4Y3O

Crystal structure of Ribosomal oxygenase NO66 in complex with substrate Rpl8 peptide and Ni(II) and cofactor N-oxalyglycine

Summary for 4Y3O

• Entry DOI: 10.2210/pdb4y3o/pdb
• Related: 4Y33 4Y4R
• Descriptor: Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66, Rpl8 peptide, NICKEL (II) ION, ... (7 entities in total)
• Functional Keywords: ribosomal oxygenase, quaternary compound structure, jmjc-domain, oxidoreductase-peptide complex, oxidoreductase/peptide
• Biological source: Homo sapiens (Human); More
• Cellular location: Nucleus, nucleolus: Q9H6W3
• Total number of polymer chains: 4
• Total formula weight: 108924.96

Authors

Wang, C.,Zhang, Q.,Zang, J. (deposition date: 2015-02-10, release date: 2015-10-07, Last modification date: 2024-03-20)

Primary citation

Wang, C.,Zhang, Q.,Hang, T.,Tao, Y.,Ma, X.,Wu, M.,Zhang, X.,Zang, J.
Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8.
Acta Crystallogr.,Sect.D, 71:1955-1964, 2015

PubMed Abstract: The JmjC domain-containing proteins belong to a large family of oxygenases possessing distinct substrate specificities which are involved in the regulation of different biological processes, such as gene transcription, RNA processing and translation. Nucleolar protein 66 (NO66) is a JmjC domain-containing protein which has been reported to be a histone demethylase and a ribosome protein 8 (Rpl8) hydroxylase. The present biochemical study confirmed the hydroxylase activity of NO66 and showed that oligomerization is required for NO66 to efficiently catalyze the hydroxylation of Rpl8. The structures of NO66(176-C) complexed with Rpl8(204-224) in a tetrameric form and of the mutant protein M2 in a dimeric form were solved. Based on the results of structural and biochemical analyses, the consensus sequence motif NHXH recognized by NO66 was confirmed. Several potential substrates of NO66 were found by a BLAST search according to the consensus sequence motif. When binding to substrate, the relative positions of each subunit in the NO66 tetramer shift. Oligomerization may facilitate the motion of each subunit in the NO66 tetramer and affect the catalytic activity.

PubMed: 26327385
DOI: 10.1107/S1399004715012948

Experimental method

X-RAY DIFFRACTION (2.2 Å)