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4nhx

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Current revision

Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with N-oxalylglycine (NOG)

Structural highlights

4nhx is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.105Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OGFD1_HUMAN Prolyl 3-hydroxylase that catalyzes 3-hydroxylation of 'Pro-62' of small ribosomal subunit RPS23, thereby regulating protein translation termination efficiency. Involved in stress granule formation.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Post-translational ribosomal protein hydroxylation is catalyzed by 2-oxoglutarate (2OG) and ferrous iron dependent oxygenases, and occurs in prokaryotes and eukaryotes. OGFOD1 catalyzes trans-3 prolyl hydroxylation at Pro62 of the small ribosomal subunit protein uS12 (RPS23) and is conserved from yeasts to humans. We describe crystal structures of the human uS12 prolyl 3-hydroxylase (OGFOD1) and its homolog from Saccharomyces cerevisiae (Tpa1p): OGFOD1 in complex with the broad-spectrum 2OG oxygenase inhibitors; N-oxalylglycine (NOG) and pyridine-2,4-dicarboxylate (2,4-PDCA) to 2.1 and 2.6 A resolution, respectively; and Tpa1p in complex with NOG, 2,4-PDCA, and 1-chloro-4-hydroxyisoquinoline-3-carbonylglycine (a more selective prolyl hydroxylase inhibitor) to 2.8, 1.9, and 1.9 A resolution, respectively. Comparison of uS12 hydroxylase structures with those of other prolyl hydroxylases, including the human hypoxia-inducible factor (HIF) prolyl hydroxylases (PHDs), reveals differences between the prolyl 3- and prolyl 4-hydroxylase active sites, which can be exploited for developing selective inhibitors of the different subfamilies.

Structure of the Ribosomal Oxygenase OGFOD1 Provides Insights into the Regio- and Stereoselectivity of Prolyl Hydroxylases.,Horita S, Scotti JS, Thinnes C, Mottaghi-Taromsari YS, Thalhammer A, Ge W, Aik W, Loenarz C, Schofield CJ, McDonough MA Structure. 2015 Feb 19. pii: S0969-2126(15)00038-6. doi:, 10.1016/j.str.2015.01.014. PMID:25728928^[4]

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

References

↑ Wehner KA, Schutz S, Sarnow P. OGFOD1, a novel modulator of eukaryotic translation initiation factor 2alpha phosphorylation and the cellular response to stress. Mol Cell Biol. 2010 Apr;30(8):2006-16. doi: 10.1128/MCB.01350-09. Epub 2010 Feb, 12. PMID:20154146 doi:http://dx.doi.org/10.1128/MCB.01350-09
↑ Singleton RS, Liu-Yi P, Formenti F, Ge W, Sekirnik R, Fischer R, Adam J, Pollard PJ, Wolf A, Thalhammer A, Loenarz C, Flashman E, Yamamoto A, Coleman ML, Kessler BM, Wappner P, Schofield CJ, Ratcliffe PJ, Cockman ME. OGFOD1 catalyzes prolyl hydroxylation of RPS23 and is involved in translation control and stress granule formation. Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4031-6. doi:, 10.1073/pnas.1314482111. Epub 2014 Feb 18. PMID:24550447 doi:http://dx.doi.org/10.1073/pnas.1314482111
↑ Loenarz C, Sekirnik R, Thalhammer A, Ge W, Spivakovsky E, Mackeen MM, McDonough MA, Cockman ME, Kessler BM, Ratcliffe PJ, Wolf A, Schofield CJ. Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy. Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4019-24. doi:, 10.1073/pnas.1311750111. Epub 2014 Feb 18. PMID:24550462 doi:http://dx.doi.org/10.1073/pnas.1311750111
↑ Horita S, Scotti JS, Thinnes C, Mottaghi-Taromsari YS, Thalhammer A, Ge W, Aik W, Loenarz C, Schofield CJ, McDonough MA. Structure of the Ribosomal Oxygenase OGFOD1 Provides Insights into the Regio- and Stereoselectivity of Prolyl Hydroxylases. Structure. 2015 Feb 19. pii: S0969-2126(15)00038-6. doi:, 10.1016/j.str.2015.01.014. PMID:25728928 doi:http://dx.doi.org/10.1016/j.str.2015.01.014

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4nhx"

Categories: Homo sapiens | Large Structures | Horita S | McDonough MA | Schofield CJ

@@ Line 1: / Line 1: @@
 ==Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with N-oxalylglycine (NOG)==
-<StructureSection load='4nhx' size='340' side='right' caption='[[4nhx]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='4nhx' size='340' side='right'caption='[[4nhx]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4nhx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NHX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NHX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4nhx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NHX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NHX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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]] 2.105&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4nhy|4nhy]], [[4nhn|4nhn]], [[4nhm|4nhm]], [[4nhl|4nhl]], [[4nhk|4nhk]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4nhx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nhx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nhx RCSB], [http://www.ebi.ac.uk/pdbsum/4nhx PDBsum]</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=4nhx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nhx OCA], [https://pdbe.org/4nhx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nhx RCSB], [https://www.ebi.ac.uk/pdbsum/4nhx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nhx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/OGFD1_HUMAN OGFD1_HUMAN]] Prolyl 3-hydroxylase that catalyzes 3-hydroxylation of 'Pro-62' of small ribosomal subunit RPS23, thereby regulating protein translation termination efficiency. Involved in stress granule formation.<ref>PMID:20154146</ref> <ref>PMID:24550447</ref> <ref>PMID:24550462</ref>
+[https://www.uniprot.org/uniprot/OGFD1_HUMAN OGFD1_HUMAN] Prolyl 3-hydroxylase that catalyzes 3-hydroxylation of 'Pro-62' of small ribosomal subunit RPS23, thereby regulating protein translation termination efficiency. Involved in stress granule formation.<ref>PMID:20154146</ref> <ref>PMID:24550447</ref> <ref>PMID:24550462</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4nhx" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Horita, S]]
+[[Category: Homo sapiens]]
-[[Category: McDonough, M A]]
+[[Category: Large Structures]]
-[[Category: Schofield, C J]]
+[[Category: Horita S]]
-[[Category: Double-stranded beta helix]]
+[[Category: McDonough MA]]
-[[Category: Jelly-roll fold]]
+[[Category: Schofield CJ]]
-[[Category: Oxidoreductase-oxidoreductase inhibitor complex]]
-[[Category: Oxygen sensing]]
-[[Category: Ribosome]]
-[[Category: Translation]]

4nhx

From Proteopedia

Current revision

Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with N-oxalylglycine (NOG)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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