3eph: Difference between revisions

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[[Image:3eph.jpg|left|200px]]


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==Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism==
The line below this paragraph, containing "STRUCTURE_3eph", creates the "Structure Box" on the page.
<StructureSection load='3eph' size='340' side='right'caption='[[3eph]], [[Resolution|resolution]] 2.95&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'>[[3eph]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EPH 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]] 2.95&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
{{STRUCTURE_3eph| PDB=3eph |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3eph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eph OCA], [https://pdbe.org/3eph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eph RCSB], [https://www.ebi.ac.uk/pdbsum/3eph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eph ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MOD5_YEAST MOD5_YEAST] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP).<ref>PMID:3031456</ref> <ref>PMID:10618371</ref> <ref>PMID:21873461</ref>
== 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/ep/3eph_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=3eph ConSurf].
<div style="clear:both"></div>


===Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism===
==See Also==
 
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
 
== References ==
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</StructureSection>
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[[Category: Large Structures]]
{{ABSTRACT_PUBMED_18852462}}
 
==About this Structure==
3EPH is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA].
 
==Reference==
Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism., Zhou C, Huang RH, Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16142-7. Epub 2008 Oct 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18852462 18852462]
[[Category: Protein complex]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: TRNA isopentenyltransferase]]
[[Category: Huang RH]]
[[Category: Huang, R H.]]
[[Category: Zhou C]]
[[Category: Zhou, C.]]
[[Category: Alternative initiation]]
[[Category: Atp-binding]]
[[Category: Cytoplasm]]
[[Category: Mitochondrion]]
[[Category: Nucleotide-binding]]
[[Category: Nucleus]]
[[Category: Transferase]]
[[Category: Transferase/rna complex]]
[[Category: Trna processing]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov  5 12:59:38 2008''

Latest revision as of 12:48, 21 February 2024

Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanismCrystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism

Structural highlights

3eph is a 4 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.95Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MOD5_YEAST Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP).[1] [2] [3]

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. ↑ Dihanich ME, Najarian D, Clark R, Gillman EC, Martin NC, Hopper AK. Isolation and characterization of MOD5, a gene required for isopentenylation of cytoplasmic and mitochondrial tRNAs of Saccharomyces cerevisiae. Mol Cell Biol. 1987 Jan;7(1):177-84. PMID:3031456
  2. ↑ Benko AL, Vaduva G, Martin NC, Hopper AK. Competition between a sterol biosynthetic enzyme and tRNA modification in addition to changes in the protein synthesis machinery causes altered nonsense suppression. Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):61-6. PMID:10618371
  3. ↑ Lamichhane TN, Blewett NH, Maraia RJ. Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases. RNA. 2011 Oct;17(10):1846-57. doi: 10.1261/rna.2628611. Epub 2011 Aug 26. PMID:21873461 doi:http://dx.doi.org/10.1261/rna.2628611

3eph, resolution 2.95Å

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