Category: pteridine]]
[[Category: riken structural genomics/proteomics initiative]]
[[Category: rsgi]]
[[Category: structural genomics]]
[[Category: tetrahydrobiopterin]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 00:14:16 2007''

Latest revision as of 16:32, 13 March 2024

Structure of GTP cyclohydrolase I from Thermus thermophilus HB8Structure of GTP cyclohydrolase I from Thermus thermophilus HB8

Structural highlights

1wm9 is a 5 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

Q5SH52_THET8

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1wm9, resolution 2.20Å

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