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==Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 at 1.65 A resolution==
==Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 at 1.65 A resolution==
<StructureSection load='2dek' size='340' side='right' caption='[[2dek]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
<StructureSection load='2dek' size='340' side='right'caption='[[2dek]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2dek]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DEK FirstGlance]. <br>
<table><tr><td colspan='2'>[[2dek]] 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=2DEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DEK FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><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]] 1.65&#8491;</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dphB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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=2dek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dek OCA], [https://pdbe.org/2dek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dek RCSB], [https://www.ebi.ac.uk/pdbsum/2dek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dek ProSAT], [https://www.topsan.org/Proteins/RSGI/2dek TOPSAN]</span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dek OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dek RCSB], [http://www.ebi.ac.uk/pdbsum/2dek PDBsum], [http://www.topsan.org/Proteins/RSGI/2dek TOPSAN]</span></td></tr>
</table>
<table>
== Function ==
[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>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/2dek_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/2dek_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata ConSurf].
</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=2dek ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Diphthine synthase]]
[[Category: Large Structures]]
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii OT3]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Shimizu K]]
[[Category: Shimizu, K.]]
[[Category: Alpha/beta fold]]
[[Category: Antiparallel beta-sheet]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Transferase]]

Latest revision as of 11:26, 25 October 2023

Crystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 at 1.65 A resolutionCrystal structure of project ID PH0725 from Pyrococcus horikoshii OT3 at 1.65 A resolution

Structural highlights

2dek 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 1.65Å
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.

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

2dek, resolution 1.65Å

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