1peg: Difference between revisions

Latest revision as of 09:42, 16 August 2023

Structural basis for the product specificity of histone lysine methyltransferases

Structural highlights

1peg is a 4 chain structure with sequence from Neurospora crassa and Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.59Å
Ligands:	SAH, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DIM5_NEUCR Histone methyltransferase that specifically trimethylates histone H3 to form H3K9me3. H3K9me3 marks chromatin regions for DNA methylation.^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

DIM-5 is a SUV39-type histone H3 Lys9 methyltransferase that is essential for DNA methylation in N. crassa. We report the structure of a ternary complex including DIM-5, S-adenosyl-L-homocysteine, and a substrate H3 peptide. The histone tail inserts as a parallel strand between two DIM-5 strands, completing a hybrid sheet. Three post-SET cysteines coordinate a zinc atom together with Cys242 from the SET signature motif (NHXCXPN) near the active site. Consequently, a narrow channel is formed to accommodate the target Lys9 side chain. The sulfur atom of S-adenosyl-L-homocysteine, where the transferable methyl group is to be attached in S-adenosyl-L-methionine, lies at the opposite end of the channel, approximately 4 A away from the target Lys9 nitrogen. Structural comparison of the active sites of DIM-5, an H3 Lys9 trimethyltransferase, and SET7/9, an H3 Lys4 monomethyltransferase, allowed us to design substitutions in both enzymes that profoundly alter their product specificities without affecting their catalytic activities.

Structural basis for the product specificity of histone lysine methyltransferases.,Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, Selker EU, Cheng X Mol Cell. 2003 Jul;12(1):177-85. PMID:12887903^[5]

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

References

↑ Tamaru H, Selker EU. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature. 2001 Nov 15;414(6861):277-83. PMID:11713521 doi:https://dx.doi.org/10.1038/35104508
↑ Tamaru H, Zhang X, McMillen D, Singh PB, Nakayama J, Grewal SI, Allis CD, Cheng X, Selker EU. Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat Genet. 2003 May;34(1):75-9. PMID:12679815 doi:https://dx.doi.org/10.1038/ng1143
↑ Zhang X, Tamaru H, Khan SI, Horton JR, Keefe LJ, Selker EU, Cheng X. Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell. 2002 Oct 4;111(1):117-27. PMID:12372305
↑ Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, Selker EU, Cheng X. Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell. 2003 Jul;12(1):177-85. PMID:12887903
↑ Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, Selker EU, Cheng X. Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell. 2003 Jul;12(1):177-85. PMID:12887903

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Tamaru H, Selker EU. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature. 2001 Nov 15;414(6861):277-83. PMID:11713521 doi:https://dx.doi.org/10.1038/35104508

[2] Tamaru H, Zhang X, McMillen D, Singh PB, Nakayama J, Grewal SI, Allis CD, Cheng X, Selker EU. Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat Genet. 2003 May;34(1):75-9. PMID:12679815 doi:https://dx.doi.org/10.1038/ng1143

[3] Zhang X, Tamaru H, Khan SI, Horton JR, Keefe LJ, Selker EU, Cheng X. Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell. 2002 Oct 4;111(1):117-27. PMID:12372305

[4] Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, Selker EU, Cheng X. Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell. 2003 Jul;12(1):177-85. PMID:12887903

[5] Zhang X, Yang Z, Khan SI, Horton JR, Tamaru H, Selker EU, Cheng X. Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell. 2003 Jul;12(1):177-85. PMID:12887903

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[2]

[3]

[4]

[5]

@@ Line 3: / Line 3: @@
 <StructureSection load='1peg' size='340' side='right'caption='[[1peg]], [[Resolution|resolution]] 2.59&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1peg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chrysonilia_crassa Chrysonilia crassa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PEG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1peg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PEG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.59&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ml9|1ml9]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Histone-lysine_N-methyltransferase Histone-lysine N-methyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.43 2.1.1.43] </span></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=1peg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1peg OCA], [https://pdbe.org/1peg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1peg RCSB], [https://www.ebi.ac.uk/pdbsum/1peg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1peg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DIM5_NEUCR DIM5_NEUCR]] Histone methyltransferase that specifically trimethylates histone H3 to form H3K9me3. H3K9me3 marks chromatin regions for DNA methylation.<ref>PMID:11713521</ref> <ref>PMID:12679815</ref> <ref>PMID:12372305</ref> <ref>PMID:12887903</ref>
+[https://www.uniprot.org/uniprot/DIM5_NEUCR DIM5_NEUCR] Histone methyltransferase that specifically trimethylates histone H3 to form H3K9me3. H3K9me3 marks chromatin regions for DNA methylation.<ref>PMID:11713521</ref> <ref>PMID:12679815</ref> <ref>PMID:12372305</ref> <ref>PMID:12887903</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Chrysonilia crassa]]
-[[Category: Histone-lysine N-methyltransferase]]
 [[Category: Large Structures]]
-[[Category: Cheng, X]]
+[[Category: Neurospora crassa]]
-[[Category: Horton, J R]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Khan, S I]]
+[[Category: Cheng X]]
-[[Category: Selker, E U]]
+[[Category: Horton JR]]
-[[Category: Tamaru, H]]
+[[Category: Khan SI]]
-[[Category: Yang, Z]]
+[[Category: Selker EU]]
-[[Category: Zhang, X]]
+[[Category: Tamaru H]]
-[[Category: A hybrid beta sheet formed by dim-5 and h3 tail]]
+[[Category: Yang Z]]
-[[Category: A suv39-type histone-h3 lys-9 methyltransferase]]
+[[Category: Zhang X]]
-[[Category: Post-set zinc-binding site]]
-[[Category: Pre-set triangular zn3cys9 zinc cluster]]
-[[Category: Set domain protein forms a knot-like substructure]]
-[[Category: Ternary structure of dim-5]]
-[[Category: Transferase]]

1peg: Difference between revisions

Latest revision as of 09:42, 16 August 2023

Structural basis for the product specificity of histone lysine methyltransferases

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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