2z2u: Difference between revisions

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[[Image:2z2u.gif|left|200px]]


{{Structure
==Crystal structure of archaeal TYW1==
|PDB= 2z2u |SIZE=350|CAPTION= <scene name='initialview01'>2z2u</scene>, resolution 2.40&Aring;
<StructureSection load='2z2u' size='340' side='right'caption='[[2z2u]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[2z2u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z2U FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
|GENE=  
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2z2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z2u OCA], [https://pdbe.org/2z2u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z2u RCSB], [https://www.ebi.ac.uk/pdbsum/2z2u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z2u ProSAT]</span></td></tr>
|DOMAIN=
</table>
|RELATEDENTRY=
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z2u OCA], [http://www.ebi.ac.uk/pdbsum/2z2u PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2z2u RCSB]</span>
[https://www.uniprot.org/uniprot/TYW1_METJA TYW1_METJA] 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]<ref>PMID:22026549</ref>
}}
== Evolutionary Conservation ==
 
[[Image:Consurf_key_small.gif|200px|right]]
'''Crystal structure of archaeal TYW1'''
Check<jmol>
 
  <jmolCheckbox>
 
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z2/2z2u_consurf.spt"</scriptWhenChecked>
==Overview==
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
Wyosine and its derivatives, such as wybutosine, found in eukaryotic and archaeal tRNAs, are tricyclic hypermodified nucleosides. In eukaryotes, wybutosine exists exclusively in position 37, 3'-adjacent to the anticodon, of tRNA(Phe), where it ensures correct translation by stabilizing the codon-anticodon base-pairing during the ribosomal decoding process. Recent studies revealed that the wyosine biosynthetic pathway consists of multistep enzymatic reactions starting from a guanosine residue. Among these steps, TYW1 catalyzes the second step to form the tricyclic ring structure, by cyclizing N(1)-methylguanosine. In this study, we solved the crystal structure of TYW1 from Methanocaldococcus jannaschii at 2.4 A resolution. TYW1 assumes an incomplete TIM barrel with (alpha/beta)(6) topology, which closely resembles the reported structures of radical SAM enzymes. Hence, TYW1 was considered to catalyze the cyclization reaction by utilizing the radical intermediate. Comparison with other radical SAM enzymes allowed us to build a model structure complexed with S-adenosylmethionine and two [4Fe-4S] clusters. Mutational analyses in yeast supported the validity of this complex model structure, which provides a structural insight into the radical reaction involving two [4Fe-4S] clusters to create a complex tricyclic base.
    <text>to colour the structure by Evolutionary Conservation</text>
 
  </jmolCheckbox>
==About this Structure==
</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=2z2u ConSurf].
2Z2U is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2U OCA].  
<div style="clear:both"></div>
 
== References ==
==Reference==
<references/>
Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA., Suzuki Y, Noma A, Suzuki T, Senda M, Senda T, Ishitani R, Nureki O, J Mol Biol. 2007 Oct 5;372(5):1204-14. Epub 2007 Jul 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17727881 17727881]
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Single protein]]
[[Category: Ishitani R]]
[[Category: Ishitani, R.]]
[[Category: Nureki O]]
[[Category: Nureki, O.]]
[[Category: Suzuki Y]]
[[Category: Suzuki, Y.]]
[[Category: metal binding protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:17:53 2008''

Latest revision as of 13:55, 13 March 2024

Crystal structure of archaeal TYW1

2z2u, resolution 2.40Å

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