1enj - Revision history

OCA at 07:05, 7 February 2024

2024-02-07T07:05:03Z

←Older revision		Revision as of 07:05, 7 February 2024
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	<StructureSection load='1enj' size='340' side='right'caption='[[1enj]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1enj' size='340' side='right'caption='[[1enj]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpt4 Bpt4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>
-	</td></tr><tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"~~><span class~~=~~'plainlinks'~~>[~~https://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)~~]~~, with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.~~1.~~25.1 3.1.25.1] </span>~~</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1enj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1enj OCA], [https://pdbe.org/1enj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1enj RCSB], [https://www.ebi.ac.uk/pdbsum/1enj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1enj 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=1enj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1enj OCA], [https://pdbe.org/1enj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1enj RCSB], [https://www.ebi.ac.uk/pdbsum/1enj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1enj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/END5_BPT4 END5_BPT4]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 17:		Line 19:
	</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=1enj ConSurf].		</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=1enj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Crystallographic study of bacteriophage T4 endonuclease V, which is involved in the initial step of the pyrimidine dimer-specific excision repair pathway, has been carried out with respect to the wild-type and three different mutant enzymes. This enzyme catalyzes the cleavage of the N-glycosyl bond at the 5'-side of the pyrimidine dimer, and subsequently incises the phosphodiester bond at the apyrimidinic site through a beta-elimination reaction. The structure of the wild-type enzyme refined at 1.45 A resolution reveals the detailed molecular architecture. The enzyme is composed of a single compact domain classified as an all-alpha structure. The molecule is stabilized mainly by three hydrophobic cores, two of which include many aromatic side-chain interactions. The structure has a unique folding motif, where the amino-terminal segment penetrates between two major alpha-helices and prevents their direct contact, and it is incompatible with the close-packing category of helices for protein folding. The concave surface, covered with many positive charges, implies an interface for DNA binding. The glycosylase catalytic center, which comprises Glu23 and the surrounding basic residues Arg3, Arg22 and Arg26, lie in this basic surface. The crystal structures of the three active-site mutants, in which Glu23 was replaced by Gln(E23Q) and Asp (E23D), respectively, and Arg3 by Gln (R3Q), have been determined at atomic resolution. The backbone structures of the E23Q and R3Q mutants were almost identical with that of the wild-type, while the E23D mutation induces a small, but significant, change in the backbone structure, such as an increase of the central kink of the H1 helix at Pro25. In the catalytic center of the glycosylase, however, these three mutations do not generate notable movements of protein atoms, except for significant shifts of some bound water molecules. Thus, the structural differences between the wild-type and each mutant are confined to the remarkably small region around their replaced chemical groups. Combined with the biochemical studies and the difference circular dichroism measurements, these results allow us to conclude that the negatively charged carboxyl group of Glu23 is essential for the cleavage of the N-glycosyl bond, and that the positively charged guanidino group of Arg3 is crucial to bind the substrate, a DNA duplex containing a pyrimidine dimer. The amino terminal alpha-amino group is located at a position approximately 4.4 A away from the carboxyl group of Glu23. These structural features are generally consistent with the reaction scheme proposed by Dodson and co-workers.
-
-	Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants.,Morikawa K, Ariyoshi M, Vassylyev DG, Matsumoto O, Katayanagi K, Ohtsuka E J Mol Biol. 1995 Jun 2;249(2):360-75. PMID:7783199<ref>PMID:7783199</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1enj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]		*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4~~]]	+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ariyoshi, M]]	+	[[Category: Ariyoshi M]]
-	[[Category: Katayanagi, K]]	+	[[Category: Katayanagi K]]
-	[[Category: Matsumoto, O]]	+	[[Category: Matsumoto O]]
-	[[Category: Morikawa, K]]	+	[[Category: Morikawa K]]
-	[[Category: Ohtsuka, E]]	+	[[Category: Ohtsuka E]]
-	[[Category: Vassylyev~~, D G]]~~	+	[[Category: Vassylyev DG]]
-	~~[[Category: Endonuclease~~]]	+

OCA at 09:39, 21 July 2021

2021-07-21T09:39:43Z

←Older revision		Revision as of 09:39, 21 July 2021
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	<StructureSection load='1enj' size='340' side='right'caption='[[1enj]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1enj' size='340' side='right'caption='[[1enj]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </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=1enj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1enj OCA], [~~http~~://pdbe.org/1enj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1enj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1enj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1enj 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=1enj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1enj OCA], [https://pdbe.org/1enj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1enj RCSB], [https://www.ebi.ac.uk/pdbsum/1enj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1enj ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 11:18, 16 October 2019

2019-10-16T11:18:43Z

←Older revision		Revision as of 11:18, 16 October 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS==		==CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS==
-	<StructureSection load='1enj' size='340' side='right' caption='[[1enj]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1enj' size='340' side='right'caption='[[1enj]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>
Line 26:		Line 26:
	</div>		</div>
	<div class="pdbe-citations 1enj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1enj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Ariyoshi, M]]		[[Category: Ariyoshi, M]]
	[[Category: Katayanagi, K]]		[[Category: Katayanagi, K]]

OCA at 07:20, 20 December 2017

2017-12-20T07:20:22Z

←Older revision		Revision as of 07:20, 20 December 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS==		==CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS==
	<StructureSection load='1enj' size='340' side='right' caption='[[1enj]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1enj' size='340' side='right' caption='[[1enj]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </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=1enj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1enj OCA], [http://pdbe.org/1enj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1enj RCSB], [http://www.ebi.ac.uk/pdbsum/1enj 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=1enj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1enj OCA], [http://pdbe.org/1enj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1enj RCSB], [http://www.ebi.ac.uk/pdbsum/1enj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1enj ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/en/1enj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/en/1enj_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 25:		Line 26:
	</div>		</div>
	<div class="pdbe-citations 1enj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1enj" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:48, 7 February 2016

2016-02-07T20:48:19Z

←Older revision		Revision as of 20:48, 7 February 2016
Line 14:		Line 14:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=1enj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:51, 10 September 2015

2015-09-10T04:51:41Z

←Older revision		Revision as of 04:51, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1enj' size='340' side='right' caption='[[1enj]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1enj' size='340' side='right' caption='[[1enj]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_t4 Enterobacteria phage t4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </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=1enj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1enj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1enj RCSB], [http://www.ebi.ac.uk/pdbsum/1enj 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=1enj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1enj OCA], [http://pdbe.org/1enj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1enj RCSB], [http://www.ebi.ac.uk/pdbsum/1enj PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 1enj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 31:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t4~~]]	+	[[Category: Bpt4]]
	[[Category: Ariyoshi, M]]		[[Category: Ariyoshi, M]]
	[[Category: Katayanagi, K]]		[[Category: Katayanagi, K]]

OCA at 19:30, 22 December 2014

2014-12-22T19:30:33Z

←Older revision		Revision as of 19:30, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1enj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1enj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1enj RCSB], [http://www.ebi.ac.uk/pdbsum/1enj 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=1enj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1enj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1enj RCSB], [http://www.ebi.ac.uk/pdbsum/1enj PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
-	[[Category: Ariyoshi, M.]]	+	[[Category: Ariyoshi, M]]
-	[[Category: Katayanagi, K.]]	+	[[Category: Katayanagi, K]]
-	[[Category: Matsumoto, O.]]	+	[[Category: Matsumoto, O]]
-	[[Category: Morikawa, K.]]	+	[[Category: Morikawa, K]]
-	[[Category: Ohtsuka, E.]]	+	[[Category: Ohtsuka, E]]
-	[[Category: Vassylyev, D G.]]	+	[[Category: Vassylyev, D G]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]

OCA at 11:30, 24 September 2014

2014-09-24T11:30:13Z

←Older revision		Revision as of 11:30, 24 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1enj.~~png\|left~~\|200px]]	+	==CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS==
		+	<StructureSection load='1enj' size='340' side='right' caption='[[1enj]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1enj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_(pyrimidine_dimer) Deoxyribonuclease (pyrimidine dimer)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.25.1 3.1.25.1] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1enj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1enj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1enj RCSB], [http://www.ebi.ac.uk/pdbsum/1enj PDBsum]</span></td></tr>
		+	<table>
		+	== 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/en/1enj_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Crystallographic study of bacteriophage T4 endonuclease V, which is involved in the initial step of the pyrimidine dimer-specific excision repair pathway, has been carried out with respect to the wild-type and three different mutant enzymes. This enzyme catalyzes the cleavage of the N-glycosyl bond at the 5'-side of the pyrimidine dimer, and subsequently incises the phosphodiester bond at the apyrimidinic site through a beta-elimination reaction. The structure of the wild-type enzyme refined at 1.45 A resolution reveals the detailed molecular architecture. The enzyme is composed of a single compact domain classified as an all-alpha structure. The molecule is stabilized mainly by three hydrophobic cores, two of which include many aromatic side-chain interactions. The structure has a unique folding motif, where the amino-terminal segment penetrates between two major alpha-helices and prevents their direct contact, and it is incompatible with the close-packing category of helices for protein folding. The concave surface, covered with many positive charges, implies an interface for DNA binding. The glycosylase catalytic center, which comprises Glu23 and the surrounding basic residues Arg3, Arg22 and Arg26, lie in this basic surface. The crystal structures of the three active-site mutants, in which Glu23 was replaced by Gln(E23Q) and Asp (E23D), respectively, and Arg3 by Gln (R3Q), have been determined at atomic resolution. The backbone structures of the E23Q and R3Q mutants were almost identical with that of the wild-type, while the E23D mutation induces a small, but significant, change in the backbone structure, such as an increase of the central kink of the H1 helix at Pro25. In the catalytic center of the glycosylase, however, these three mutations do not generate notable movements of protein atoms, except for significant shifts of some bound water molecules. Thus, the structural differences between the wild-type and each mutant are confined to the remarkably small region around their replaced chemical groups. Combined with the biochemical studies and the difference circular dichroism measurements, these results allow us to conclude that the negatively charged carboxyl group of Glu23 is essential for the cleavage of the N-glycosyl bond, and that the positively charged guanidino group of Arg3 is crucial to bind the substrate, a DNA duplex containing a pyrimidine dimer. The amino terminal alpha-amino group is located at a position approximately 4.4 A away from the carboxyl group of Glu23. These structural features are generally consistent with the reaction scheme proposed by Dodson and co-workers.

-	~~{{STRUCTURE_1enj\| PDB=1enj \| SCENE= }}~~	+	Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants.,Morikawa K, Ariyoshi M, Vassylyev DG, Matsumoto O, Katayanagi K, Ohtsuka E J Mol Biol. 1995 Jun 2;249(2):360-75. PMID:7783199<ref>PMID:7783199</ref>

-	~~===CRYSTAL STRUCTURE OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME FROM BACTERIOPHAGE T4: REFINEMENT AT 1.45 ANGSTROMS AND X-RAY ANALYSIS OF THE THREE ACTIVE SITE MUTANTS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7783199}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1enj]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA].~~	+

	==See Also==		==See Also==
	*[[Endonuclease\|Endonuclease]]		*[[Endonuclease\|Endonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:007783199<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Ariyoshi, M.]]		[[Category: Ariyoshi, M.]]

OCA at 07:49, 20 October 2012

2012-10-20T07:49:32Z

←Older revision		Revision as of 07:49, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1enj]] is a 1 chain structure ~~of [[Endonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA].	+	[[1enj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENJ OCA].

	==See Also==		==See Also==

OCA: Protected "1enj" [edit=sysop:move=sysop]

2012-07-25T17:35:01Z

Protected "1enj" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:35, 25 July 2012