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| | ==THE STRUCTURE OF THE YRDC GENE PRODUCT FROM E.COLI== | | ==THE STRUCTURE OF THE YRDC GENE PRODUCT FROM E.COLI== |
| - | <StructureSection load='1hru' size='340' side='right' caption='[[1hru]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='1hru' size='340' side='right'caption='[[1hru]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1hru]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HRU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1HRU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1hru]] is a 2 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=1HRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HRU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YRDC ([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'>[https://proteopedia.org/fgij/fg.htm?mol=1hru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hru OCA], [https://pdbe.org/1hru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hru RCSB], [https://www.ebi.ac.uk/pdbsum/1hru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hru ProSAT], [https://www.topsan.org/Proteins/MCSG/1hru TOPSAN]</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=1hru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hru OCA], [http://pdbe.org/1hru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1hru RCSB], [http://www.ebi.ac.uk/pdbsum/1hru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1hru ProSAT], [http://www.topsan.org/Proteins/MCSG/1hru TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RIMN_ECOLI RIMN_ECOLI]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Binds ATP, and to fully modified tRNA(Thr) and partially modified tRNA(Thr). Could also be required for the maturation of 16S rRNA. Binds to double-stranded RNA but does not interact tightly with either of the ribosomal subunits, or the 70S particles.<ref>PMID:15716138</ref> <ref>PMID:19287007</ref> | + | [https://www.uniprot.org/uniprot/TSAC_ECOLI TSAC_ECOLI] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, bicarbonate/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of pyrophosphate. Is also able to catalyze the reverse reaction in vitro, i.e. the formation of ATP from TC-AMP and PPi. Shows higher affinity for the full-length tRNA(Thr) lacking only the t(6)A37 modification than for its fully modified counterpart. Could also be required for the maturation of 16S rRNA. Binds to double-stranded RNA but does not interact tightly with either of the ribosomal subunits, or the 70S particles.[HAMAP-Rule:MF_01852]<ref>PMID:15716138</ref> <ref>PMID:19287007</ref> <ref>PMID:21285948</ref> <ref>PMID:22378793</ref> <ref>PMID:23072323</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hr/1hru_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hr/1hru_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Anderson, W F]] | + | [[Category: Large Structures]] |
| - | [[Category: Bushueva, T]] | + | [[Category: Anderson WF]] |
| - | [[Category: Egli, M]] | + | [[Category: Bushueva T]] |
| - | [[Category: Joachimiak, A]] | + | [[Category: Egli M]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Joachimiak A]] |
| - | [[Category: Sanishvili, R]] | + | [[Category: Sanishvili R]] |
| - | [[Category: Teplova, M]] | + | [[Category: Teplova M]] |
| - | [[Category: Tereshko, V]] | + | [[Category: Tereshko V]] |
| - | [[Category: Mcsg]]
| + | |
| - | [[Category: Protein folding]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Rna]]
| + | |
| - | [[Category: Sua5]]
| + | |
| - | [[Category: Unknown function]]
| + | |
| - | [[Category: Yrdc]]
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| Structural highlights
Function
TSAC_ECOLI Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, bicarbonate/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of pyrophosphate. Is also able to catalyze the reverse reaction in vitro, i.e. the formation of ATP from TC-AMP and PPi. Shows higher affinity for the full-length tRNA(Thr) lacking only the t(6)A37 modification than for its fully modified counterpart. Could also be required for the maturation of 16S rRNA. Binds to double-stranded RNA but does not interact tightly with either of the ribosomal subunits, or the 70S particles.[HAMAP-Rule:MF_01852][1] [2] [3] [4] [5]
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
The yrdC family of genes codes for proteins that occur both independently and as a domain in proteins that have been implicated in regulation. An example for the latter case is the sua5 gene from yeast. SuaS was identified as a suppressor of a translation initiation defect in cytochrome c and is required for normal growth in yeast (Na JG, Pinto I, Hampsey M, 1992, Genetics 11:791-801). However, the function of the Sua5 protein remains unknown; Sua5 could act either at the transcriptional or the posttranscriptional levels to compensate for an aberrant translation start codon in the cyc gene. To potentially learn more about the function of YrdC and proteins featuring this domain, the crystal structure of the YrdC protein from Escherichia coli was determined at a resolution of 2.0 A. YrdC adopts a new fold with no obvious similarity to those of other proteins with known three-dimensional (3D) structure. The protein features a large concave surface on one side that exhibits a positive electrostatic potential. The dimensions of this depression, its curvature, and the fact that conserved basic amino acids are located at its floor suggest that YrdC may be a nucleic acid binding protein. An investigation of YrdC's binding affinities for single- and double-stranded RNA and DNA fragments as well as tRNAs demonstrates that YrdC binds preferentially to double-stranded RNA. Our work provides evidence that 3D structures of functionally uncharacterized gene products with unique sequences can yield novel folds and functional insights.
The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding.,Teplova M, Tereshko V, Sanishvili R, Joachimiak A, Bushueva T, Anderson WF, Egli M Protein Sci. 2000 Dec;9(12):2557-66. PMID:11206077[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kaczanowska M, Ryden-Aulin M. The YrdC protein--a putative ribosome maturation factor. Biochim Biophys Acta. 2005 Feb 14;1727(2):87-96. Epub 2004 Dec 31. PMID:15716138 doi:http://dx.doi.org/S0167-4781(04)00263-5
- ↑ El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crecy-Lagard V. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. Nucleic Acids Res. 2009 May;37(9):2894-909. doi: 10.1093/nar/gkp152. Epub 2009, Mar 13. PMID:19287007 doi:http://dx.doi.org/10.1093/nar/gkp152
- ↑ El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG, de Crecy-Lagard V. A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J. 2011 Mar 2;30(5):882-93. doi: 10.1038/emboj.2010.363. Epub 2011 Feb 1. PMID:21285948 doi:10.1038/emboj.2010.363
- ↑ Deutsch C, El Yacoubi B, de Crecy-Lagard V, Iwata-Reuyl D. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem. 2012 Apr 20;287(17):13666-73. doi: 10.1074/jbc.M112.344028. Epub, 2012 Feb 29. PMID:22378793 doi:http://dx.doi.org/10.1074/jbc.M112.344028
- ↑ Lauhon CT. Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Biochemistry. 2012 Nov 6;51(44):8950-63. doi: 10.1021/bi301233d. Epub 2012 Oct, 26. PMID:23072323 doi:http://dx.doi.org/10.1021/bi301233d
- ↑ Teplova M, Tereshko V, Sanishvili R, Joachimiak A, Bushueva T, Anderson WF, Egli M. The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. Protein Sci. 2000 Dec;9(12):2557-66. PMID:11206077
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