4y3o

From Proteopedia

(Difference between revisions)

Revision as of 18:05, 26 April 2023

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

Structural highlights

4y3o 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.
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIOX1_HUMAN Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Specifically demethylates 'Lys-4' (H3K4me) and 'Lys-36' (H3K36me) of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 'Lys-4' (H3K4me3) and monomethylated H3 'Lys-4' (H3K4me1) residues, while it has weaker activity for dimethylated H3 'Lys-36' (H3K36me2). Also catalyzes the hydroxylation of 60S ribosomal protein L8 on 'His-216'. Acts as a regulator of osteoblast differentiation via its interaction with SP7/OSX by demethylating H3K4me and H3K36me, thereby inhibiting SP7/OSX-mediated promoter activation (By similarity). May also play a role in ribosome biogenesis and in the replication or remodeling of certain heterochromatic region. Participates in MYC-induced transcriptional activation.^[1] ^[2] ^[3]

Publication Abstract from PubMed

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.

Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8.,Wang C, Zhang Q, Hang T, Tao Y, Ma X, Wu M, Zhang X, Zang J Acta Crystallogr D Biol Crystallogr. 2015 Sep 1;71(Pt 9):1955-64. doi:, 10.1107/S1399004715012948. Epub 2015 Aug 28. PMID:26327385^[4]

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

References

↑ Eilbracht J, Reichenzeller M, Hergt M, Schnolzer M, Heid H, Stohr M, Franke WW, Schmidt-Zachmann MS. NO66, a highly conserved dual location protein in the nucleolus and in a special type of synchronously replicating chromatin. Mol Biol Cell. 2004 Apr;15(4):1816-32. Epub 2004 Jan 23. PMID:14742713 doi:http://dx.doi.org/10.1091/mbc.E03-08-0623
↑ Suzuki C, Takahashi K, Hayama S, Ishikawa N, Kato T, Ito T, Tsuchiya E, Nakamura Y, Daigo Y. Identification of Myc-associated protein with JmjC domain as a novel therapeutic target oncogene for lung cancer. Mol Cancer Ther. 2007 Feb;6(2):542-51. PMID:17308053 doi:http://dx.doi.org/10.1158/1535-7163.MCT-06-0659
↑ Ge W, Wolf A, Feng T, Ho CH, Sekirnik R, Zayer A, Granatino N, Cockman ME, Loenarz C, Loik ND, Hardy AP, Claridge TD, Hamed RB, Chowdhury R, Gong L, Robinson CV, Trudgian DC, Jiang M, Mackeen MM, McCullagh JS, Gordiyenko Y, Thalhammer A, Yamamoto A, Yang M, Liu-Yi P, Zhang Z, Schmidt-Zachmann M, Kessler BM, Ratcliffe PJ, Preston GM, Coleman ML, Schofield CJ. Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans. Nat Chem Biol. 2012 Dec;8(12):960-2. doi: 10.1038/nchembio.1093. Epub 2012 Oct, 28. PMID:23103944 doi:10.1038/nchembio.1093
↑ 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 D Biol Crystallogr. 2015 Sep 1;71(Pt 9):1955-64. doi:, 10.1107/S1399004715012948. Epub 2015 Aug 28. PMID:26327385 doi:http://dx.doi.org/10.1107/S1399004715012948

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/4y3o"

Categories: Homo sapiens | Large Structures | Wang C | Zang J | Zhang Q

@@ Line 3: / Line 3: @@
 <StructureSection load='4y3o' size='340' side='right'caption='[[4y3o]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4y3o]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y3O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y3O FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4y3o]] is a 4 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=4Y3O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y3O FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4y33|4y33]], [[4y4r|4y4r]]</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=4y3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y3o OCA], [https://pdbe.org/4y3o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y3o RCSB], [https://www.ebi.ac.uk/pdbsum/4y3o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y3o ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NO66, C14orf169, MAPJD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4y3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y3o OCA], [http://pdbe.org/4y3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y3o RCSB], [http://www.ebi.ac.uk/pdbsum/4y3o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y3o ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NO66_HUMAN NO66_HUMAN]] Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Specifically demethylates 'Lys-4' (H3K4me) and 'Lys-36' (H3K36me) of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 'Lys-4' (H3K4me3) and monomethylated H3 'Lys-4' (H3K4me1) residues, while it has weaker activity for dimethylated H3 'Lys-36' (H3K36me2). Also catalyzes the hydroxylation of 60S ribosomal protein L8 on 'His-216'. Acts as a regulator of osteoblast differentiation via its interaction with SP7/OSX by demethylating H3K4me and H3K36me, thereby inhibiting SP7/OSX-mediated promoter activation (By similarity). May also play a role in ribosome biogenesis and in the replication or remodeling of certain heterochromatic region. Participates in MYC-induced transcriptional activation.<ref>PMID:14742713</ref> <ref>PMID:17308053</ref> <ref>PMID:23103944</ref>
+[https://www.uniprot.org/uniprot/RIOX1_HUMAN RIOX1_HUMAN] Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Specifically demethylates 'Lys-4' (H3K4me) and 'Lys-36' (H3K36me) of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 'Lys-4' (H3K4me3) and monomethylated H3 'Lys-4' (H3K4me1) residues, while it has weaker activity for dimethylated H3 'Lys-36' (H3K36me2). Also catalyzes the hydroxylation of 60S ribosomal protein L8 on 'His-216'. Acts as a regulator of osteoblast differentiation via its interaction with SP7/OSX by demethylating H3K4me and H3K36me, thereby inhibiting SP7/OSX-mediated promoter activation (By similarity). May also play a role in ribosome biogenesis and in the replication or remodeling of certain heterochromatic region. Participates in MYC-induced transcriptional activation.<ref>PMID:14742713</ref> <ref>PMID:17308053</ref> <ref>PMID:23103944</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Wang, C]]
+[[Category: Wang C]]
-[[Category: Zang, J]]
+[[Category: Zang J]]
-[[Category: Zhang, Q]]
+[[Category: Zhang Q]]
-[[Category: Jmjc-domain]]
-[[Category: Oxidoreductase-peptide complex]]
-[[Category: Quaternary compound structure]]
-[[Category: Ribosomal oxygenase]]

4y3o

From Proteopedia

Revision as of 18:05, 26 April 2023

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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