1v9k

From Proteopedia

(Difference between revisions)

Current revision

The crystal structure of the catalytic domain of pseudouridine synthase RluC from Escherichia coli

Structural highlights

1v9k 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:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RLUC_ECOLI Responsible for synthesis of pseudouridine from uracil at positions 955, 2504 and 2580 in 23S ribosomal RNA.

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 most frequent modification of RNA, the conversion of uridine bases to pseudouridines, is found in all living organisms and often in highly conserved locations in ribosomal and transfer RNA. RluC and RluD are homologous enzymes which each convert three specific uridine bases in Escherichia coli ribosomal 23S RNA to pseudouridine: bases 955, 2504, and 2580 in the case of RluC and 1911, 1915, and 1917 in the case of RluD. Both have an N-terminal S4 RNA binding domain. While the loss of RluC has little phenotypic effect, loss of RluD results in a much reduced growth rate. We have determined the crystal structures of the catalytic domain of RluC, and full-length RluD. The S4 domain of RluD appears to be highly flexible or unfolded and is completely invisible in the electron density map. Despite the conserved topology shared by the two proteins, the surface shape and charge distribution are very different. The models suggest significant differences in substrate binding by different pseudouridine synthases.

Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli.,Mizutani K, Machida Y, Unzai S, Park SY, Tame JR Biochemistry. 2004 Apr 20;43(15):4454-63. PMID:15078091^[1]

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

References

↑ Mizutani K, Machida Y, Unzai S, Park SY, Tame JR. Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli. Biochemistry. 2004 Apr 20;43(15):4454-63. PMID:15078091 doi:10.1021/bi036079c

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1v9k"

@@ Line 3: / Line 3: @@
 <StructureSection load='1v9k' size='340' side='right'caption='[[1v9k]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1v9k]] 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=1V9K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1V9K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1v9k]] 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=1V9K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9K FirstGlance]. <br>
-</td></tr><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>
+</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='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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RLUC ([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=1v9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9k OCA], [https://pdbe.org/1v9k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9k RCSB], [https://www.ebi.ac.uk/pdbsum/1v9k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9k 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=1v9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9k OCA], [http://pdbe.org/1v9k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v9k RCSB], [http://www.ebi.ac.uk/pdbsum/1v9k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9k ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RLUC_ECOLI RLUC_ECOLI]] Responsible for synthesis of pseudouridine from uracil at positions 955, 2504 and 2580 in 23S ribosomal RNA.
+[https://www.uniprot.org/uniprot/RLUC_ECOLI RLUC_ECOLI] Responsible for synthesis of pseudouridine from uracil at positions 955, 2504 and 2580 in 23S ribosomal RNA.
 == 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/v9/1v9k_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: Machida Y]]
-[[Category: Machida, Y]]
+[[Category: Mizutani K]]
-[[Category: Mizutani, K]]
+[[Category: Park S-Y]]
-[[Category: Park, S Y]]
+[[Category: Tame JRH]]
-[[Category: Tame, J R.H]]
+[[Category: Unzai S]]
-[[Category: Unzai, S]]
-[[Category: Lyase]]
-[[Category: Pseudouridine syntase]]
-[[Category: Rna binding]]

1v9k

From Proteopedia

Current revision

The crystal structure of the catalytic domain of pseudouridine synthase RluC from Escherichia coli

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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