3ufb - Revision history

OCA at 08:38, 20 March 2024

OCA — Wed, 20 Mar 2024 08:38:34 GMT

←Older revision		Revision as of 08:38, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3ufb' size='340' side='right'caption='[[3ufb]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3ufb' size='340' side='right'caption='[[3ufb]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ufb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Vibvy Vibvy~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UFB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ufb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus_YJ016 Vibrio vulnificus YJ016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UFB FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>VV0266 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=196600 VIBVY])</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]] 1.8Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Site~~-~~specific_DNA-methyltransferase_(adenine-specific) Site-specific DNA-methyltransferase (adenine-specific)]~~, ~~with EC number~~ [~~https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.~~1.~~1.72 2.1.1.72] </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=3ufb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ufb OCA], [https://pdbe.org/3ufb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ufb RCSB], [https://www.ebi.ac.uk/pdbsum/3ufb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ufb 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=3ufb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ufb OCA], [https://pdbe.org/3ufb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ufb RCSB], [https://www.ebi.ac.uk/pdbsum/3ufb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ufb ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q7MPU6_VIBVY Q7MPU6_VIBVY]
-	In multifunctional type I restriction enzymes, active methyltransferases (MTases) are constituted of methylation (HsdM) and specificity (HsdS) subunits. In this study, the crystal structure of a putative HsdM subunit from Vibrio vulnificus YJ016 (vvHsdM) was elucidated at a resolution of 1.80 A. A cofactor-binding site for S-adenosyl-L-methionine (SAM, a methyl-group donor) is formed within the C-terminal domain of an alpha/beta-fold, in which a number of residues are conserved, including the GxGG and (N/D)PP(F/Y) motifs, which are likely to interact with several functional moieties of the SAM methyl-group donor. Comparison with the N6 DNA MTase of Thermus aquaticus and other HsdM structures suggests that two aromatic rings (Phe199 and Phe312) in the motifs that are conserved among the HsdMs may sandwich both sides of the adenine ring of the recognition sequence so that a conserved Asn residue (Asn309) can interact with the N6 atom of the target adenine base (a methyl-group acceptor) and locate the target adenine base close to the transferred SAM methyl group.	+
-		+
-	Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.,Park SY, Lee HJ, Song JM, Sun J, Hwang HJ, Nishi K, Kim JS Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):~~1570-7. doi:, 10.1107~~/~~S0907444912038826. Epub 2012 Oct 18. PMID:23090406<ref>PMID:23090406<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3ufb" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Vibvy~~]]	+	[[Category: Vibrio vulnificus YJ016]]
-	[[Category: Kim~~, J S~~]]	+	[[Category: Kim JS]]
-	[[Category: Lee~~, H J~~]]	+	[[Category: Lee HJ]]
-	[[Category: Nishi, K]]	+	[[Category: Nishi K]]
-	[[Category: Park~~, S Y~~]]	+	[[Category: Park SY]]
-	[[Category: Song~~, J M~~]]	+	[[Category: Song JM]]
-	[[Category: Sun, J]]	+	[[Category: Sun J]]
-	~~[[Category: Methyltransferase activity]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:10, 13 July 2022

OCA — Wed, 13 Jul 2022 06:10:53 GMT

←Older revision		Revision as of 06:10, 13 July 2022
Line 1:		Line 1:

	==Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016==		==Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016==
-	<StructureSection load='3ufb' size='340' side='right' caption='[[3ufb]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='3ufb' size='340' side='right'caption='[[3ufb]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ufb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Vibvy Vibvy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UFB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3UFB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ufb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibvy Vibvy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UFB FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VV0266 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196600 VIBVY])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VV0266 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196600 VIBVY])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Site-specific_DNA-methyltransferase_(adenine-specific) Site-specific DNA-methyltransferase (adenine-specific)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.72 2.1.1.72] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Site-specific_DNA-methyltransferase_(adenine-specific) Site-specific DNA-methyltransferase (adenine-specific)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.72 2.1.1.72] </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=3ufb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ufb OCA], [~~http~~://pdbe.org/3ufb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ufb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ufb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ufb 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=3ufb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ufb OCA], [https://pdbe.org/3ufb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ufb RCSB], [https://www.ebi.ac.uk/pdbsum/3ufb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ufb ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Vibvy]]		[[Category: Vibvy]]
	[[Category: Kim, J S]]		[[Category: Kim, J S]]

OCA at 21:53, 5 August 2016

OCA — Fri, 05 Aug 2016 21:53:22 GMT

←Older revision		Revision as of 21:53, 5 August 2016
Line 1:		Line 1:
-	[[Image:3ufb.jpg\|left\|200px]]

-	~~{{STRUCTURE_3ufb~~\| ~~PDB~~=3ufb \| ~~SCENE~~= }}	+	==Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016==
		+	<StructureSection load='3ufb' size='340' side='right' caption='[[3ufb]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ufb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibvy Vibvy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UFB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UFB FirstGlance]. <br>
		+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VV0266 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196600 VIBVY])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Site-specific_DNA-methyltransferase_(adenine-specific) Site-specific DNA-methyltransferase (adenine-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.72 2.1.1.72] </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=3ufb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ufb OCA], [http://pdbe.org/3ufb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ufb RCSB], [http://www.ebi.ac.uk/pdbsum/3ufb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ufb ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In multifunctional type I restriction enzymes, active methyltransferases (MTases) are constituted of methylation (HsdM) and specificity (HsdS) subunits. In this study, the crystal structure of a putative HsdM subunit from Vibrio vulnificus YJ016 (vvHsdM) was elucidated at a resolution of 1.80 A. A cofactor-binding site for S-adenosyl-L-methionine (SAM, a methyl-group donor) is formed within the C-terminal domain of an alpha/beta-fold, in which a number of residues are conserved, including the GxGG and (N/D)PP(F/Y) motifs, which are likely to interact with several functional moieties of the SAM methyl-group donor. Comparison with the N6 DNA MTase of Thermus aquaticus and other HsdM structures suggests that two aromatic rings (Phe199 and Phe312) in the motifs that are conserved among the HsdMs may sandwich both sides of the adenine ring of the recognition sequence so that a conserved Asn residue (Asn309) can interact with the N6 atom of the target adenine base (a methyl-group acceptor) and locate the target adenine base close to the transferred SAM methyl group.

-	~~===Crystal structure~~ of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016~~===~~	+	Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.,Park SY, Lee HJ, Song JM, Sun J, Hwang HJ, Nishi K, Kim JS Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1570-7. doi:, 10.1107/S0907444912038826. Epub 2012 Oct 18. PMID:23090406<ref>PMID:23090406</ref>

-		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~==About this Structure==~~	+	</div>
-	~~[[3ufb]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Vibrio_vulnificus_yj016 Vibrio vulnificus yj016]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca~~-~~bin~~/~~ocashort?id~~=~~3UFB OCA].~~	+	<div class="pdbe-citations 3ufb" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Vibrio vulnificus yj016~~]]	+	== References ==
-	[[Category: Kim, J S.]]	+	<references/>
-	[[Category: Lee, H J.]]	+	__TOC__
-	[[Category: Nishi, K.]]	+	</StructureSection>
-	[[Category: Park, S Y.]]	+	[[Category: Vibvy]]
-	[[Category: Song, J M.]]	+	[[Category: Kim, J S]]
-	[[Category: Sun, J.]]	+	[[Category: Lee, H J]]
		+	[[Category: Nishi, K]]
		+	[[Category: Park, S Y]]
		+	[[Category: Song, J M]]
		+	[[Category: Sun, J]]
	[[Category: Methyltransferase activity]]		[[Category: Methyltransferase activity]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 13:53, 8 November 2012

OCA — Thu, 08 Nov 2012 13:53:24 GMT

←Older revision		Revision as of 13:53, 8 November 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3ufb.jpg\|left\|200px]]

-	~~The entry~~ 3ufb ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_3ufb\| PDB=3ufb \| SCENE= }}

-	~~Authors: Park, S.Y., Lee, H.J., Sun, J., Nishi, K., Song, J.M., Kim, J.S.~~	+	===Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016===

-	~~Description: Crystal structure of~~ a ~~modification subunit of a putative type I restriction enzyme~~ from Vibrio vulnificus ~~YJ016~~	+
		+	==About this Structure==
		+	[[3ufb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_vulnificus_yj016 Vibrio vulnificus yj016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UFB OCA].
		+	[[Category: Vibrio vulnificus yj016]]
		+	[[Category: Kim, J S.]]
		+	[[Category: Lee, H J.]]
		+	[[Category: Nishi, K.]]
		+	[[Category: Park, S Y.]]
		+	[[Category: Song, J M.]]
		+	[[Category: Sun, J.]]
		+	[[Category: Methyltransferase activity]]
		+	[[Category: Transferase]]

OCA at 07:34, 7 December 2011

OCA — Wed, 07 Dec 2011 07:34:57 GMT

←Older revision		Revision as of 07:34, 7 December 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3ufb is ON HOLD	+	The entry 3ufb is ON HOLD until Paper Publication

	Authors: Park, S.Y., Lee, H.J., Sun, J., Nishi, K., Song, J.M., Kim, J.S.		Authors: Park, S.Y., Lee, H.J., Sun, J., Nishi, K., Song, J.M., Kim, J.S.

	Description: Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016		Description: Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016

OCA: Protected "3ufb" [edit=sysop:move=sysop]

OCA — Wed, 09 Nov 2011 11:17:55 GMT

Protected "3ufb" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:17, 9 November 2011

OCA: New page: '''Unreleased structure''' The entry 3ufb is ON HOLD Authors: Park, S.Y., Lee, H.J., Sun, J., Nishi, K., Song, J.M., Kim, J.S. Description: Crystal structure of a modification subunit ...

OCA — Wed, 09 Nov 2011 11:17:54 GMT

New page: '''Unreleased structure''' The entry 3ufb is ON HOLD Authors: Park, S.Y., Lee, H.J., Sun, J., Nishi, K., Song, J.M., Kim, J.S. Description: Crystal structure of a modification subunit ...

New page

'''Unreleased structure'''

The entry 3ufb is ON HOLD

Authors: Park, S.Y., Lee, H.J., Sun, J., Nishi, K., Song, J.M., Kim, J.S.

Description: Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016