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2yx0

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[[Image:2yx0.gif|left|200px]]
 
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{{Structure
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==Crystal structure of P. horikoshii TYW1==
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|PDB= 2yx0 |SIZE=350|CAPTION= <scene name='initialview01'>2yx0</scene>, resolution 2.21&Aring;
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<StructureSection load='2yx0' size='340' side='right'caption='[[2yx0]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[2yx0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX0 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2YX0 FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2yx0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx0 OCA], [http://pdbe.org/2yx0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yx0 RCSB], [http://www.ebi.ac.uk/pdbsum/2yx0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yx0 ProSAT], [http://www.topsan.org/Proteins/RSGI/2yx0 TOPSAN]</span></td></tr>
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|GENE=
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</table>
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|DOMAIN=
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== Function ==
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|RELATEDENTRY=
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[[http://www.uniprot.org/uniprot/TYW1_PYRHO TYW1_PYRHO]] Component of the wyosine derivatives biosynthesis pathway that catalyzes the condensation of N-methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine (imG-14) on guanosine-37 of tRNA(Phe).[HAMAP-Rule:MF_01921]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yx0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx0 OCA], [http://www.ebi.ac.uk/pdbsum/2yx0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2yx0 RCSB]</span>
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== Evolutionary Conservation ==
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}}
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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'''Crystal structure of P. horikoshii TYW1'''
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yx/2yx0_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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==Overview==
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2yx0 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
Wye bases are tricyclic bases that are found in archaeal and eukaryotic tRNAs. The most modified wye base, wybutosine, which appears at position 37 (the 3'-adjacent position to the anticodon), is known to be important for translational reading-frame maintenance. Saccharomyces cerevisiae TYW1 catalyzes the tri-ring-formation step in wye-base biosynthesis, with the substrate tRNA bearing N(1)-methylated G37. Here, the crystal structure of the archaeal TYW1 homologue from Pyrococcus horikoshii is reported at 2.2 A resolution. The amino-acid sequence of P. horikoshii TYW1 suggested that it is a radical-AdoMet enzyme and the tertiary structure of P. horikoshii TYW1 indeed shares the modified TIM-barrel structure found in other radical-AdoMet enzymes. Radical-AdoMet enzymes generally contain one or two iron-sulfur (FeS) clusters. The tertiary structure of P. horikoshii TYW1 revealed two FeS cluster sites, each containing three cysteine residues. One FeS cluster site was expected from the amino-acid sequence and the other involves cysteine residues that are dispersed throughout the sequence. The existence of two FeS clusters was confirmed from the anomalous Fourier electron-density map. By superposing the P. horikoshii TYW1 tertiary structure on those of other radical-AdoMet enzymes, the AdoMet molecule, which is necessary for the reactions of radical-AdoMet enzymes, was modelled in P. horikoshii TYW1. Surface plots of conservation rates and electrostatic potentials revealed the highly conserved and positively charged active-site hollow. On the basis of the surface properties, a docking model of P. horikoshii TYW1, the tRNA, the FeS clusters and the AdoMet molecule was constructed, with the nucleoside at position 37 of tRNA flipped out from the canonical tRNA structure.
Wye bases are tricyclic bases that are found in archaeal and eukaryotic tRNAs. The most modified wye base, wybutosine, which appears at position 37 (the 3'-adjacent position to the anticodon), is known to be important for translational reading-frame maintenance. Saccharomyces cerevisiae TYW1 catalyzes the tri-ring-formation step in wye-base biosynthesis, with the substrate tRNA bearing N(1)-methylated G37. Here, the crystal structure of the archaeal TYW1 homologue from Pyrococcus horikoshii is reported at 2.2 A resolution. The amino-acid sequence of P. horikoshii TYW1 suggested that it is a radical-AdoMet enzyme and the tertiary structure of P. horikoshii TYW1 indeed shares the modified TIM-barrel structure found in other radical-AdoMet enzymes. Radical-AdoMet enzymes generally contain one or two iron-sulfur (FeS) clusters. The tertiary structure of P. horikoshii TYW1 revealed two FeS cluster sites, each containing three cysteine residues. One FeS cluster site was expected from the amino-acid sequence and the other involves cysteine residues that are dispersed throughout the sequence. The existence of two FeS clusters was confirmed from the anomalous Fourier electron-density map. By superposing the P. horikoshii TYW1 tertiary structure on those of other radical-AdoMet enzymes, the AdoMet molecule, which is necessary for the reactions of radical-AdoMet enzymes, was modelled in P. horikoshii TYW1. Surface plots of conservation rates and electrostatic potentials revealed the highly conserved and positively charged active-site hollow. On the basis of the surface properties, a docking model of P. horikoshii TYW1, the tRNA, the FeS clusters and the AdoMet molecule was constructed, with the nucleoside at position 37 of tRNA flipped out from the canonical tRNA structure.
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==About this Structure==
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Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis.,Goto-Ito S, Ishii R, Ito T, Shibata R, Fusatomi E, Sekine SI, Bessho Y, Yokoyama S Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1059-68. Epub 2007, Sep 19. PMID:17881823<ref>PMID:17881823</ref>
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2YX0 is a [[Single protein]] structure of 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=2YX0 OCA].
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==Reference==
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Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis., Goto-Ito S, Ishii R, Ito T, Shibata R, Fusatomi E, Sekine SI, Bessho Y, Yokoyama S, Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1059-68. Epub 2007, Sep 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17881823 17881823]
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[[Category: Pyrococcus horikoshii]]
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[[Category: Single protein]]
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[[Category: Bessho, Y.]]
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[[Category: Fusatomi, E.]]
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[[Category: Goto-Ito, S.]]
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[[Category: Ishii, R.]]
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[[Category: Ito, T.]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Sekine, S.]]
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[[Category: Shibata, R.]]
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[[Category: Yokoyama, S.]]
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[[Category: metal binding protein]]
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[[Category: national project on protein structural and functional analyse]]
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[[Category: nppsfa]]
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[[Category: predicted trna modification enzyme]]
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[[Category: radical sam enzyme]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rsgi]]
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[[Category: structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:16:13 2008''
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2yx0" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Pyrococcus shinkaii]]
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[[Category: Large Structures]]
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[[Category: Bessho, Y]]
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[[Category: Fusatomi, E]]
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[[Category: Goto-Ito, S]]
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[[Category: Ishii, R]]
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[[Category: Ito, T]]
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[[Category: Structural genomic]]
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[[Category: Sekine, S]]
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[[Category: Shibata, R]]
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[[Category: Yokoyama, S]]
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[[Category: Metal binding protein]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Nppsfa]]
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[[Category: Predicted trna modification enzyme]]
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[[Category: Radical sam enzyme]]
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[[Category: Rsgi]]

Current revision

Crystal structure of P. horikoshii TYW1

PDB ID 2yx0

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