7dn7 - Revision history

OCA at 16:36, 29 November 2023

OCA — Wed, 29 Nov 2023 16:36:45 GMT

←Older revision		Revision as of 16:36, 29 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7dn7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6laq 6laq] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ql6 3ql6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DN7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DN7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7dn7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6laq 6laq] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ql6 3ql6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DN7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DN7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OSM:1-(OXIDOSULFANYL)METHANAMINE'>OSM</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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]] 1.7Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OSM:1-(OXIDOSULFANYL)METHANAMINE'>OSM</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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=7dn7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dn7 OCA], [https://pdbe.org/7dn7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dn7 RCSB], [https://www.ebi.ac.uk/pdbsum/7dn7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dn7 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=7dn7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dn7 OCA], [https://pdbe.org/7dn7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dn7 RCSB], [https://www.ebi.ac.uk/pdbsum/7dn7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dn7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PERL_BOVIN PERL_BOVIN]] LPO is an antimicrobial agent. It is thought to help protect the udder from infection and promote growth in newborn calves.	+	[https://www.uniprot.org/uniprot/PERL_BOVIN PERL_BOVIN] LPO is an antimicrobial agent. It is thought to help protect the udder from infection and promote growth in newborn calves.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 28:
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Peroxidase]]~~	+	[[Category: Kaur P]]
-	[[Category: Kaur, P]]	+	[[Category: Sharma S]]
-	[[Category: Sharma, S]]	+	[[Category: Singh AK]]
-	[[Category: Singh~~, A K~~]]	+	[[Category: Singh PK]]
-	[[Category: Singh~~, P K~~]]	+	[[Category: Singh RP]]
-	[[Category: Singh~~, R P~~]]	+	[[Category: Singh TP]]
-	[[Category: Singh~~, T P]]~~	+
-	~~[[Category: Lactoperoxidase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:06, 14 July 2021

OCA — Wed, 14 Jul 2021 10:06:12 GMT

←Older revision		Revision as of 10:06, 14 July 2021
Line 1:		Line 1:

	==Crystal structure of ternary complexes of lactoperoxidase with hydrogen peroxide at 1.70 A resolution==		==Crystal structure of ternary complexes of lactoperoxidase with hydrogen peroxide at 1.70 A resolution==
-	<StructureSection load='7dn7' size='340' side='right'caption='[[7dn7]]' scene=''>	+	<StructureSection load='7dn7' size='340' side='right'caption='[[7dn7]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6laq 6laq] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ql6 3ql6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DN7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7DN7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dn7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6laq 6laq] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ql6 3ql6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DN7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DN7 FirstGlance]. <br>
-	</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=7dn7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dn7 OCA], [~~http~~://pdbe.org/7dn7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7dn7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7dn7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7dn7 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OSM:1-(OXIDOSULFANYL)METHANAMINE'>OSM</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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'>[https://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </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=7dn7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dn7 OCA], [https://pdbe.org/7dn7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dn7 RCSB], [https://www.ebi.ac.uk/pdbsum/7dn7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dn7 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/PERL_BOVIN PERL_BOVIN]] LPO is an antimicrobial agent. It is thought to help protect the udder from infection and promote growth in newborn calves.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lactoperoxidase (LPO) is a mammalian heme peroxidase which catalyzes the conversion of thiocyanate (SCN ) and iodide (I(-)) by hydrogen peroxide (H2O2) into antimicrobial hypothiocyanite (OSCN ) and hypoiodite (IO(-)). The prosthetic heme group is covalently attached to LPO through two ester linkages involving conserved glutamate and aspartate residues. On the proximal side, His351 is coordinated to heme iron while His 109 is located in the substrate binding site on the distal heme side. We report here the first structure of the ternary complex of LPO with iodide (I(-)) and H2O2 at 1.77 A resolution. LPO was crystallized with ammonium iodide and the crystals were soaked in the reservoir solution containing H2O2. Structure determination showed the presence of an iodide ion and a H2O2 molecule in the substrate binding site. The iodide ion occupied the position which is stabilized by the interactions with heme moiety, His109, Arg255 and Glu258 while H2O2 was held between the heme iron and His109. The presence of I(-) in the distal heme cavity seems to screen the positive charge of Arg255 thus suppressing the proton transfer from H2O2 to His109. This prevents compound I formation and allows trapping of a stable enzyme-substrate (LPO-I(-)-H2O2) ternary complex. This stable geometrical arrangement of H2O2 in the distal heme cavity of LPO is similar to that of H2O2 in the structure of the transient intermediate of the palm tree heme peroxidase. The biochemical studies showed that the catalytic activity of LPO decreased when the samples of LPO were preincubated with ammonium iodide.
		+
		+	Structure of a ternary complex of lactoperoxidase with iodide and hydrogen peroxide at 1.77 A resolution.,Singh PK, Sharma P, Bhushan A, Kaur P, Sharma S, Singh TP J Inorg Biochem. 2021 Apr 18;220:111461. doi: 10.1016/j.jinorgbio.2021.111461. PMID:33882424<ref>PMID:33882424</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dn7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lactoperoxidase\|Lactoperoxidase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kaur P]]	+	[[Category: Peroxidase]]
-	[[Category: Sharma S]]	+	[[Category: Kaur, P]]
-	[[Category: Singh AK]]	+	[[Category: Sharma, S]]
-	[[Category: Singh PK]]	+	[[Category: Singh, A K]]
-	[[Category: Singh RP]]	+	[[Category: Singh, P K]]
-	[[Category: Singh TP]]	+	[[Category: Singh, R P]]
		+	[[Category: Singh, T P]]
		+	[[Category: Lactoperoxidase]]
		+	[[Category: Oxidoreductase]]

OCA at 06:42, 30 December 2020

OCA — Wed, 30 Dec 2020 06:42:28 GMT

←Older revision		Revision as of 06:42, 30 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7dn7 ~~is ON HOLD~~	+	==Crystal structure of ternary complexes of lactoperoxidase with hydrogen peroxide at 1.70 A resolution==
-		+	<StructureSection load='7dn7' size='340' side='right'caption='[[7dn7]]' scene=''>
-	~~Authors~~: ~~Singh, P~~.K.~~, Singh, A~~.K., ~~Singh, R~~.P., ~~Kaur~~, P., ~~Sharma, S~~., ~~Singh, T~~.P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6laq 6laq] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ql6 3ql6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DN7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7DN7 FirstGlance]. <br>
-	~~Description: Crystal structure of ternary complexes of lactoperoxidase with hydrogen peroxide at 1.70 A resolution~~	+	</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=7dn7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dn7 OCA], [http://pdbe.org/7dn7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7dn7 RCSB], [http://www.ebi.ac.uk/pdbsum/7dn7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7dn7 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Singh,~~ P.K]]	+	__TOC__
-	[[Category: Sharma, S]]	+	</StructureSection>
-	[[Category: Singh~~, R.P~~]]	+	[[Category: Large Structures]]
-	[[Category: Singh~~, T.P~~]]	+	[[Category: Kaur P]]
-	[[Category: Singh~~, A.K~~]]	+	[[Category: Sharma S]]
-	[[Category: ~~Kaur, P~~]]	+	[[Category: Singh AK]]
		+	[[Category: Singh PK]]
		+	[[Category: Singh RP]]
		+	[[Category: Singh TP]]

OCA: Protected "7dn7" [edit=sysop:move=sysop]

OCA — Wed, 16 Dec 2020 11:07:51 GMT

Protected "7dn7" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:07, 16 December 2020

OCA: New page: '''Unreleased structure''' The entry 7dn7 is ON HOLD Authors: Singh, P.K., Singh, A.K., Singh, R.P., Kaur, P., Sharma, S., Singh, T.P. Description: Crystal structure of ternary complex...

OCA — Wed, 16 Dec 2020 11:07:50 GMT

New page: '''Unreleased structure''' The entry 7dn7 is ON HOLD Authors: Singh, P.K., Singh, A.K., Singh, R.P., Kaur, P., Sharma, S., Singh, T.P. Description: Crystal structure of ternary complex...

New page

'''Unreleased structure'''

The entry 7dn7 is ON HOLD

Authors: Singh, P.K., Singh, A.K., Singh, R.P., Kaur, P., Sharma, S., Singh, T.P.

Description: Crystal structure of ternary complexes of lactoperoxidase with hydrogen peroxide at 1.70 A resolution
[[Category: Unreleased Structures]]
[[Category: Singh, P.K]]
[[Category: Sharma, S]]
[[Category: Singh, R.P]]
[[Category: Singh, T.P]]
[[Category: Singh, A.K]]
[[Category: Kaur, P]]