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3rib

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{{STRUCTURE_3rib| PDB=3rib | SCENE= }}
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==Human lysine methyltransferase Smyd2 in complex with AdoHcy==
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===Human lysine methyltransferase Smyd2 in complex with AdoHcy===
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<StructureSection load='3rib' size='340' side='right' caption='[[3rib]], [[Resolution|resolution]] 2.79&Aring;' scene=''>
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{{ABSTRACT_PUBMED_21724641}}
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3rib]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RIB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RIB FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SMYD2, KMT3C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
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<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=3rib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rib OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rib RCSB], [http://www.ebi.ac.uk/pdbsum/3rib PDBsum]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The SET- and myeloid-Nervy-DEAF-1 (MYND)-domain containing (Smyd) lysine methyltransferases 1-3 share relatively high sequence similarity but exhibit divergence in the substrate specificity. Here we report the crystal structure of the full-length human Smyd2 in complex with S-adenosyl-L-homocysteine (AdoHcy). Although the Smyd1-3 enzymes are similar in the overall structure, detailed comparisons demonstrate that they differ substantially in the potential substrate-binding site. The binding site of Smyd3 consists mainly of a deep and narrow pocket, while those of Smyd1 and Smyd2 consist of a comparable pocket and a long groove. In addition, Smyd2, which has lysine methyltransferase activity on histone H3-lysine 36, exhibits substantial differences in the wall of the substrate-binding pocket compared with those of Smyd1 and Smyd3 which have activity specifically on histone H3-lysine 4. The differences in the substrate-binding site might account for the observed divergence in the specificity and methylation state of the substrates. Further modeling study of Smyd2 in complex with a p53 peptide indicates that mono-methylation of p53-Lys(372) might result in steric conflict of the methyl group with the surrounding residues of Smyd2, providing a structural explanation for the inhibitory effect of the SET7/9-mediated mono-methylation of p53-Lys(372) on the Smyd2-mediated methylation of p53-Lys(370).
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==Function==
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Structure of human lysine methyltransferase Smyd2 reveals insights into the substrate divergence in Smyd proteins.,Xu S, Zhong C, Zhang T, Ding J J Mol Cell Biol. 2011 Jul 1. PMID:21724641<ref>PMID:21724641</ref>
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[[http://www.uniprot.org/uniprot/SMYD2_HUMAN SMYD2_HUMAN]] Protein-lysine N-methyltransferase that methylates both histones and non-histone proteins. Specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). Has also methyltransferase activity toward non-histone proteins such as p53/TP53 and RB1. Monomethylates 'Lys-370' of p53/TP53, leading to decreased DNA-binding activity and subsequent transcriptional regulation activity of p53/TP53. Monomethylates 'Lys-860' of RB1/RB.<ref>PMID:17108971</ref> <ref>PMID:17805299</ref> <ref>PMID:18065756</ref> <ref>PMID:20870719</ref>
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[3rib]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RIB OCA].
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</div>
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==Reference==
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==See Also==
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<ref group="xtra">PMID:021724641</ref><references group="xtra"/><references/>
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*[[Histone methyltransferase|Histone methyltransferase]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Ding, J.]]
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[[Category: Ding, J]]
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[[Category: Xu, S.]]
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[[Category: Xu, S]]
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[[Category: Zhang, T.]]
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[[Category: Zhang, T]]
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[[Category: Zhong, C.]]
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[[Category: Zhong, C]]
[[Category: H3k36]]
[[Category: H3k36]]
[[Category: H3k4]]
[[Category: H3k4]]

Revision as of 10:23, 19 December 2014

Human lysine methyltransferase Smyd2 in complex with AdoHcy

3rib, resolution 2.79Å

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