4hdu - Revision history

OCA at 15:04, 20 September 2023

2023-09-20T15:04:29Z

←Older revision		Revision as of 15:04, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4hdu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HDU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HDU FirstGlance]. <br>		<table><tr><td colspan='2'>[[4hdu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HDU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HDU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</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]] 2.848Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</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=4hdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hdu OCA], [https://pdbe.org/4hdu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hdu RCSB], [https://www.ebi.ac.uk/pdbsum/4hdu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hdu 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=4hdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hdu OCA], [https://pdbe.org/4hdu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hdu RCSB], [https://www.ebi.ac.uk/pdbsum/4hdu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hdu ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:11, 3 November 2022

2022-11-03T08:11:59Z

←Older revision		Revision as of 08:11, 3 November 2022
Line 1:		Line 1:

	==Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2-aminopurine==		==Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2-aminopurine==
-	<StructureSection load='4hdu' size='340' side='right' caption='[[4hdu]], [[Resolution\|resolution]] 2.85Å' scene=''>	+	<StructureSection load='4hdu' size='340' side='right'caption='[[4hdu]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4hdu]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cbs_356 Cbs 356~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HDU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4HDU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4hdu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HDU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HDU FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hdv\|4hdv]]</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=4hdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hdu OCA], [https://pdbe.org/4hdu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hdu RCSB], [https://www.ebi.ac.uk/pdbsum/4hdu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hdu ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">atl1, SPAC1250.04c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])~~</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=4hdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hdu OCA], [~~http~~://pdbe.org/4hdu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4hdu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4hdu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4hdu ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ATL1_SCHPO ATL1_SCHPO]] Acts as a DNA damage recognition factor. Required for DNA repair from mutagenic O(6)-alkylguanine adducts. Binds O(6)-alkylguanine lesions providing a signal for other DNA repair pathways.	+	[https://www.uniprot.org/uniprot/ATL1_SCHPO ATL1_SCHPO] Acts as a DNA damage recognition factor. Required for DNA repair from mutagenic O(6)-alkylguanine adducts. Binds O(6)-alkylguanine lesions providing a signal for other DNA repair pathways.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cbs 356~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Tainer, J A~~]]	+	[[Category: Schizosaccharomyces pombe]]
-	[[Category: ~~Tubbs, J L~~]]	+	[[Category: Tainer JA]]
-	[[Category: ~~Alkylation]]~~	+	[[Category: Tubbs JL]]
-	~~[[Category: Alkyltransferase]]~~	+
-	~~[[Category: Base repair]]~~	+
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Guanine]]~~	+
-	~~[[Category: Ner]]~~	+
-	~~[[Category: Nucleotide excision repair~~]]	+

OCA at 18:26, 4 August 2016

2016-08-04T18:26:34Z

←Older revision		Revision as of 18:26, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2-aminopurine==		==Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2-aminopurine==
	<StructureSection load='4hdu' size='340' side='right' caption='[[4hdu]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='4hdu' size='340' side='right' caption='[[4hdu]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4hdu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Schizosaccharomyces_pombe Schizosaccharomyces pombe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HDU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HDU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4hdu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HDU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HDU FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hdv\|4hdv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hdv\|4hdv]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">atl1, SPAC1250.04c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 ~~Schizosaccharomyces pombe~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">atl1, SPAC1250.04c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</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=4hdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hdu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hdu RCSB], [http://www.ebi.ac.uk/pdbsum/4hdu 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=4hdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hdu OCA], [http://pdbe.org/4hdu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hdu RCSB], [http://www.ebi.ac.uk/pdbsum/4hdu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hdu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4hdu" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Schizosaccharomyces pombe~~]]	+	[[Category: Cbs 356]]
	[[Category: Tainer, J A]]		[[Category: Tainer, J A]]
	[[Category: Tubbs, J L]]		[[Category: Tubbs, J L]]

OCA at 11:54, 25 December 2014

2014-12-25T11:54:11Z

←Older revision		Revision as of 11:54, 25 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4hdu.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2-aminopurine==
		+	<StructureSection load='4hdu' size='340' side='right' caption='[[4hdu]], [[Resolution\|resolution]] 2.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4hdu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HDU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HDU FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4hdv\|4hdv]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">atl1, SPAC1250.04c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 Schizosaccharomyces pombe])</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=4hdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hdu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hdu RCSB], [http://www.ebi.ac.uk/pdbsum/4hdu PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ATL1_SCHPO ATL1_SCHPO]] Acts as a DNA damage recognition factor. Required for DNA repair from mutagenic O(6)-alkylguanine adducts. Binds O(6)-alkylguanine lesions providing a signal for other DNA repair pathways.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Alkyltransferase-like (ATL) proteins in Schizosaccharomyces pombe (Atl1) and Thermus thermophilus (TTHA1564) protect against the adverse effects of DNA alkylation damage by flagging O(6)-alkylguanine lesions for nucleotide excision repair (NER). We show that both ATL proteins bind with high affinity to oligodeoxyribonucleotides containing O(6)-alkylguanines differing in size, polarity, and charge of the alkyl group. However, Atl1 shows a greater ability than TTHA1564 to distinguish between O(6)-alkylguanine and guanine and in an unprecedented mechanism uses Arg69 to probe the electrostatic potential surface of O(6)-alkylguanine, as determined using molecular mechanics calculations. An unexpected consequence of this feature is the recognition of 2,6-diaminopurine and 2-aminopurine, as confirmed in crystal structures of respective Atl1-DNA complexes. O(6)-Alkylguanine and guanine discrimination is diminished for Atl1 R69A and R69F mutants, and S. pombe R69A and R69F mutants are more sensitive toward alkylating agent toxicity, revealing the key role of Arg69 in identifying O(6)-alkylguanines critical for NER recognition.

-	~~{{STRUCTURE_4hdu\| PDB=4hdu \| SCENE= }}~~	+	Alkyltransferase-like protein (Atl1) distinguishes alkylated guanines for DNA repair using cation-pi interactions.,Wilkinson OJ, Latypov V, Tubbs JL, Millington CL, Morita R, Blackburn H, Marriott A, McGown G, Thorncroft M, Watson AJ, Connolly BA, Grasby JA, Masui R, Hunter CA, Tainer JA, Margison GP, Williams DM Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):18755-60. doi:, 10.1073/pnas.1209451109. Epub 2012 Oct 29. PMID:23112169<ref>PMID:23112169</ref>

-	~~===Crystal structure~~ of S. ~~pombe ATL1 in complex with damaged DNA containing 2-aminopurine===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_23112169}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[4hdu]] is a 3 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HDU OCA].~~	+	</StructureSection>
	[[Category: Schizosaccharomyces pombe]]		[[Category: Schizosaccharomyces pombe]]
-	[[Category: Tainer, J A.]]	+	[[Category: Tainer, J A]]
-	[[Category: Tubbs, J L.]]	+	[[Category: Tubbs, J L]]
	[[Category: Alkylation]]		[[Category: Alkylation]]
	[[Category: Alkyltransferase]]		[[Category: Alkyltransferase]]

OCA at 09:30, 2 January 2013

2013-01-02T09:30:48Z

←Older revision		Revision as of 09:30, 2 January 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4hdu.jpg\|left\|200px]]

-	~~The entry~~ 4hdu ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4hdu\| PDB=4hdu \| SCENE= }}

-	~~Authors: Tubbs, J.L., Tainer, J.A~~.	+	===Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2-aminopurine===

-	~~Description: Crystal~~ structure ~~of S~~. pombe ~~ATL1 in complex with damaged DNA containing 2~~-~~aminopurine~~	+	{{ABSTRACT_PUBMED_23112169}}
		+
		+	==About this Structure==
		+	[[4hdu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HDU OCA].
		+	[[Category: Schizosaccharomyces pombe]]
		+	[[Category: Tainer, J A.]]
		+	[[Category: Tubbs, J L.]]
		+	[[Category: Alkylation]]
		+	[[Category: Alkyltransferase]]
		+	[[Category: Base repair]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Dna damage]]
		+	[[Category: Dna repair]]
		+	[[Category: Guanine]]
		+	[[Category: Ner]]
		+	[[Category: Nucleotide excision repair]]

OCA at 09:03, 21 November 2012

2012-11-21T09:03:37Z

←Older revision		Revision as of 09:03, 21 November 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Tubbs, J.L., Tainer, J.A.		Authors: Tubbs, J.L., Tainer, J.A.

	Description: Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2-aminopurine		Description: Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2-aminopurine

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

2012-10-10T07:00:54Z

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

←Older revision

Revision as of 07:00, 10 October 2012

OCA: New page: '''Unreleased structure''' The entry 4hdu is ON HOLD Authors: Tubbs, J.L., Tainer, J.A. Description: Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2-aminopu...

2012-10-10T07:00:53Z

New page: '''Unreleased structure''' The entry 4hdu is ON HOLD Authors: Tubbs, J.L., Tainer, J.A. Description: Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2-aminopu...

New page

'''Unreleased structure'''

The entry 4hdu is ON HOLD

Authors: Tubbs, J.L., Tainer, J.A.

Description: Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2-aminopurine