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[[Image:1ml9.gif|left|200px]]


{{Structure
==Structure of the Neurospora SET domain protein DIM-5, a histone lysine methyltransferase==
|PDB= 1ml9 |SIZE=350|CAPTION= <scene name='initialview01'>1ml9</scene>, resolution 1.98&Aring;
<StructureSection load='1ml9' size='340' side='right'caption='[[1ml9]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
|SITE=
== Structural highlights ==
|LIGAND= <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
<table><tr><td colspan='2'>[[1ml9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ML9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ML9 FirstGlance]. <br>
|ACTIVITY= <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><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ml9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ml9 OCA], [https://pdbe.org/1ml9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ml9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ml9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ml9 ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ml9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ml9 OCA], [http://www.ebi.ac.uk/pdbsum/1ml9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ml9 RCSB]</span>
== 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>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ml/1ml9_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ml9 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
AdoMet-dependent methylation of histones is part of the "histone code" that can profoundly influence gene expression. We describe the crystal structure of Neurospora DIM-5, a histone H3 lysine 9 methyltranferase (HKMT), determined at 1.98 A resolution, as well as results of biochemical characterization and site-directed mutagenesis of key residues. This SET domain protein bears no structural similarity to previously characterized AdoMet-dependent methyltransferases but includes notable features such as a triangular Zn3Cys9 zinc cluster in the pre-SET domain and a AdoMet binding site in the SET domain essential for methyl transfer. The structure suggests a mechanism for the methylation reaction and provides the structural basis for functional characterization of the HKMT family and the SET domain.


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


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ml9" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
AdoMet-dependent methylation of histones is part of the "histone code" that can profoundly influence gene expression. We describe the crystal structure of Neurospora DIM-5, a histone H3 lysine 9 methyltranferase (HKMT), determined at 1.98 A resolution, as well as results of biochemical characterization and site-directed mutagenesis of key residues. This SET domain protein bears no structural similarity to previously characterized AdoMet-dependent methyltransferases but includes notable features such as a triangular Zn3Cys9 zinc cluster in the pre-SET domain and a AdoMet binding site in the SET domain essential for methyl transfer. The structure suggests a mechanism for the methylation reaction and provides the structural basis for functional characterization of the HKMT family and the SET domain.
*[[Histone methyltransferase 3D structures|Histone methyltransferase 3D structures]]
 
== References ==
==About this Structure==
<references/>
1ML9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ML9 OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase., Zhang X, Tamaru H, Khan SI, Horton JR, Keefe LJ, Selker EU, Cheng X, Cell. 2002 Oct 4;111(1):117-27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12372305 12372305]
[[Category: Histone-lysine N-methyltransferase]]
[[Category: Neurospora crassa]]
[[Category: Neurospora crassa]]
[[Category: Single protein]]
[[Category: Cheng X]]
[[Category: Cheng, X.]]
[[Category: Horton JR]]
[[Category: Horton, J R.]]
[[Category: Keefe LJ]]
[[Category: Keefe, L J.]]
[[Category: Khan SI]]
[[Category: Khan, S I.]]
[[Category: Selker EU]]
[[Category: Selker, E U.]]
[[Category: Tamaru H]]
[[Category: Tamaru, H.]]
[[Category: Zhang X]]
[[Category: Zhang, X.]]
[[Category: adomet-dependent methyltransferase histone h3 lysine-9 methylation]]
[[Category: dim-5]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:17:34 2008''

Latest revision as of 09:30, 12 February 2025

Structure of the Neurospora SET domain protein DIM-5, a histone lysine methyltransferaseStructure of the Neurospora SET domain protein DIM-5, a histone lysine methyltransferase

Structural highlights

1ml9 is a 1 chain structure with sequence from Neurospora crassa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.98Å
Ligands:
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

AdoMet-dependent methylation of histones is part of the "histone code" that can profoundly influence gene expression. We describe the crystal structure of Neurospora DIM-5, a histone H3 lysine 9 methyltranferase (HKMT), determined at 1.98 A resolution, as well as results of biochemical characterization and site-directed mutagenesis of key residues. This SET domain protein bears no structural similarity to previously characterized AdoMet-dependent methyltransferases but includes notable features such as a triangular Zn3Cys9 zinc cluster in the pre-SET domain and a AdoMet binding site in the SET domain essential for methyl transfer. The structure suggests a mechanism for the methylation reaction and provides the structural basis for functional characterization of the HKMT family and the SET domain.

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

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

See Also

References

  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:http://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:http://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, 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

1ml9, resolution 1.98Å

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