6f4t: Difference between revisions

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==Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5)==

== Structural highlights ==

<table><tr><td colspan='2'>[[6f4t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F4T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6F4T FirstGlance]. <br>

<table><tr><td colspan='2'>[[6f4t]] is a 2 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=6F4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6F4T FirstGlance]. <br>

</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'~~>~~GOL</scene>, <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>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.22Å</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6f4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f4t OCA], [https://pdbe.org/6f4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6f4t RCSB], [https://www.ebi.ac.uk/pdbsum/6f4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6f4t ProSAT]</span></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=6f4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f4t OCA], [~~http~~://pdbe.org/6f4t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6f4t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6f4t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6f4t ProSAT]</span></td></tr>

</table>

== Function ==

[~~[http~~://www.uniprot.org/uniprot/KDM8_HUMAN 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. [[http://www.uniprot.org/uniprot/RCCD1_HUMAN 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).<ref>PMID:24981860</ref> <ref>PMID:28455245</ref>

[https://www.uniprot.org/uniprot/KDM8_HUMAN 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.

== Publication Abstract from PubMed ==

Line 21:

Line 19:

</div>

==See Also==

*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]

== References ==

__TOC__

</StructureSection>

[[Category: ~~50S ribosomal protein L16 3-hydroxylase~~]]

[[Category: Homo sapiens]]

[[Category: ~~Chowdhury, R~~]]

[[Category: Large Structures]]

[[Category: ~~Islam, M S~~]]

[[Category: Chowdhury R]]

[[Category: ~~Schofield, C J~~]]

[[Category: Islam MS]]

[[Category: ~~2-oxoglutarate]]~~

[[Category: Schofield CJ]]

~~[[Category: 40s ribosomal protein s6]]~~

~~[[Category: Arginine hydroxylation]]~~

~~[[Category: Arginyl c-3 hydroxylase]]~~

~~[[Category: Beta-hydroxylation]]~~

~~[[Category: Cancer]]~~

~~[[Category: Cell structure]]~~

~~[[Category: Cytoplasm]]~~

~~[[Category: Development]]~~

~~[[Category: Dioxygenase]]~~

~~[[Category: Dna-binding]]~~

~~[[Category: Dsbh]]~~

~~[[Category: Epigenetic regulation]]~~

~~[[Category: Facial triad]]~~

~~[[Category: Hydroxylation]]~~

~~[[Category: Hypoxia]]~~

~~[[Category: Iron]]~~

~~[[Category: Jmjc]]~~

~~[[Category: Jmjc demethylase]]~~

~~[[Category: Jmjc domain]]~~

~~[[Category: Jmjc domain-containing protein 5]]~~

~~[[Category: Jmjc hydroxylase]]~~

~~[[Category: Jmjd5]]~~

~~[[Category: Kdm]]~~

~~[[Category: Kdm8]]~~

~~[[Category: Lysine-specific demethylase 8]]~~

~~[[Category: Metal-binding]]~~

~~[[Category: Non-heme]]~~

~~[[Category: Oxidoreductase]]~~

~~[[Category: Oxygenase]]~~

~~[[Category: Phosphorylation]]~~

~~[[Category: Polymorphism]]~~

~~[[Category: Post-translational modification]]~~

~~[[Category: Ptm]]~~

~~[[Category: Rcc1 domain-containing protein 1]]~~

~~[[Category: Rccd1]]~~

~~[[Category: Regulator of chromosome condensation]]~~

~~[[Category: Ribosome biogenesis]]~~

~~[[Category: Rps6]]~~

~~[[Category: Signaling]]~~

~~[[Category: Transcription]]~~

~~[[Category: Transcription activator/inhibitor]]~~

~~[[Category: Translation~~]]

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@@ Line 1: / Line 1: @@
 ==Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5)==
-<StructureSection load='6f4t' size='340' side='right' caption='[[6f4t]], [[Resolution|resolution]] 1.22&Aring;' scene=''>
+<StructureSection load='6f4t' size='340' side='right'caption='[[6f4t]], [[Resolution|resolution]] 1.22&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6f4t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F4T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6f4t]] is a 2 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=6F4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6F4T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.22&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6f4m|6f4m]], [[6f4n|6f4n]], [[6f4o|6f4o]], [[6f4p|6f4p]], [[6f4q|6f4q]], [[6f4r|6f4r]], [[6f4s|6f4s]]</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=6f4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f4t OCA], [https://pdbe.org/6f4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6f4t RCSB], [https://www.ebi.ac.uk/pdbsum/6f4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6f4t ProSAT]</span></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=6f4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f4t OCA], [http://pdbe.org/6f4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f4t RCSB], [http://www.ebi.ac.uk/pdbsum/6f4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f4t ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KDM8_HUMAN 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. [[http://www.uniprot.org/uniprot/RCCD1_HUMAN 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).<ref>PMID:24981860</ref> <ref>PMID:28455245</ref>
+[https://www.uniprot.org/uniprot/KDM8_HUMAN 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.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 19: @@
 </div>
 <div class="pdbe-citations 6f4t" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: 50S ribosomal protein L16 3-hydroxylase]]
+[[Category: Homo sapiens]]
-[[Category: Chowdhury, R]]
+[[Category: Large Structures]]
-[[Category: Islam, M S]]
+[[Category: Chowdhury R]]
-[[Category: Schofield, C J]]
+[[Category: Islam MS]]
-[[Category: 2-oxoglutarate]]
+[[Category: Schofield CJ]]
-[[Category: 40s ribosomal protein s6]]
-[[Category: Arginine hydroxylation]]
-[[Category: Arginyl c-3 hydroxylase]]
-[[Category: Beta-hydroxylation]]
-[[Category: Cancer]]
-[[Category: Cell structure]]
-[[Category: Cytoplasm]]
-[[Category: Development]]
-[[Category: Dioxygenase]]
-[[Category: Dna-binding]]
-[[Category: Dsbh]]
-[[Category: Epigenetic regulation]]
-[[Category: Facial triad]]
-[[Category: Hydroxylation]]
-[[Category: Hypoxia]]
-[[Category: Iron]]
-[[Category: Jmjc]]
-[[Category: Jmjc demethylase]]
-[[Category: Jmjc domain]]
-[[Category: Jmjc domain-containing protein 5]]
-[[Category: Jmjc hydroxylase]]
-[[Category: Jmjd5]]
-[[Category: Kdm]]
-[[Category: Kdm8]]
-[[Category: Lysine-specific demethylase 8]]
-[[Category: Metal-binding]]
-[[Category: Non-heme]]
-[[Category: Oxidoreductase]]
-[[Category: Oxygenase]]
-[[Category: Phosphorylation]]
-[[Category: Polymorphism]]
-[[Category: Post-translational modification]]
-[[Category: Ptm]]
-[[Category: Rcc1 domain-containing protein 1]]
-[[Category: Rccd1]]
-[[Category: Regulator of chromosome condensation]]
-[[Category: Ribosome biogenesis]]
-[[Category: Rps6]]
-[[Category: Signaling]]
-[[Category: Transcription]]
-[[Category: Transcription activator/inhibitor]]
-[[Category: Translation]]