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| | ==Crystal structure of Escherichia coli ribosomal oxygenase YcfD== | | ==Crystal structure of Escherichia coli ribosomal oxygenase YcfD== |
| - | <StructureSection load='4nub' size='340' side='right' caption='[[4nub]], [[Resolution|resolution]] 2.70Å' scene=''> | + | <StructureSection load='4nub' size='340' side='right'caption='[[4nub]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4nub]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NUB OCA]. <br> | + | <table><tr><td colspan='2'>[[4nub]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NUB FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</td></tr> |
| - | <tr><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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b1128, JW1114, ycfD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4nub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nub OCA], [https://pdbe.org/4nub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nub RCSB], [https://www.ebi.ac.uk/pdbsum/4nub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nub ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr> | + | </table> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4nub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nub OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nub RCSB], [http://www.ebi.ac.uk/pdbsum/4nub PDBsum]</span></td></tr> | + | == Function == |
| - | <table> | + | [https://www.uniprot.org/uniprot/ROXA_ECOLI ROXA_ECOLI] Growth-regulating oxygenase that catalyzes the hydroxylation of ribosomal protein uL16 on 'Arg-81'.<ref>PMID:23103944</ref> <ref>PMID:24530688</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | Structure and Functional Analysis of YcfD, a Novel 2-Oxoglutarate/Fe-Dependent Oxygenase Involved in Translational Regulation in Escherichiacoli.,van Staalduinen L, Novakowski SK, Jia Z J Mol Biol. 2014 Feb 13. pii: S0022-2836(14)00074-6. doi:, 10.1016/j.jmb.2014.02.008. PMID:24530688<ref>PMID:24530688</ref> | | Structure and Functional Analysis of YcfD, a Novel 2-Oxoglutarate/Fe-Dependent Oxygenase Involved in Translational Regulation in Escherichiacoli.,van Staalduinen L, Novakowski SK, Jia Z J Mol Biol. 2014 Feb 13. pii: S0022-2836(14)00074-6. doi:, 10.1016/j.jmb.2014.02.008. PMID:24530688<ref>PMID:24530688</ref> |
| | | | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4nub" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: BSGI, Montreal-Kingston Bacterial Structural Genomics Initiative.]] | + | [[Category: Large Structures]] |
| - | [[Category: Jia, Z.]] | + | [[Category: Jia Z]] |
| - | [[Category: Staalduinen, L M.Van.]] | + | [[Category: Van staalduinen LM]] |
| - | [[Category: 2og/fe2+ dependent oxygenase]]
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| - | [[Category: Beta-barrel]]
| + | |
| - | [[Category: Bsgi]]
| + | |
| - | [[Category: Cupin]]
| + | |
| - | [[Category: Jelly roll]]
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| - | [[Category: Montreal-kingston bacterial structural genomics initiative]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Ribosomal protein l-16]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| Structural highlights
Function
ROXA_ECOLI Growth-regulating oxygenase that catalyzes the hydroxylation of ribosomal protein uL16 on 'Arg-81'.[1] [2]
Publication Abstract from PubMed
The 2-oxoglutarate (2OG)/Fe2+-dependent oxygenases (2OG oxygenases) are a large family of proteins that share a similar overall three-dimensional structure and catalyze a diverse array of oxidation reactions. The Jumonji C (JmjC)-domain-containing proteins represent an important subclass of the 2OG oxygenase family that typically catalyze protein hydroxylation; however, recently, other reactions have been identified, such as tRNA modification. The Escherichiacoli gene, ycfD, was predicted to be a JmjC-domain-containing protein of unknown function based on primary sequence. Recently, YcfD was determined to act as a ribosomal oxygenase, hydroxylating an arginine residue on the 50S ribosomal protein L-16 (RL-16). We have determined the crystal structure of YcfD at 2.7A resolution, revealing that YcfD is structurally similar to known JmjC proteins and possesses the characteristic double-stranded beta-helix fold or cupin domain. Separate from the cupin domain, an additional globular module termed alpha-helical arm mediates dimerization of YcfD. We further have shown that 2OG binds to YcfD using isothermal titration calorimetry and identified key binding residues using mutagenesis that, together with the iron location and structural similarity with other cupin family members, allowed identification of the active site. Structural homology to ribosomal assembly proteins combined with GST (glutathione S-transferase)-YcfD pull-down of a ribosomal protein and docking of RL-16 to the YcfD active site support the role of YcfD in regulation of bacterial ribosome assembly. Furthermore, overexpression of YcfD is shown to inhibit cell growth signifying a toxic effect on ribosome assembly.
Structure and Functional Analysis of YcfD, a Novel 2-Oxoglutarate/Fe-Dependent Oxygenase Involved in Translational Regulation in Escherichiacoli.,van Staalduinen L, Novakowski SK, Jia Z J Mol Biol. 2014 Feb 13. pii: S0022-2836(14)00074-6. doi:, 10.1016/j.jmb.2014.02.008. PMID:24530688[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ge W, Wolf A, Feng T, Ho CH, Sekirnik R, Zayer A, Granatino N, Cockman ME, Loenarz C, Loik ND, Hardy AP, Claridge TD, Hamed RB, Chowdhury R, Gong L, Robinson CV, Trudgian DC, Jiang M, Mackeen MM, McCullagh JS, Gordiyenko Y, Thalhammer A, Yamamoto A, Yang M, Liu-Yi P, Zhang Z, Schmidt-Zachmann M, Kessler BM, Ratcliffe PJ, Preston GM, Coleman ML, Schofield CJ. Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans. Nat Chem Biol. 2012 Dec;8(12):960-2. doi: 10.1038/nchembio.1093. Epub 2012 Oct, 28. PMID:23103944 doi:10.1038/nchembio.1093
- ↑ van Staalduinen L, Novakowski SK, Jia Z. Structure and Functional Analysis of YcfD, a Novel 2-Oxoglutarate/Fe-Dependent Oxygenase Involved in Translational Regulation in Escherichiacoli. J Mol Biol. 2014 Feb 13. pii: S0022-2836(14)00074-6. doi:, 10.1016/j.jmb.2014.02.008. PMID:24530688 doi:http://dx.doi.org/10.1016/j.jmb.2014.02.008
- ↑ van Staalduinen L, Novakowski SK, Jia Z. Structure and Functional Analysis of YcfD, a Novel 2-Oxoglutarate/Fe-Dependent Oxygenase Involved in Translational Regulation in Escherichiacoli. J Mol Biol. 2014 Feb 13. pii: S0022-2836(14)00074-6. doi:, 10.1016/j.jmb.2014.02.008. PMID:24530688 doi:http://dx.doi.org/10.1016/j.jmb.2014.02.008
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