6f4r

From Proteopedia

(Difference between revisions)

Revision as of 06:10, 12 June 2019

Human JMJD5 (N308C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-3)

Structural highlights

6f4r is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:
Related:	6f4m, 6f4n, 6f4o, 6f4p, 6f4q, 6f4s, 6f4t
Gene:	KDM8, JMJD5 (HUMAN)
Activity:	50S ribosomal protein L16 3-hydroxylase, with EC number 1.14.11.47
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[KDM8_HUMAN] Histone demethylase required for G2/M phase cell cycle progression. Specifically demethylates dimethylated 'Lys-36' (H3K36me2) of histone H3, an epigenetic repressive mark, thereby acting as a transcription activator. Regulates expression of CCNA1 (cyclin-A1), leading to regulate cancer cell proliferation. [RCCD1_HUMAN] Acts as a coregulator of KDM8 to promote histone demethylase activity on di- and trimethylated 'Lys-36' (H3K36me2/me3) of histone H3 (PubMed:24981860). Plays a role in transcriptional repression of satellite repeats, possibly by regulating H3K36 methylation levels in centromeric regions together with KDM8 (PubMed:24981860). Possibly together with KDM8, involved in proper mitotic spindle organization and chromosome segregation (PubMed:24981860). Plays a role in regulating alpha-tubulin deacetylation and cytoskeletal microtubule stability and thereby promoting cell migration and TGF-beta-induced epithelial to mesenchymal transition (EMT), potentially through the inhibition of KDM8 (PubMed:28455245).^[1] ^[2]

Publication Abstract from PubMed

Oxygenase-catalysed post-translational modifications of basic protein residues, including lysyl hydroxylations and N(epsilon)-methyl lysyl demethylations, have important cellular roles. Jumonji-C (JmjC) domain-containing protein 5 (JMJD5), which genetic studies reveal is essential in animal development, is reported as a histone N(epsilon)-methyl lysine demethylase (KDM). Here we report how extensive screening with peptides based on JMJD5 interacting proteins led to the finding that JMJD5 catalyses stereoselective C-3 hydroxylation of arginine residues in sequences from human regulator of chromosome condensation domain-containing protein 1 (RCCD1) and ribosomal protein S6 (RPS6). High-resolution crystallographic analyses reveal overall fold, active site and substrate binding/product release features supporting the assignment of JMJD5 as an arginine hydroxylase rather than a KDM. The results will be useful in the development of selective oxygenase inhibitors for the treatment of cancer and genetic diseases.

JMJD5 is a human arginyl C-3 hydroxylase.,Wilkins SE, Islam S, Gannon JM, Markolovic S, Hopkinson RJ, Ge W, Schofield CJ, Chowdhury R Nat Commun. 2018 Mar 21;9(1):1180. doi: 10.1038/s41467-018-03410-w. PMID:29563586^[3]

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

References

↑ Marcon E, Ni Z, Pu S, Turinsky AL, Trimble SS, Olsen JB, Silverman-Gavrila R, Silverman-Gavrila L, Phanse S, Guo H, Zhong G, Guo X, Young P, Bailey S, Roudeva D, Zhao D, Hewel J, Li J, Graslund S, Paduch M, Kossiakoff AA, Lupien M, Emili A, Wodak SJ, Greenblatt J. Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. Cell Rep. 2014 Jul 10;8(1):297-310. doi: 10.1016/j.celrep.2014.05.050. Epub 2014 , Jun 26. PMID:24981860 doi:http://dx.doi.org/10.1016/j.celrep.2014.05.050
↑ Wu J, He Z, Yang XM, Li KL, Wang DL, Sun FL. RCCD1 depletion attenuates TGF-beta-induced EMT and cell migration by stabilizing cytoskeletal microtubules in NSCLC cells. Cancer Lett. 2017 Aug 1;400:18-29. doi: 10.1016/j.canlet.2017.04.021. Epub 2017, Apr 26. PMID:28455245 doi:http://dx.doi.org/10.1016/j.canlet.2017.04.021
↑ Wilkins SE, Islam S, Gannon JM, Markolovic S, Hopkinson RJ, Ge W, Schofield CJ, Chowdhury R. JMJD5 is a human arginyl C-3 hydroxylase. Nat Commun. 2018 Mar 21;9(1):1180. doi: 10.1038/s41467-018-03410-w. PMID:29563586 doi:http://dx.doi.org/10.1038/s41467-018-03410-w

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6f4r"

@@ Line 1: / Line 1: @@
 ==Human JMJD5 (N308C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-3)==
-<StructureSection load='6f4r' size='340' side='right' caption='[[6f4r]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
+<StructureSection load='6f4r' size='340' side='right'caption='[[6f4r]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6f4r]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F4R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6f4r]] is a 2 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=6F4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F4R FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6f4m|6f4m]], [[6f4n|6f4n]], [[6f4o|6f4o]], [[6f4p|6f4p]], [[6f4q|6f4q]], [[6f4s|6f4s]], [[6f4t|6f4t]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KDM8, JMJD5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/50S_ribosomal_protein_L16_3-hydroxylase 50S ribosomal protein L16 3-hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.47 1.14.11.47] </span></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=6f4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f4r OCA], [http://pdbe.org/6f4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f4r RCSB], [http://www.ebi.ac.uk/pdbsum/6f4r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f4r ProSAT]</span></td></tr>
@@ Line 21: / Line 22: @@
 </div>
 <div class="pdbe-citations 6f4r" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Jumonji domain-containing protein|Jumonji domain-containing protein]]
 == References ==
 <references/>
@@ Line 26: / Line 30: @@
 </StructureSection>
 [[Category: 50S ribosomal protein L16 3-hydroxylase]]
-[[Category: CHOWDHURY, R]]
+[[Category: Human]]
+[[Category: Large Structures]]
+[[Category: Chowdhury, R]]
 [[Category: Islam, M S]]
-[[Category: SCHOFIELD, C J]]
+[[Category: Schofield, C J]]
 [[Category: 2-oxoglutarate]]
 [[Category: 40s ribosomal protein s6]]

6f4r

From Proteopedia

Revision as of 06:10, 12 June 2019

Human JMJD5 (N308C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-3)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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