2d1p: Difference between revisions

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[[Image:2d1p.gif|left|200px]]


{{Structure
==crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification==
|PDB= 2d1p |SIZE=350|CAPTION= <scene name='initialview01'>2d1p</scene>, resolution 2.15&Aring;
<StructureSection load='2d1p' size='340' side='right'caption='[[2d1p]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>
<table><tr><td colspan='2'>[[2d1p]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1P 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]] 2.15&#8491;</td></tr>
|GENE= yheN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), yheM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), yheL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [https://pdbe.org/2d1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [https://www.ebi.ac.uk/pdbsum/2d1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1p ProSAT]</span></td></tr>
 
</table>
'''crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification'''
== Function ==
 
[https://www.uniprot.org/uniprot/TUSD_ECOLI TUSD_ECOLI] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Accepts sulfur from TusA and transfers it in turn to TusE.<ref>PMID:16387657</ref>
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
Uridine at wobble position 34 of tRNA(Lys), tRNA(Glu), and tRNA(Gln) is exclusively modified into 2-thiouridine (s2U), which is crucial for both precise codon recognition and recognition by the cognate aminoacyl-tRNA synthetases. Recent Escherichia coli genetic studies revealed that the products of five novel genes, tusABCDE, function in the s2U modification. Here, we solved the 2.15 angstroms crystal structure of the E. coli TusBCD complex, a sulfur transfer mediator, forming a heterohexamer composed of a dimer of the heterotrimer. Structure-based sequence alignment suggested two putative active site Cys residues, Cys79 (in TusC) and Cys78 (in TusD), which are exposed on the hexameric complex. In vivo mutant analyses revealed that only Cys78, in the TusD subunit, participates in sulfur transfer during the s2U modification process. Since the single Cys acts as a catalytic residue, we proposed that TusBCD mediates sulfur relay via a putative persulfide state of the TusD subunit.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/2d1p_consurf.spt"</scriptWhenChecked>
2D1P is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex., Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O, Structure. 2006 Feb;14(2):357-66. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16472754 16472754]
</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=2d1p ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Fukai, S.]]
[[Category: Fukai S]]
[[Category: Ikeuchi, Y.]]
[[Category: Ikeuchi Y]]
[[Category: Numata, T.]]
[[Category: Numata T]]
[[Category: Nureki, O.]]
[[Category: Nureki O]]
[[Category: Suzuki, T.]]
[[Category: Suzuki T]]
[[Category: SO4]]
[[Category: structural genomic]]
[[Category: sulfur transfer]]
[[Category: trna modification]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:22:12 2008''

Latest revision as of 13:45, 13 March 2024

crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification

2d1p, resolution 2.15Å

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