1szw: Difference between revisions

Latest revision as of 08:49, 6 November 2024

Crystal structure of E. coli tRNA pseudouridine synthase TruD

Structural highlights

1szw is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TRUD_ECOLI Responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs.^[1]

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

Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine in structural RNA. The pseudouridine synthase TruD, that modifies U13 in tRNA, belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life. We report here the crystal structure of Escherichia coli TruD at 2.0 A resolution. The structure reveals an overall V-shaped molecule with an RNA-binding cleft formed between two domains: a catalytic domain and an insertion domain. The catalytic domain has a fold similar to that of the catalytic domains of previously characterised pseudouridine synthases, whereas the insertion domain displays a novel fold.

X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold.,Ericsson UB, Nordlund P, Hallberg BM FEBS Lett. 2004 May 7;565(1-3):59-64. PMID:15135053^[2]

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

References

↑ Kaya Y, Ofengand J. A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. RNA. 2003 Jun;9(6):711-21. PMID:12756329
↑ Ericsson UB, Nordlund P, Hallberg BM. X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. FEBS Lett. 2004 May 7;565(1-3):59-64. PMID:15135053 doi:10.1016/j.febslet.2004.03.085

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kaya Y, Ofengand J. A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. RNA. 2003 Jun;9(6):711-21. PMID:12756329

[2] Ericsson UB, Nordlund P, Hallberg BM. X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. FEBS Lett. 2004 May 7;565(1-3):59-64. PMID:15135053 doi:10.1016/j.febslet.2004.03.085

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='1szw' size='340' side='right'caption='[[1szw]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1szw]] 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=1SZW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SZW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1szw]] 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=1SZW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SZW FirstGlance]. <br>
-</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>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1sb7|1sb7]], [[1si7|1si7]]</div></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></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TRUD ([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=1szw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szw OCA], [https://pdbe.org/1szw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1szw RCSB], [https://www.ebi.ac.uk/pdbsum/1szw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1szw ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1szw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1szw OCA], [http://pdbe.org/1szw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1szw RCSB], [http://www.ebi.ac.uk/pdbsum/1szw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1szw ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TRUD_ECOLI TRUD_ECOLI]] Responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs.<ref>PMID:12756329</ref>
+[https://www.uniprot.org/uniprot/TRUD_ECOLI TRUD_ECOLI] Responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs.<ref>PMID:12756329</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sz/1szw_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>
    </jmolCheckbox>
@@ Line 39: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Pseudouridylate synthase]]
+[[Category: Ericsson UB]]
-[[Category: Ericsson, U B]]
+[[Category: Hallberg BM]]
-[[Category: Hallberg, B M]]
+[[Category: Nordlund P]]
-[[Category: Nordlund, P]]
-[[Category: SPINE, Structural Proteomics in Europe]]
-[[Category: Lyase]]
-[[Category: Novel fold]]
-[[Category: Pseudouridine synthase]]
-[[Category: Rna modification]]
-[[Category: Spine]]
-[[Category: Structural genomic]]
-[[Category: Structural proteomics in europe]]
-[[Category: Trud]]

1szw: Difference between revisions

Latest revision as of 08:49, 6 November 2024

Crystal structure of E. coli tRNA pseudouridine synthase TruD

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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