2d1p: Difference between revisions

Revision as of 06:18, 30 May 2018

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

Structural highlights

2d1p is a 9 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	SO4
Gene:	yheN ("Bacillus coli" Migula 1895), yheM ("Bacillus coli" Migula 1895), yheL ("Bacillus coli" Migula 1895)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] [TUSB_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.^[2] [TUSC_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.^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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:16472754^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell. 2006 Jan 6;21(1):97-108. PMID:16387657 doi:https://dx.doi.org/S1097-2765(05)01761-2
↑ Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell. 2006 Jan 6;21(1):97-108. PMID:16387657 doi:https://dx.doi.org/S1097-2765(05)01761-2
↑ Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell. 2006 Jan 6;21(1):97-108. PMID:16387657 doi:https://dx.doi.org/S1097-2765(05)01761-2
↑ Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O. Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex. Structure. 2006 Feb;14(2):357-66. PMID:16472754 doi:10.1016/j.str.2005.11.009

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell. 2006 Jan 6;21(1):97-108. PMID:16387657 doi:https://dx.doi.org/S1097-2765(05)01761-2

[2] Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell. 2006 Jan 6;21(1):97-108. PMID:16387657 doi:https://dx.doi.org/S1097-2765(05)01761-2

[3] Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell. 2006 Jan 6;21(1):97-108. PMID:16387657 doi:https://dx.doi.org/S1097-2765(05)01761-2

[4] Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O. Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex. Structure. 2006 Feb;14(2):357-66. PMID:16472754 doi:10.1016/j.str.2005.11.009

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification==
 <StructureSection load='2d1p' size='340' side='right' caption='[[2d1p]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yheN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yheM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yheL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [http://pdbe.org/2d1p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [http://www.ebi.ac.uk/pdbsum/2d1p PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [http://pdbe.org/2d1p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [http://www.ebi.ac.uk/pdbsum/2d1p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1p ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/2d1p_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/2d1p_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/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=2d1p ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">

2d1p: Difference between revisions

Revision as of 06:18, 30 May 2018

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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