6bpi: Difference between revisions

Revision as of 08:39, 27 December 2017

Crystal structure of SETDB1 Tudor domain with aryl triazole fragment peptide conjugates

Structural highlights

6bpi is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	EDO, SO4, UNX
NonStd Res:	E2G, MLY
Related:	6au2, 6au3
Activity:	Histone-lysine N-methyltransferase, with EC number 2.1.1.43
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SETB1_HUMAN] Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. H3 'Lys-9' trimethylation is coordinated with DNA methylation. Probably forms a complex with MBD1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Its activity is dependent on MBD1 and is heritably maintained through DNA replication by being recruited by CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor recruited by KRAB zinc-finger proteins.^[1] ^[2] ^[3] ^[4]

References

↑ Ayyanathan K, Lechner MS, Bell P, Maul GG, Schultz DC, Yamada Y, Tanaka K, Torigoe K, Rauscher FJ 3rd. Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation. Genes Dev. 2003 Aug 1;17(15):1855-69. Epub 2003 Jul 17. PMID:12869583 doi:https://dx.doi.org/10.1101/gad.1102803
↑ Wang H, An W, Cao R, Xia L, Erdjument-Bromage H, Chatton B, Tempst P, Roeder RG, Zhang Y. mAM facilitates conversion by ESET of dimethyl to trimethyl lysine 9 of histone H3 to cause transcriptional repression. Mol Cell. 2003 Aug;12(2):475-87. PMID:14536086
↑ Sarraf SA, Stancheva I. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol Cell. 2004 Aug 27;15(4):595-605. PMID:15327775 doi:https://dx.doi.org/10.1016/j.molcel.2004.06.043
↑ Takada I, Mihara M, Suzawa M, Ohtake F, Kobayashi S, Igarashi M, Youn MY, Takeyama K, Nakamura T, Mezaki Y, Takezawa S, Yogiashi Y, Kitagawa H, Yamada G, Takada S, Minami Y, Shibuya H, Matsumoto K, Kato S. A histone lysine methyltransferase activated by non-canonical Wnt signalling suppresses PPAR-gamma transactivation. Nat Cell Biol. 2007 Nov;9(11):1273-85. Epub 2007 Oct 21. PMID:17952062 doi:https://dx.doi.org/10.1038/ncb1647

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OCA

[1] Ayyanathan K, Lechner MS, Bell P, Maul GG, Schultz DC, Yamada Y, Tanaka K, Torigoe K, Rauscher FJ 3rd. Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation. Genes Dev. 2003 Aug 1;17(15):1855-69. Epub 2003 Jul 17. PMID:12869583 doi:https://dx.doi.org/10.1101/gad.1102803

[2] Wang H, An W, Cao R, Xia L, Erdjument-Bromage H, Chatton B, Tempst P, Roeder RG, Zhang Y. mAM facilitates conversion by ESET of dimethyl to trimethyl lysine 9 of histone H3 to cause transcriptional repression. Mol Cell. 2003 Aug;12(2):475-87. PMID:14536086

[3] Sarraf SA, Stancheva I. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol Cell. 2004 Aug 27;15(4):595-605. PMID:15327775 doi:https://dx.doi.org/10.1016/j.molcel.2004.06.043

[4] Takada I, Mihara M, Suzawa M, Ohtake F, Kobayashi S, Igarashi M, Youn MY, Takeyama K, Nakamura T, Mezaki Y, Takezawa S, Yogiashi Y, Kitagawa H, Yamada G, Takada S, Minami Y, Shibuya H, Matsumoto K, Kato S. A histone lysine methyltransferase activated by non-canonical Wnt signalling suppresses PPAR-gamma transactivation. Nat Cell Biol. 2007 Nov;9(11):1273-85. Epub 2007 Oct 21. PMID:17952062 doi:https://dx.doi.org/10.1038/ncb1647

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[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6bpi is ON HOLD
+==Crystal structure of SETDB1 Tudor domain with aryl triazole fragment peptide conjugates==
+<StructureSection load='6bpi' size='340' side='right' caption='[[6bpi]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
-Authors: MADER, P., Mendoza-Sanchez, R., DONG, A., DOBROVETSKY, E., IQBAL, A., CORLESS, V., TEMPEL, W., LIEW, S.K., SMIL, D., DELA SENA, C.C., KENNEDY, S., DIAZ, D.B., SCHAPIRA, M., VEDADI, M., BROWN, P.J., Santhakumar, V., FRYE, S., Bountra, C., Edwards, A.M., YUDIN, A.K., Arrowsmith, C.H., Structural Genomics Consortium (SGC)
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6bpi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BPI FirstGlance]. <br>
-Description: Crystal structure of SETDB1 Tudor domain with aryl triazole fragment peptide conjugates
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-[[Category: Unreleased Structures]]
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=E2G:'>E2G</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr>
-[[Category: Frye, S]]
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6au2|6au2]], [[6au3|6au3]]</td></tr>
-[[Category: Diaz, D.B]]
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43] </span></td></tr>
-[[Category: Arrowsmith, C.H]]
+<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=6bpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bpi OCA], [http://pdbe.org/6bpi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bpi RCSB], [http://www.ebi.ac.uk/pdbsum/6bpi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bpi ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/SETB1_HUMAN SETB1_HUMAN]] Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. H3 'Lys-9' trimethylation is coordinated with DNA methylation. Probably forms a complex with MBD1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Its activity is dependent on MBD1 and is heritably maintained through DNA replication by being recruited by CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor recruited by KRAB zinc-finger proteins.<ref>PMID:12869583</ref> <ref>PMID:14536086</ref> <ref>PMID:15327775</ref> <ref>PMID:17952062</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Histone-lysine N-methyltransferase]]
+[[Category: Arrowsmith, C H]]
+[[Category: BROWN, P J]]
+[[Category: Bountra, C]]
+[[Category: CORLESS, V]]
+[[Category: DIAZ, D B]]
+[[Category: DOBROVETSKY, E]]
+[[Category: DONG, A]]
+[[Category: Edwards, A M]]
+[[Category: FRYE, S]]
+[[Category: IQBAL, A]]
+[[Category: KENNEDY, S]]
+[[Category: LIEW, S K]]
+[[Category: MADER, P]]
+[[Category: Mendoza-Sanchez, R]]
+[[Category: SCHAPIRA, M]]
+[[Category: SENA, C C.DELA]]
+[[Category: Structural genomic]]
+[[Category: SMIL, D]]
 [[Category: Santhakumar, V]]
-[[Category: Kennedy, S]]
+[[Category: TEMPEL, W]]
-[[Category: Iqbal, A]]
+[[Category: VEDADI, M]]
-[[Category: Dong, A]]
+[[Category: YUDIN, A K]]
-[[Category: Vedadi, M]]
+[[Category: Epigenetic]]
-[[Category: Brown, P.J]]
+[[Category: Fragment hit]]
-[[Category: Smil, D]]
+[[Category: Methyl lysine reader]]
-[[Category: Mendoza-Sanchez, R]]
+[[Category: Setdb1 tudor]]
-[[Category: Corless, V]]
+[[Category: Sgc]]
-[[Category: Liew, S.K]]
+[[Category: Transferase]]
-[[Category: Yudin, A.K]]
-[[Category: Schapira, M]]
-[[Category: Edwards, A.M]]
-[[Category: Dobrovetsky, E]]
-[[Category: Structural Genomics Consortium (Sgc)]]
-[[Category: Dela Sena, C.C]]
-[[Category: Mader, P]]
-[[Category: Bountra, C]]
-[[Category: Tempel, W]]

6bpi: Difference between revisions

Revision as of 08:39, 27 December 2017

Crystal structure of SETDB1 Tudor domain with aryl triazole fragment peptide conjugates

Structural highlights

Function

References

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