5zhz - Revision history

OCA at 08:56, 22 November 2023

OCA — Wed, 22 Nov 2023 08:56:20 GMT

←Older revision		Revision as of 08:56, 22 November 2023
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	<StructureSection load='5zhz' size='340' side='right'caption='[[5zhz]], [[Resolution\|resolution]] 1.18Å' scene=''>		<StructureSection load='5zhz' size='340' side='right'caption='[[5zhz]], [[Resolution\|resolution]] 1.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zhz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZHZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZHZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zhz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZHZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZHZ 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]] 1.18Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)]~~, ~~with EC number [http~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2]~~ </~~span~~></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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5zhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhz OCA], [~~http~~://pdbe.org/5zhz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zhz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zhz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhz 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=5zhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhz OCA], [https://pdbe.org/5zhz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zhz RCSB], [https://www.ebi.ac.uk/pdbsum/5zhz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/END4_MYCTU END4_MYCTU]] Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin.[HAMAP-Rule:MF_00152]	+	[https://www.uniprot.org/uniprot/END4_MYCTU END4_MYCTU] Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin.[HAMAP-Rule:MF_00152]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5zhz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zhz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Apurinic/apyrimidinic endonuclease 3D structures\|Apurinic/apyrimidinic endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li, S]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Rao, Z]]	+	[[Category: Li S]]
-	[[Category: Wang, H]]	+	[[Category: Rao Z]]
-	[[Category: Xu, Y]]	+	[[Category: Wang H]]
-	[[Category: Yan, M]]	+	[[Category: Xu Y]]
-	[[Category: Yang, H]]	+	[[Category: Yan M]]
-	[[Category: Zhang, W]]	+	[[Category: Yang H]]
-	[[Category: Zhou, W]]	+	[[Category: Zhang W]]
-	~~[[Category: Dna binding protein]]~~	+	[[Category: Zhou W]]
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Endonuclease iv]]~~	+
-	~~[[Category: Tim fold~~]]	+

OCA at 21:19, 28 October 2020

OCA — Wed, 28 Oct 2020 21:19:52 GMT

←Older revision		Revision as of 21:19, 28 October 2020
Line 1:		Line 1:

	==Crystal structure of the apurinic/apyrimidinic endonuclease IV from Mycobacterium tuberculosis==		==Crystal structure of the apurinic/apyrimidinic endonuclease IV from Mycobacterium tuberculosis==
-	<StructureSection load='5zhz' size='340' side='right' caption='[[5zhz]], [[Resolution\|resolution]] 1.18Å' scene=''>	+	<StructureSection load='5zhz' size='340' side='right'caption='[[5zhz]], [[Resolution\|resolution]] 1.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zhz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZHZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZHZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zhz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZHZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZHZ 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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </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=5zhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhz OCA], [http://pdbe.org/5zhz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zhz RCSB], [http://www.ebi.ac.uk/pdbsum/5zhz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhz ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5zhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhz OCA], [http://pdbe.org/5zhz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zhz RCSB], [http://www.ebi.ac.uk/pdbsum/5zhz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Li, S]]		[[Category: Li, S]]
	[[Category: Rao, Z]]		[[Category: Rao, Z]]

OCA at 05:56, 4 April 2018

OCA — Wed, 04 Apr 2018 05:56:45 GMT

←Older revision		Revision as of 05:56, 4 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zhz is ~~ON HOLD~~	+	==Crystal structure of the apurinic/apyrimidinic endonuclease IV from Mycobacterium tuberculosis==
		+	<StructureSection load='5zhz' size='340' side='right' caption='[[5zhz]], [[Resolution\|resolution]] 1.18Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zhz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZHZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZHZ 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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_IV_(phage-T(4)-induced) Deoxyribonuclease IV (phage-T(4)-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.2 3.1.21.2] </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=5zhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zhz OCA], [http://pdbe.org/5zhz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zhz RCSB], [http://www.ebi.ac.uk/pdbsum/5zhz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zhz ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/END4_MYCTU END4_MYCTU]] Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin.[HAMAP-Rule:MF_00152]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Endonuclease IV is a typical endonuclease of the apurinic-apyrimidinic (AP) or abasic endonuclease superfamily. It repairs damaged DNA through base excision repair by cleaving the DNA backbone immediately 5' of an AP site. In Mycobacterium tuberculosis, endonuclease IV is the major AP endonuclease. This enzyme is absent from mammalian cells, making it an attractive target for anti-tuberculosis drug development. In this study, the structure of the recombinant endonuclease IV from M. tuberculosis (MtbEndo IV) was determined at a high resolution of 1.18A. MtbEndo IV was found to have a classical alpha8beta8-fold TIM barrel with loops on its surface connecting the alpha-helices and beta-strands that constitute a groove for DNA binding. Three zinc ions were identified at the active site. A comparison between the structures of MtbEndo IV and Escherichia coli End IV suggested that Gln32 of MtbEndo IV may plays a role in regulating substrate binding.

-	~~Authors: Zhang~~, W~~., Yueyang, X., Mengrong~~, Y., ~~Shanshan~~, L., ~~Huiying~~, ~~W., Haitao, Y.~~, Zhou, W., Rao, Z.	+	Crystal structure of the apurinic/apyrimidinic endonuclease IV from Mycobacterium tuberculosis.,Zhang W, Xu Y, Yan M, Li S, Wang H, Yang H, Zhou W, Rao Z Biochem Biophys Res Commun. 2018 Mar 25;498(1):111-118. doi:, 10.1016/j.bbrc.2018.02.181. Epub 2018 Feb 27. PMID:29496453<ref>PMID:29496453</ref>

-	~~Description: Crystal structure~~ of the ~~apurinic~~/~~apyrimidinic endonuclease IV from Mycobacterium tuberculosis~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Haitao, Y]]~~	+	<div class="pdbe-citations 5zhz" style="background-color:#fffaf0;"></div>
-	~~[[Category: Huiying, W]]~~	+	== References ==
-	~~[[Category: Mengrong, Y]]~~	+	<references/>
-	~~[[Category: Zhou, W]]~~	+	__TOC__
-	[[Category: ~~Yueyang~~, X]]	+	</StructureSection>
		+	[[Category: Li, S]]
	[[Category: Rao, Z]]		[[Category: Rao, Z]]
		+	[[Category: Wang, H]]
		+	[[Category: Xu, Y]]
		+	[[Category: Yan, M]]
		+	[[Category: Yang, H]]
	[[Category: Zhang, W]]		[[Category: Zhang, W]]
-	[[Category: ~~Shanshan~~, L]]	+	[[Category: Zhou, W]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna repair]]
		+	[[Category: Endonuclease iv]]
		+	[[Category: Tim fold]]

OCA: Protected "5zhz" [edit=sysop:move=sysop]

OCA — Wed, 21 Mar 2018 06:01:51 GMT

Protected "5zhz" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:01, 21 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zhz is ON HOLD Authors: Zhang, W., Yueyang, X., Mengrong, Y., Shanshan, L., Huiying, W., Haitao, Y., Zhou, W., Rao, Z. Description: Crystal struct...

OCA — Wed, 21 Mar 2018 06:01:50 GMT

New page: '''Unreleased structure''' The entry 5zhz is ON HOLD Authors: Zhang, W., Yueyang, X., Mengrong, Y., Shanshan, L., Huiying, W., Haitao, Y., Zhou, W., Rao, Z. Description: Crystal struct...

New page

'''Unreleased structure'''

The entry 5zhz is ON HOLD

Authors: Zhang, W., Yueyang, X., Mengrong, Y., Shanshan, L., Huiying, W., Haitao, Y., Zhou, W., Rao, Z.

Description: Crystal structure of the apurinic/apyrimidinic endonuclease IV from Mycobacterium tuberculosis
[[Category: Unreleased Structures]]
[[Category: Haitao, Y]]
[[Category: Huiying, W]]
[[Category: Mengrong, Y]]
[[Category: Zhou, W]]
[[Category: Yueyang, X]]
[[Category: Rao, Z]]
[[Category: Zhang, W]]
[[Category: Shanshan, L]]