3K2O

Structure of an oxygenase

Summary for 3K2O

• Entry DOI: 10.2210/pdb3k2o/pdb
• Descriptor: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6, NICKEL (II) ION, SODIUM ION, ... (8 entities in total)
• Functional Keywords: structural genomics consortium, sgc, chromatin regulator, developmental protein, differentiation, dioxygenase, iron, metal-binding, mrna processing, mrna splicing, nucleus, oxidoreductase, transcription, transcription regulation
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus, nucleoplasm: Q6NYC1
• Total number of polymer chains: 2
• Total formula weight: 80666.06

Authors

Krojer, T.,McDonough, M.A.,Clifton, I.J.,Mantri, M.,Ng, S.S.,Pike, A.C.W.,Butler, D.S.,Webby, C.J.,Kochan, G.,Bhatia, C.,Bray, J.E.,Chaikuad, A.,Gileadi, O.,von Delft, F.,Weigelt, J.,Arrowsmith, C.H.,Bountra, C.,Edwards, A.M.,Schofield, C.J.,Kavanagh, K.L.,Oppermann, U.,Structural Genomics Consortium (SGC) (deposition date: 2009-09-30, release date: 2009-11-03, Last modification date: 2024-11-13)

Primary citation

Mantri, M.,Krojer, T.,Bagg, E.A.,Webby, C.A.,Butler, D.S.,Kochan, G.,Kavanagh, K.L.,Oppermann, U.,McDonough, M.A.,Schofield, C.J.
Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6.
J.Mol.Biol., 401:211-222, 2010

PubMed Abstract: Lysyl and prolyl hydroxylations are well-known post-translational modifications to animal and plant proteins with extracellular roles. More recent work has indicated that the hydroxylation of intracellular animal proteins may be common. JMJD6 catalyses the iron- and 2-oxoglutarate-dependent hydroxylation of lysyl residues in arginine-serine-rich domains of RNA-splicing-related proteins. We report crystallographic studies on the catalytic domain of JMJD6 in complex with Ni(II) substituting for Fe(II). Together with mutational studies, the structural data suggest how JMJD6 binds its lysyl residues such that it can catalyse C-5 hydroxylation rather than N(varepsilon)-demethylation, as for analogous enzymes.

PubMed: 20685276
DOI: 10.1016/j.jmb.2010.05.054

Experimental method

X-RAY DIFFRACTION (1.75 Å)