4nhy

From Proteopedia

Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with pyridine-2,4-dicarboxylic acid (2,4-PDCA)

PDB ID 4nhy

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Structural highlights

4nhy is a 4 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 2.603Å
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