|
|
| Line 3: |
Line 3: |
| | <StructureSection load='1v9f' size='340' side='right'caption='[[1v9f]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='1v9f' size='340' side='right'caption='[[1v9f]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1v9f]] is a 1 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=1V9F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1V9F FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1v9f]] is a 1 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=1V9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9F FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 1.7Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RLUD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=1v9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9f OCA], [https://pdbe.org/1v9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9f RCSB], [https://www.ebi.ac.uk/pdbsum/1v9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9f ProSAT]</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=1v9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9f OCA], [http://pdbe.org/1v9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v9f RCSB], [http://www.ebi.ac.uk/pdbsum/1v9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9f ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RLUD_ECOLI RLUD_ECOLI]] Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA. Isomerization occurs as a late step during the assembly of the large ribosomal subunit.<ref>PMID:11087118</ref> <ref>PMID:17937767</ref> | + | [https://www.uniprot.org/uniprot/RLUD_ECOLI RLUD_ECOLI] Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA. Isomerization occurs as a late step during the assembly of the large ribosomal subunit.<ref>PMID:11087118</ref> <ref>PMID:17937767</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 38: |
Line 37: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[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 synthase]]
| + | |
| - | [[Category: Rna binding]]
| + | |
| Structural highlights
Function
RLUD_ECOLI Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA. Isomerization occurs as a late step during the assembly of the large ribosomal subunit.[1] [2]
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wrzesinski J, Bakin A, Ofengand J, Lane BG. Isolation and properties of Escherichia coli 23S-RNA pseudouridine 1911, 1915, 1917 synthase (RluD). IUBMB Life. 2000 Jul;50(1):33-7. PMID:11087118 doi:http://dx.doi.org/10.1080/15216540050176566
- ↑ Leppik M, Peil L, Kipper K, Liiv A, Remme J. Substrate specificity of the pseudouridine synthase RluD in Escherichia coli. FEBS J. 2007 Nov;274(21):5759-66. Epub 2007 Oct 12. PMID:17937767 doi:http://dx.doi.org/10.1111/j.1742-4658.2007.06101.x
- ↑ 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
|
