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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]] 2.70&Aring;' scene=''>
<StructureSection load='4nub' size='340' side='right'caption='[[4nub]], [[Resolution|resolution]] 2.70&Aring;' 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]] 2.7&#8491;</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&reg;/PubMed&reg;, 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]]
[[Category: Beta-barrel]]
[[Category: Bsgi]]
[[Category: Cupin]]
[[Category: Jelly roll]]
[[Category: Montreal-kingston bacterial structural genomics initiative]]
[[Category: Oxidoreductase]]
[[Category: Ribosomal protein l-16]]
[[Category: Structural genomic]]
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