3f2k: Difference between revisions

Revision as of 09:22, 23 February 2022

Structure of the transposase domain of human Histone-lysine N-methyltransferase SETMAR

Structural highlights

3f2k is a 3 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	MG
NonStd Res:	MSE
Gene:	SETMAR (HUMAN)
Activity:	Histone-lysine N-methyltransferase, with EC number 2.1.1.43
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SETMR_HUMAN] Histone methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3, 2 specific tags for epigenetic transcriptional activation. Specifically mediates dimethylation of H3 'Lys-36'. Has sequence-specific DNA-binding activity and recognizes the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. Has DNA nicking activity. Has in vivo end joining activity and may mediate genomic integration of foreign DNA.^[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.

References

↑ Lee SH, Oshige M, Durant ST, Rasila KK, Williamson EA, Ramsey H, Kwan L, Nickoloff JA, Hromas R. The SET domain protein Metnase mediates foreign DNA integration and links integration to nonhomologous end-joining repair. Proc Natl Acad Sci U S A. 2005 Dec 13;102(50):18075-80. Epub 2005 Dec 6. PMID:16332963 doi:10.1073/pnas.0503676102
↑ Cordaux R, Udit S, Batzer MA, Feschotte C. Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proc Natl Acad Sci U S A. 2006 May 23;103(21):8101-6. Epub 2006 May 3. PMID:16672366 doi:0601161103
↑ Roman Y, Oshige M, Lee YJ, Goodwin K, Georgiadis MM, Hromas RA, Lee SH. Biochemical characterization of a SET and transposase fusion protein, Metnase: its DNA binding and DNA cleavage activity. Biochemistry. 2007 Oct 9;46(40):11369-76. Epub 2007 Sep 18. PMID:17877369 doi:10.1021/bi7005477
↑ Miskey C, Papp B, Mates L, Sinzelle L, Keller H, Izsvak Z, Ivics Z. The ancient mariner sails again: transposition of the human Hsmar1 element by a reconstructed transposase and activities of the SETMAR protein on transposon ends. Mol Cell Biol. 2007 Jun;27(12):4589-600. Epub 2007 Apr 2. PMID:17403897 doi:10.1128/MCB.02027-06

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OCA

[1] Lee SH, Oshige M, Durant ST, Rasila KK, Williamson EA, Ramsey H, Kwan L, Nickoloff JA, Hromas R. The SET domain protein Metnase mediates foreign DNA integration and links integration to nonhomologous end-joining repair. Proc Natl Acad Sci U S A. 2005 Dec 13;102(50):18075-80. Epub 2005 Dec 6. PMID:16332963 doi:10.1073/pnas.0503676102

[2] Cordaux R, Udit S, Batzer MA, Feschotte C. Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proc Natl Acad Sci U S A. 2006 May 23;103(21):8101-6. Epub 2006 May 3. PMID:16672366 doi:0601161103

[3] Roman Y, Oshige M, Lee YJ, Goodwin K, Georgiadis MM, Hromas RA, Lee SH. Biochemical characterization of a SET and transposase fusion protein, Metnase: its DNA binding and DNA cleavage activity. Biochemistry. 2007 Oct 9;46(40):11369-76. Epub 2007 Sep 18. PMID:17877369 doi:10.1021/bi7005477

[4] Miskey C, Papp B, Mates L, Sinzelle L, Keller H, Izsvak Z, Ivics Z. The ancient mariner sails again: transposition of the human Hsmar1 element by a reconstructed transposase and activities of the SETMAR protein on transposon ends. Mol Cell Biol. 2007 Jun;27(12):4589-600. Epub 2007 Apr 2. PMID:17403897 doi:10.1128/MCB.02027-06

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==Structure of the transposase domain of human Histone-lysine N-methyltransferase SETMAR==
-<StructureSection load='3f2k' size='340' side='right' caption='[[3f2k]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<StructureSection load='3f2k' size='340' side='right'caption='[[3f2k]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3f2k]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F2K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3f2k]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F2K FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SETMAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SETMAR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<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>
+<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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3f2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2k OCA], [http://pdbe.org/3f2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3f2k RCSB], [http://www.ebi.ac.uk/pdbsum/3f2k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3f2k ProSAT]</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=3f2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2k OCA], [https://pdbe.org/3f2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f2k RCSB], [https://www.ebi.ac.uk/pdbsum/3f2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f2k ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SETMR_HUMAN SETMR_HUMAN]] Histone methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3, 2 specific tags for epigenetic transcriptional activation. Specifically mediates dimethylation of H3 'Lys-36'. Has sequence-specific DNA-binding activity and recognizes the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. Has DNA nicking activity. Has in vivo end joining activity and may mediate genomic integration of foreign DNA.<ref>PMID:16332963</ref> <ref>PMID:16672366</ref> <ref>PMID:17877369</ref> <ref>PMID:17403897</ref>
+[[https://www.uniprot.org/uniprot/SETMR_HUMAN SETMR_HUMAN]] Histone methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3, 2 specific tags for epigenetic transcriptional activation. Specifically mediates dimethylation of H3 'Lys-36'. Has sequence-specific DNA-binding activity and recognizes the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. Has DNA nicking activity. Has in vivo end joining activity and may mediate genomic integration of foreign DNA.<ref>PMID:16332963</ref> <ref>PMID:16672366</ref> <ref>PMID:17877369</ref> <ref>PMID:17403897</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 24: / Line 24: @@
 ==See Also==
-*[[Histone methyltransferase|Histone methyltransferase]]
+*[[Histone methyltransferase 3D structures|Histone methyltransferase 3D structures]]
 == References ==
 <references/>
@@ Line 31: / Line 31: @@
 [[Category: Histone-lysine N-methyltransferase]]
 [[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Amaya, M F]]
 [[Category: Arrowsmith, C H]]

3f2k: Difference between revisions

Revision as of 09:22, 23 February 2022

Structure of the transposase domain of human Histone-lysine N-methyltransferase SETMAR

Structural highlights

Function

Evolutionary Conservation

See Also

References

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