4zbz - Revision history

OCA at 15:43, 8 November 2023

OCA — Wed, 08 Nov 2023 15:43:28 GMT

←Older revision		Revision as of 15:43, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4zbz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZBZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4zbz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZBZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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=4zbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zbz OCA], [https://pdbe.org/4zbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zbz RCSB], [https://www.ebi.ac.uk/pdbsum/4zbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zbz 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=4zbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zbz OCA], [https://pdbe.org/4zbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zbz RCSB], [https://www.ebi.ac.uk/pdbsum/4zbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zbz ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:48, 10 May 2023

OCA — Wed, 10 May 2023 07:48:21 GMT

←Older revision		Revision as of 07:48, 10 May 2023
Line 1:		Line 1:

	==Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free form, X-ray wavelength=1.5418)==		==Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free form, X-ray wavelength=1.5418)==
-	<StructureSection load='4zbz' size='340' side='right' caption='[[4zbz]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4zbz' size='340' side='right'caption='[[4zbz]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zbz]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sulto Sulto~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZBZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ZBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zbz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZBZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zbx\|4zbx]], [[4zby\|4zby]]</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=4zbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zbz OCA], [https://pdbe.org/4zbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zbz RCSB], [https://www.ebi.ac.uk/pdbsum/4zbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zbz ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STK_22380 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273063 SULTO])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </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=4zbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zbz OCA], [~~http~~://pdbe.org/4zbz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4zbz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4zbz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4zbz ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/UDGA_SULTO UDGA_SULTO] Removes uracil bases that are present in DNA as a result of either deamination of cytosine or misincorporation of dUMP instead of dTMP.<ref>PMID:26318717</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4zbz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4zbz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sulto~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Uracil-DNA glycosylase~~]]	+	[[Category: Sulfurisphaera tokodaii str. 7]]
-	[[Category: Kawai, A]]	+	[[Category: Kawai A]]
-	[[Category: Miyamoto, S]]	+	[[Category: Miyamoto S]]
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Uracil-dna glycosylase~~]]	+

OCA at 16:22, 16 November 2017

OCA — Thu, 16 Nov 2017 16:22:18 GMT

←Older revision		Revision as of 16:22, 16 November 2017
Line 1:		Line 1:
		+
	==Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free form, X-ray wavelength=1.5418)==		==Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free form, X-ray wavelength=1.5418)==
	<StructureSection load='4zbz' size='340' side='right' caption='[[4zbz]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4zbz' size='340' side='right' caption='[[4zbz]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zbz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zbz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulto Sulto]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZBZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zbx\|4zbx]], [[4zby\|4zby]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zbx\|4zbx]], [[4zby\|4zby]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">STK_22380 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273063 SULTO])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </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=4zbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zbz OCA], [http://pdbe.org/4zbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zbz RCSB], [http://www.ebi.ac.uk/pdbsum/4zbz PDBsum]</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=4zbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zbz OCA], [http://pdbe.org/4zbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zbz RCSB], [http://www.ebi.ac.uk/pdbsum/4zbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zbz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Sulto]]
	[[Category: Uracil-DNA glycosylase]]		[[Category: Uracil-DNA glycosylase]]
	[[Category: Kawai, A]]		[[Category: Kawai, A]]

OCA at 06:42, 30 September 2015

OCA — Wed, 30 Sep 2015 06:42:51 GMT

←Older revision		Revision as of 06:42, 30 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zbx\|4zbx]], [[4zby\|4zby]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zbx\|4zbx]], [[4zby\|4zby]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </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=4zbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4zbz RCSB], [http://www.ebi.ac.uk/pdbsum/4zbz PDBsum]</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=4zbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zbz OCA], [http://pdbe.org/4zbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zbz RCSB], [http://www.ebi.ac.uk/pdbsum/4zbz PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Uracil-DNA glycosylases (UDGs) excise uracil from DNA by catalyzing the N-glycosidic bond hydrolysis. Here we report the first crystal structures of an archaeal UDG (stoUDG). Compared with other UDGs, stoUDG has a different structure of the leucine-intercalation loop, which is important for DNA binding. The stoUDG-DNA complex model indicated that Leu169, Tyr170, and Asn171 in the loop are involved in DNA intercalation. Mutational analysis showed that Tyr170 is critical for substrate DNA recognition. These results indicate that Tyr170 occupies the intercalation site formed after the structural change of the leucine-intercalation loop required for the catalysis.
		+
		+	Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus tokodaii and a function of tyrosine 170 in DNA binding.,Kawai A, Higuchi S, Tsunoda M, Nakamura KT, Yamagata Y, Miyamoto S FEBS Lett. 2015 Sep 14;589(19 Pt B):2675-82. doi: 10.1016/j.febslet.2015.08.019. , Epub 2015 Aug 28. PMID:26318717<ref>PMID:26318717</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4zbz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:21, 9 September 2015

OCA — Wed, 09 Sep 2015 11:21:40 GMT

←Older revision		Revision as of 11:21, 9 September 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free form, X-ray wavelength=1.5418)==
-		+	<StructureSection load='4zbz' size='340' side='right' caption='[[4zbz]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~The entry~~ 4zbz is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4zbz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZBZ FirstGlance]. <br>
-	~~Authors~~: ~~Kawai~~, A., ~~Miyamoto~~, S.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zbx\|4zbx]], [[4zby\|4zby]]</td></tr>
-	~~Description~~: ~~Family 4 uracil~~-DNA glycosylase ~~from Sulfolobus tokodaii (free form~~, X-~~ray wavelength~~=1.~~5418)~~	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase Uracil-DNA glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.27 3.2.2.27] </span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=4zbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4zbz RCSB], [http://www.ebi.ac.uk/pdbsum/4zbz PDBsum]</span></td></tr>
-	[[Category: ~~Miyamoto, S~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Uracil-DNA glycosylase]]
	[[Category: Kawai, A]]		[[Category: Kawai, A]]
		+	[[Category: Miyamoto, S]]
		+	[[Category: Dna repair]]
		+	[[Category: Hydrolase]]
		+	[[Category: Uracil-dna glycosylase]]

OCA at 10:10, 30 April 2015

OCA — Thu, 30 Apr 2015 10:10:12 GMT

←Older revision		Revision as of 10:10, 30 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4zbz is ON HOLD	+	The entry 4zbz is ON HOLD until Paper Publication

	Authors: Kawai, A., Miyamoto, S.		Authors: Kawai, A., Miyamoto, S.

OCA: Protected "4zbz" [edit=sysop:move=sysop]

OCA — Wed, 22 Apr 2015 11:41:39 GMT

Protected "4zbz" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:41, 22 April 2015

OCA: New page: '''Unreleased structure''' The entry 4zbz is ON HOLD Authors: Kawai, A., Miyamoto, S. Description: Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free form, X-ray wavelength...

OCA — Wed, 22 Apr 2015 11:41:38 GMT

New page: '''Unreleased structure''' The entry 4zbz is ON HOLD Authors: Kawai, A., Miyamoto, S. Description: Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free form, X-ray wavelength...

New page

'''Unreleased structure'''

The entry 4zbz is ON HOLD

Authors: Kawai, A., Miyamoto, S.

Description: Family 4 uracil-DNA glycosylase from Sulfolobus tokodaii (free form, X-ray wavelength=1.5418)
[[Category: Unreleased Structures]]
[[Category: Miyamoto, S]]
[[Category: Kawai, A]]