6jqq - Revision history

OCA at 10:18, 22 November 2023

OCA — Wed, 22 Nov 2023 10:18:29 GMT

←Older revision		Revision as of 10:18, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6jqq' size='340' side='right'caption='[[6jqq]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6jqq' size='340' side='right'caption='[[6jqq]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jqq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JQQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jqq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_ISC7 Escherichia coli ISC7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JQQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1~~,2~~-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 2.4Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/Catalase Catalase]~~, ~~with EC number [http~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=6jqq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jqq OCA], [~~http~~://pdbe.org/6jqq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jqq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jqq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jqq 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=6jqq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jqq OCA], [https://pdbe.org/6jqq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jqq RCSB], [https://www.ebi.ac.uk/pdbsum/6jqq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jqq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/W1F4G9_ECOLX W1F4G9_ECOLX]] Serves to protect cells from the toxic effects of hydrogen peroxide.[PIRNR:PIRNR038927]	+	[https://www.uniprot.org/uniprot/W1F4G9_ECOLX W1F4G9_ECOLX] Serves to protect cells from the toxic effects of hydrogen peroxide.[PIRNR:PIRNR038927]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	BACKGROUND: Catalase is a ubiquitous enzyme present in both the prokaryotic and eukaryotic cells of aerobic organisms. It serves, in part, to protect the cell from the toxic effects of small peroxides. Escherichia coli produces two catalases, HPI and HPII, that are quite distinct from other catalases in physical structure and catalytic properties. HPII, studied in this work, is encoded by the katE gene, and has been characterized as an oligomeric, monofunctional catalase containing one cis-heme d prosthetic group per subunit of 753 residues. RESULTS: The crystal structure of catalase HPII from E. coli has been determined to 2.8 A resolution. The asymmetric unit of the crystal contains a whole molecule, which is a tetramer with accurate 222 point group symmetry. In the model built, that includes residues 27-753 and one heme group per monomer, strict non-crystallographic symmetry has been maintained. The crystallographic agreement R-factor is 20.1% for 58,477 reflections in the resolution shell 8.0-2.8 A. CONCLUSIONS: Despite differences in size and chemical properties, which were suggestive of a unique catalase, the deduced structure of HPII is related to the structure of catalase from Penicillium vitale, whose sequence is not yet known. In particular, both molecules have an additional C-terminal domain that is absent in the bovine catalase. This extra domain contains a Rossmann fold but no bound nucleotides have been detected, and its physiological role is unknown. In HPII, the heme group is modified to a heme d and inverted with respect to the orientation determined in all previously reported heme catalases. HPII is the largest catalase for which the structure has been determined to almost atomic resolution.	+

-	~~Crystal structure of catalase HPII from Escherichia coli.,Bravo J, Verdaguer N, Tormo J, Betzel C, Switala J, Loewen PC, Fita I Structure. 1995 May 15;3(5):491-502. PMID:7663946<ref>PMID:7663946</ref>~~	+	==See Also==
-		+	*[[Catalase 3D structures\|Catalase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6jqq" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Catalase~~]]	+	[[Category: Escherichia coli ISC7]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cho, H S]]	+	[[Category: Cho H-S]]
-	[[Category: Park~~, J B]]~~	+	[[Category: Park JB]]
-	~~[[Category: Kate]]~~	+
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:05, 1 April 2020

OCA — Wed, 01 Apr 2020 09:05:40 GMT

←Older revision		Revision as of 09:05, 1 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jqq is ~~ON HOLD until Paper~~ Publication	+	==KatE H392C from Escherichia coli==
		+	<StructureSection load='6jqq' size='340' side='right'caption='[[6jqq]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6jqq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JQQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JQQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </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=6jqq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jqq OCA], [http://pdbe.org/6jqq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jqq RCSB], [http://www.ebi.ac.uk/pdbsum/6jqq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jqq ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/W1F4G9_ECOLX W1F4G9_ECOLX]] Serves to protect cells from the toxic effects of hydrogen peroxide.[PIRNR:PIRNR038927]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Catalase is a ubiquitous enzyme present in both the prokaryotic and eukaryotic cells of aerobic organisms. It serves, in part, to protect the cell from the toxic effects of small peroxides. Escherichia coli produces two catalases, HPI and HPII, that are quite distinct from other catalases in physical structure and catalytic properties. HPII, studied in this work, is encoded by the katE gene, and has been characterized as an oligomeric, monofunctional catalase containing one cis-heme d prosthetic group per subunit of 753 residues. RESULTS: The crystal structure of catalase HPII from E. coli has been determined to 2.8 A resolution. The asymmetric unit of the crystal contains a whole molecule, which is a tetramer with accurate 222 point group symmetry. In the model built, that includes residues 27-753 and one heme group per monomer, strict non-crystallographic symmetry has been maintained. The crystallographic agreement R-factor is 20.1% for 58,477 reflections in the resolution shell 8.0-2.8 A. CONCLUSIONS: Despite differences in size and chemical properties, which were suggestive of a unique catalase, the deduced structure of HPII is related to the structure of catalase from Penicillium vitale, whose sequence is not yet known. In particular, both molecules have an additional C-terminal domain that is absent in the bovine catalase. This extra domain contains a Rossmann fold but no bound nucleotides have been detected, and its physiological role is unknown. In HPII, the heme group is modified to a heme d and inverted with respect to the orientation determined in all previously reported heme catalases. HPII is the largest catalase for which the structure has been determined to almost atomic resolution.

-	~~Authors: Park~~, J~~.B.~~, ~~Cho~~, H.-S.	+	Crystal structure of catalase HPII from Escherichia coli.,Bravo J, Verdaguer N, Tormo J, Betzel C, Switala J, Loewen PC, Fita I Structure. 1995 May 15;3(5):491-502. PMID:7663946<ref>PMID:7663946</ref>

-	~~Description~~: ~~KatE H392C from Escherichia coli~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Cho, H.-S]]	+	<div class="pdbe-citations 6jqq" style="background-color:#fffaf0;"></div>
-	[[Category: Park, J.B]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Catalase]]
		+	[[Category: Large Structures]]
		+	[[Category: Cho, H S]]
		+	[[Category: Park, J B]]
		+	[[Category: Kate]]
		+	[[Category: Mutant]]
		+	[[Category: Oxidoreductase]]

OCA at 03:57, 17 April 2019

OCA — Wed, 17 Apr 2019 03:57:51 GMT

←Older revision		Revision as of 03:57, 17 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6jqq is ON HOLD	+	The entry 6jqq is ON HOLD until Paper Publication

	Authors: Park, J.B., Cho, H.-S.		Authors: Park, J.B., Cho, H.-S.

OCA: Protected "6jqq" [edit=sysop:move=sysop]

OCA — Wed, 10 Apr 2019 05:23:08 GMT

Protected "6jqq" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:23, 10 April 2019

OCA: New page: '''Unreleased structure''' The entry 6jqq is ON HOLD Authors: Park, J.B., Cho, H.-S. Description: KatE H392C from Escherichia coli Category: Unreleased Structures [[Category: Cho, ...

OCA — Wed, 10 Apr 2019 05:23:07 GMT

New page: '''Unreleased structure''' The entry 6jqq is ON HOLD Authors: Park, J.B., Cho, H.-S. Description: KatE H392C from Escherichia coli Category: Unreleased Structures [[Category: Cho, ...

New page

'''Unreleased structure'''

The entry 6jqq is ON HOLD

Authors: Park, J.B., Cho, H.-S.

Description: KatE H392C from Escherichia coli
[[Category: Unreleased Structures]]
[[Category: Cho, H.-S]]
[[Category: Park, J.B]]