2dv4: Difference between revisions

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New page: left|200px<br /><applet load="2dv4" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dv4, resolution 2.20Å" /> '''Crystal structure of...
 
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[[Image:2dv4.jpg|left|200px]]<br /><applet load="2dv4" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2dv4, resolution 2.20&Aring;" />
'''Crystal structure of Leu65 to Gln mutant of Diphthine synthase'''<br />


==About this Structure==
==Crystal structure of Leu65 to Gln mutant of Diphthine synthase==
2DV4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] with SO4, CL, SAH, MES and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Diphthine_synthase Diphthine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.98 2.1.1.98] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DV4 OCA].
<StructureSection load='2dv4' size='340' side='right'caption='[[2dv4]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
[[Category: Diphthine synthase]]
== Structural highlights ==
[[Category: Pyrococcus horikoshii]]
<table><tr><td colspan='2'>[[2dv4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DV4 FirstGlance]. <br>
[[Category: Single protein]]
</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>
[[Category: Kunishima, N.]]
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
[[Category: Matsuura, Y.]]
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dv4 OCA], [https://pdbe.org/2dv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dv4 RCSB], [https://www.ebi.ac.uk/pdbsum/2dv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dv4 ProSAT], [https://www.topsan.org/Proteins/RSGI/2dv4 TOPSAN]</span></td></tr>
[[Category: Mizutani, H.]]
</table>
[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
== Function ==
[[Category: CL]]
[https://www.uniprot.org/uniprot/DPHB_PYRHO DPHB_PYRHO] S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the trimethylation of the amino group of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine. The three successive methylation reactions represent the second step of diphthamide biosynthesis.<ref>PMID:20873788</ref>
[[Category: GOL]]
== Evolutionary Conservation ==
[[Category: MES]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: SAH]]
Check<jmol>
[[Category: SO4]]
  <jmolCheckbox>
[[Category: national project on protein structural and functional analyses]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/2dv4_consurf.spt"</scriptWhenChecked>
[[Category: nppsfa]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: riken structural genomics/proteomics initiative]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: rsgi]]
  </jmolCheckbox>
[[Category: structural genomics]]
</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=2dv4 ConSurf].
[[Category: transferase]]
<div style="clear:both"></div>


''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:47:55 2007''
==See Also==
*[[Diphthine synthase|Diphthine synthase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus horikoshii OT3]]
[[Category: Kunishima N]]
[[Category: Matsuura Y]]
[[Category: Mizutani H]]

Latest revision as of 11:30, 25 October 2023

Crystal structure of Leu65 to Gln mutant of Diphthine synthaseCrystal structure of Leu65 to Gln mutant of Diphthine synthase

Structural highlights

2dv4 is a 2 chain structure with sequence from Pyrococcus horikoshii OT3. 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

DPHB_PYRHO S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the trimethylation of the amino group of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine. The three successive methylation reactions represent the second step of diphthamide biosynthesis.[1]

Evolutionary Conservation

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

See Also

References

  1. ↑ Zhu X, Kim J, Su X, Lin H. Reconstitution of diphthine synthase activity in vitro. Biochemistry. 2010 Nov 9;49(44):9649-57. doi: 10.1021/bi100812h. PMID:20873788 doi:http://dx.doi.org/10.1021/bi100812h

2dv4, resolution 2.20Å

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