4mb7 - Revision history

OCA at 12:25, 1 March 2024

2024-03-01T12:25:07Z

←Older revision		Revision as of 12:25, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4mb7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MB7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4mb7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MB7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.04Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4mb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mb7 OCA], [https://pdbe.org/4mb7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mb7 RCSB], [https://www.ebi.ac.uk/pdbsum/4mb7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mb7 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=4mb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mb7 OCA], [https://pdbe.org/4mb7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mb7 RCSB], [https://www.ebi.ac.uk/pdbsum/4mb7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mb7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/YL720_MIMIV YL720_MIMIV]		[https://www.uniprot.org/uniprot/YL720_MIMIV YL720_MIMIV]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Assault to DNA that leads to oxidative base damage is repaired by the base excision repair (BER) pathway with specialized enzymes called DNA glycosylases catalyzing the first step of this pathway. These glycosylases can be categorized into two families: the HhH superfamily, which includes endonuclease III (or Nth), and the Fpg/Nei family, which comprises formamidopyrimidine DNA glycosylase (or Fpg) and endonuclease VIII (or Nei). In humans there are three Nei-like (NEIL) glycosylases: NEIL1, 2, and 3. Here we present the first crystal structure of a viral ortholog of the human NEIL2/NEIL3 proteins, Mimivirus Nei2 (MvNei2), determined at 2.04A resolution. The C-terminal region of the MvNei2 enzyme comprises two conserved DNA binding motifs: the helix-two-turns-helix (H2TH) motif and a C-H-C-C type zinc-finger similar to that of human NEIL2. The N-terminal region of MvNei2 is most closely related to NEIL3. Like NEIL3, MvNei2 bears a valine at position 2 instead of the usual proline and it lacks two of the three conserved void-filling residues present in other members of the Fpg/Nei family. Mutational analysis of the only conserved void-filling residue methionine 72 to alanine yields an MvNei2 variant with impaired glycosylase activity. Mutation of the adjacent His73 causes the enzyme to be more productive thereby suggesting a plausible role for this residue in the DNA lesion search process.
-
-	Structural investigation of a viral ortholog of human NEIL2/3 DNA glycosylases.,Prakash A, Eckenroth BE, Averill AM, Imamura K, Wallace SS, Doublie S DNA Repair (Amst). 2013 Oct 10. pii: S1568-7864(13)00234-6. doi:, 10.1016/j.dnarep.2013.09.004. PMID:24120312<ref>PMID:24120312</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4mb7" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:07, 21 December 2022

2022-12-21T11:07:08Z

←Older revision		Revision as of 11:07, 21 December 2022
Line 1:		Line 1:

	==Crystal Structure of a viral DNA glycosylase==		==Crystal Structure of a viral DNA glycosylase==
-	<StructureSection load='4mb7' size='340' side='right' caption='[[4mb7]], [[Resolution\|resolution]] 2.04Å' scene=''>	+	<StructureSection load='4mb7' size='340' side='right'caption='[[4mb7]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4mb7]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Apmv Apmv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MB7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4MB7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4mb7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MB7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease VIII (nei) 2, MIMI_L720 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</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=4mb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mb7 OCA], [https://pdbe.org/4mb7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mb7 RCSB], [https://www.ebi.ac.uk/pdbsum/4mb7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mb7 ProSAT]</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=4mb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mb7 OCA], [~~http~~://pdbe.org/4mb7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4mb7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4mb7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4mb7 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/YL720_MIMIV YL720_MIMIV]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Apmv~~]]	+	[[Category: Acanthamoeba polyphaga mimivirus]]
-	[[Category: ~~Doublie, S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Eckenroth, B E~~]]	+	[[Category: Doublie S]]
-	[[Category: ~~Prakash, A~~]]	+	[[Category: Eckenroth BE]]
-	[[Category: ~~Dna glycosylase]]~~	+	[[Category: Prakash A]]
-	~~[[Category: H2th-motif]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Zinc-finger domain~~]]	+

OCA at 14:24, 11 August 2016

2016-08-11T14:24:16Z

←Older revision		Revision as of 14:24, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of a viral DNA glycosylase==		==Crystal Structure of a viral DNA glycosylase==
	<StructureSection load='4mb7' size='340' side='right' caption='[[4mb7]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='4mb7' size='340' side='right' caption='[[4mb7]], [[Resolution\|resolution]] 2.04Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease VIII (nei) 2, MIMI_L720 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease VIII (nei) 2, MIMI_L720 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</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=4mb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mb7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mb7 RCSB], [http://www.ebi.ac.uk/pdbsum/4mb7 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=4mb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mb7 OCA], [http://pdbe.org/4mb7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mb7 RCSB], [http://www.ebi.ac.uk/pdbsum/4mb7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mb7 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4mb7" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:40, 5 January 2015

2015-01-05T08:40:47Z

←Older revision		Revision as of 08:40, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4mb7~~\| ~~PDB~~=4mb7 \| ~~SCENE~~= }}	+	==Crystal Structure of a viral DNA glycosylase==
-	===~~Crystal Structure~~ of a viral DNA glycosylase~~===~~	+	<StructureSection load='4mb7' size='340' side='right' caption='[[4mb7]], [[Resolution\|resolution]] 2.04Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24120312}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4mb7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Apmv Apmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MB7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MB7 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Endonuclease VIII (nei) 2, MIMI_L720 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</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=4mb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mb7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mb7 RCSB], [http://www.ebi.ac.uk/pdbsum/4mb7 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Assault to DNA that leads to oxidative base damage is repaired by the base excision repair (BER) pathway with specialized enzymes called DNA glycosylases catalyzing the first step of this pathway. These glycosylases can be categorized into two families: the HhH superfamily, which includes endonuclease III (or Nth), and the Fpg/Nei family, which comprises formamidopyrimidine DNA glycosylase (or Fpg) and endonuclease VIII (or Nei). In humans there are three Nei-like (NEIL) glycosylases: NEIL1, 2, and 3. Here we present the first crystal structure of a viral ortholog of the human NEIL2/NEIL3 proteins, Mimivirus Nei2 (MvNei2), determined at 2.04A resolution. The C-terminal region of the MvNei2 enzyme comprises two conserved DNA binding motifs: the helix-two-turns-helix (H2TH) motif and a C-H-C-C type zinc-finger similar to that of human NEIL2. The N-terminal region of MvNei2 is most closely related to NEIL3. Like NEIL3, MvNei2 bears a valine at position 2 instead of the usual proline and it lacks two of the three conserved void-filling residues present in other members of the Fpg/Nei family. Mutational analysis of the only conserved void-filling residue methionine 72 to alanine yields an MvNei2 variant with impaired glycosylase activity. Mutation of the adjacent His73 causes the enzyme to be more productive thereby suggesting a plausible role for this residue in the DNA lesion search process.

-	~~==About this Structure==~~	+	Structural investigation of a viral ortholog of human NEIL2/3 DNA glycosylases.,Prakash A, Eckenroth BE, Averill AM, Imamura K, Wallace SS, Doublie S DNA Repair (Amst). 2013 Oct 10. pii: S1568-7864(13)00234-6. doi:, 10.1016/j.dnarep.2013.09.004. PMID:24120312<ref>PMID:24120312</ref>
-	~~[[4mb7]] is~~ a ~~1 chain structure with sequence from [http:/~~/en.~~wikipedia~~.~~org/wiki/Apmv Apmv]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=4MB7 OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024120312</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Apmv]]		[[Category: Apmv]]
-	[[Category: Doublie, S.]]	+	[[Category: Doublie, S]]
-	[[Category: Eckenroth, B E.]]	+	[[Category: Eckenroth, B E]]
-	[[Category: Prakash, A.]]	+	[[Category: Prakash, A]]
	[[Category: Dna glycosylase]]		[[Category: Dna glycosylase]]
	[[Category: H2th-motif]]		[[Category: H2th-motif]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Zinc-finger domain]]		[[Category: Zinc-finger domain]]

OCA at 12:19, 11 December 2013

2013-12-11T12:19:01Z

←Older revision		Revision as of 12:19, 11 December 2013
Line 4:		Line 4:

	==About this Structure==		==About this Structure==
-	[[4mb7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MB7 OCA].	+	[[4mb7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Apmv Apmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MB7 OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:024120312</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:024120312</ref><references group="xtra"/><references/>
-	[[Category: ~~Acanthamoeba polyphaga mimivirus~~]]	+	[[Category: Apmv]]
	[[Category: Doublie, S.]]		[[Category: Doublie, S.]]
	[[Category: Eckenroth, B E.]]		[[Category: Eckenroth, B E.]]

OCA at 09:38, 30 October 2013

2013-10-30T09:38:45Z

←Older revision		Revision as of 09:38, 30 October 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4mb7\| PDB=4mb7 \| SCENE= }}
		+	===Crystal Structure of a viral DNA glycosylase===
		+	{{ABSTRACT_PUBMED_24120312}}

-	~~The entry~~ 4mb7 is ~~ON HOLD~~	+	==About this Structure==
		+	[[4mb7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MB7 OCA].

-	~~Authors~~: ~~Prakash~~, A., Eckenroth, B.E., ~~Doublie, S~~.	+	==Reference==
-		+	<ref group="xtra">PMID:024120312</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal Structure of a viral DNA~~ glycosylase	+	[[Category: Acanthamoeba polyphaga mimivirus]]
		+	[[Category: Doublie, S.]]
		+	[[Category: Eckenroth, B E.]]
		+	[[Category: Prakash, A.]]
		+	[[Category: Dna glycosylase]]
		+	[[Category: H2th-motif]]
		+	[[Category: Hydrolase]]
		+	[[Category: Zinc-finger domain]]

OCA at 04:49, 12 September 2013

2013-09-12T04:49:15Z

←Older revision		Revision as of 04:49, 12 September 2013
Line 3:		Line 3:
	The entry 4mb7 is ON HOLD		The entry 4mb7 is ON HOLD

-	Authors: Prakash, A., Eckenroth, B.E. , Doublie, S.	+	Authors: Prakash, A., Eckenroth, B.E., Doublie, S.

	Description: Crystal Structure of a viral DNA glycosylase		Description: Crystal Structure of a viral DNA glycosylase

OCA: Protected "4mb7" [edit=sysop:move=sysop]

2013-08-28T06:56:09Z

Protected "4mb7" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:56, 28 August 2013

OCA: New page: '''Unreleased structure''' The entry 4mb7 is ON HOLD Authors: Prakash, A., Eckenroth, B.E. , Doublie, S. Description: Crystal Structure of a viral DNA glycosylase

2013-08-28T06:56:08Z

New page: '''Unreleased structure''' The entry 4mb7 is ON HOLD Authors: Prakash, A., Eckenroth, B.E. , Doublie, S. Description: Crystal Structure of a viral DNA glycosylase

New page

'''Unreleased structure'''

The entry 4mb7 is ON HOLD

Authors: Prakash, A., Eckenroth, B.E. , Doublie, S.

Description: Crystal Structure of a viral DNA glycosylase