1hru: Difference between revisions

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-{{Seed}}
-[[Image:1hru.png|left|200px]]
-<!--
+==THE STRUCTURE OF THE YRDC GENE PRODUCT FROM E.COLI==
-The line below this paragraph, containing "STRUCTURE_1hru", creates the "Structure Box" on the page.
+<StructureSection load='1hru' size='340' side='right'caption='[[1hru]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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&#8491;</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>
-{{STRUCTURE_1hru|  PDB=1hru  |  SCENE=  }}
+<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>
+</table>
+== Function ==
+[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 ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <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/initialview03.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/main_output.php?pdb_ID=1hru ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== 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 E.COLI===
+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<ref>PMID:11206077</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_11206077}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1hru" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11206077 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11206077}}
+__TOC__
+</StructureSection>
-==About this Structure==
-HRU is a [[Single protein]] structure of sequence 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=1HRU OCA].
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/11206077 11206077]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Anderson, W F.]]
+[[Category: Anderson WF]]
-[[Category: Bushueva, T.]]
+[[Category: Bushueva T]]
-[[Category: Egli, M.]]
+[[Category: Egli M]]
-[[Category: Joachimiak, A.]]
+[[Category: Joachimiak A]]
-[[Category: MCSG, Midwest Center for Structural Genomics.]]
+[[Category: Sanishvili R]]
-[[Category: Sanishvili, R.]]
+[[Category: Teplova M]]
-[[Category: Teplova, M.]]
+[[Category: Tereshko V]]
-[[Category: Tereshko, V.]]
-[[Category: Mcsg]]
-[[Category: Midwest center for structural genomic]]
-[[Category: Protein folding]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Rna]]
-[[Category: Structural genomic]]
-[[Category: Sua5]]
-[[Category: Yrdc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 08:36:04 2008''