7cne - Revision history

OCA at 16:11, 29 November 2023

2023-11-29T16:11:23Z

←Older revision		Revision as of 16:11, 29 November 2023
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	<StructureSection load='7cne' size='340' side='right'caption='[[7cne]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='7cne' size='340' side='right'caption='[[7cne]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7cne]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"streptomyces_griseocarneus"_benedict_et_al._1950 "streptomyces~~ griseocarneus~~" benedict et al. 1950~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wcx 3wcx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7CNE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7cne]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_griseocarneus Streptomyces griseocarneus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wcx 3wcx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CNE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EPE:4~~-(2~~-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>smc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~51201~~ "~~Streptomyces griseocarneus~~" ~~Benedict et al. 1950])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12]~~ </~~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=7cne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cne OCA], [https://pdbe.org/7cne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cne RCSB], [https://www.ebi.ac.uk/pdbsum/7cne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cne 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=7cne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cne OCA], [~~http~~://pdbe.org/7cne PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7cne RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7cne PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7cne ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A6P7M9_9ACTN A6P7M9_9ACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Streptomyces griseocarneus benedict et al. 1950]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Sphingomyelin phosphodiesterase]]
-	[[Category: Fujisawa, I]]
-	[[Category: Murayama, K]]
-	[[Category: Sugimori, D]]
-	[[Category: Hydrolase]]
-	[[Category: Metal-binding site]]
-	[[Category: Sphingomyelinase c]]
	[[Category: Streptomyces griseocarneus]]		[[Category: Streptomyces griseocarneus]]
		+	[[Category: Fujisawa I]]
		+	[[Category: Murayama K]]
		+	[[Category: Sugimori D]]

OCA at 06:04, 20 January 2021

2021-01-20T06:04:48Z

←Older revision		Revision as of 06:04, 20 January 2021
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	==Crystal Structure of Sphingomyelinase C from Streptomyces griseocarneus==		==Crystal Structure of Sphingomyelinase C from Streptomyces griseocarneus==
-	<StructureSection load='7cne' size='340' side='right'caption='[[7cne]]' scene=''>	+	<StructureSection load='7cne' size='340' side='right'caption='[[7cne]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wcx 3wcx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7CNE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7cne]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_griseocarneus"_benedict_et_al._1950 "streptomyces griseocarneus" benedict et al. 1950]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wcx 3wcx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7CNE 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=7cne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cne OCA], [http://pdbe.org/7cne PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7cne RCSB], [http://www.ebi.ac.uk/pdbsum/7cne PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7cne 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">smc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=51201 "Streptomyces griseocarneus" Benedict et al. 1950])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphingomyelin_phosphodiesterase Sphingomyelin phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.12 3.1.4.12] </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=7cne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cne OCA], [http://pdbe.org/7cne PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7cne RCSB], [http://www.ebi.ac.uk/pdbsum/7cne PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7cne ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Sphingomyelinase C (SMC) hydrolyzes sphingomyelin to ceramide and phosphocholine. Prokaryotic SMCs share sequence homology with mammalian SMCs that have enzymatic pH optima at neutral pH. SMC from the nonpathogenic prokaryote Streptomyces griseocarneus shows notable enzymatic features such as higher optimum pH and thermostability than other prokaryotic SMCs. Determination of the three-dimensional structure of S. griseocarneus-SMC (Sg-SMC) and comparison with other SMC structures represents a promising strategy to elucidate the unique enzymatic features of Sg-SMC on a structural basis. Therefore, we determined the crystal structure of Sg-SMC at 2.0 A resolution by X-ray crystallography. Comparison of the Sg-SMC structure with three other structurally known SMCs from Listeria ivanovii, Bacillus cereus, and Staphylococcus aureus indicated that Sg-SMC is more diverse in sequence and that structural differences in the main chain between these SMCs are primarily located on the molecular surface distant from the active site. Comparison of the surface area of the four SMCs revealed that Sg-SMC has the most compact structure, which may contribute to the enhanced thermostability of Sg-SMC. Regarding the hydrogen bond network in the active site of Sg-SMC, a basic amino acid, Arg278, is involved, whereas the corresponding residue in other SMCs (Ser or Asn) does not form hydrogen bonds with metal-coordinating water molecules. Hydrogen bond formation between Arg278 and a Mg(2+) ion-coordinating water molecule may be responsible for the higher optimal pH of Sg-SMC compared to that of other SMCs.
		+
		+	Structural basis for the high thermal stability and optimum pH of sphingomyelinase C from Streptomyces griseocarneus.,Fujisawa I, Hamana H, Tomita Y, Matsumoto Y, Murayama K, Sugimori D J Biosci Bioeng. 2020 Oct 3. pii: S1389-1723(20)30354-6. doi:, 10.1016/j.jbiosc.2020.09.005. PMID:33023861<ref>PMID:33023861</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7cne" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Sphingomyelinase\|Sphingomyelinase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Streptomyces griseocarneus benedict et al. 1950]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fujisawa I]]	+	[[Category: Sphingomyelin phosphodiesterase]]
-	[[Category: Murayama K]]	+	[[Category: Fujisawa, I]]
-	[[Category: Sugimori D]]	+	[[Category: Murayama, K]]
		+	[[Category: Sugimori, D]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metal-binding site]]
		+	[[Category: Sphingomyelinase c]]
		+	[[Category: Streptomyces griseocarneus]]

OCA at 20:27, 28 October 2020

2020-10-28T20:27:59Z

←Older revision		Revision as of 20:27, 28 October 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7cne ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of Sphingomyelinase C from Streptomyces griseocarneus==
-		+	<StructureSection load='7cne' size='340' side='right'caption='[[7cne]]' scene=''>
-	~~Authors~~: ~~Murayama~~, K., ~~Fujisawa~~, I., ~~Sugimori~~, D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3wcx 3wcx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7CNE FirstGlance]. <br>
-	~~Description: Crystal Structure of Sphingomyelinase C from Streptomyces griseocarneus~~	+	</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=7cne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cne OCA], [http://pdbe.org/7cne PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7cne RCSB], [http://www.ebi.ac.uk/pdbsum/7cne PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7cne ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Murayama, K~~]]	+	__TOC__
-	[[Category: ~~Fujisawa, I~~]]	+	</StructureSection>
-	[[Category: Sugimori, D]]	+	[[Category: Large Structures]]
		+	[[Category: Fujisawa I]]
		+	[[Category: Murayama K]]
		+	[[Category: Sugimori D]]

OCA at 04:41, 19 August 2020

2020-08-19T04:41:39Z

←Older revision		Revision as of 04:41, 19 August 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7cne is ON HOLD	+	The entry 7cne is ON HOLD until Paper Publication

	Authors: Murayama, K., Fujisawa, I., Sugimori, D.		Authors: Murayama, K., Fujisawa, I., Sugimori, D.
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	Description: Crystal Structure of Sphingomyelinase C from Streptomyces griseocarneus		Description: Crystal Structure of Sphingomyelinase C from Streptomyces griseocarneus
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Sugimori, D]]
-	[[Category: Fujisawa, I]]
	[[Category: Murayama, K]]		[[Category: Murayama, K]]
		+	[[Category: Fujisawa, I]]
		+	[[Category: Sugimori, D]]

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

2020-08-05T04:12:32Z

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

←Older revision

Revision as of 04:12, 5 August 2020

OCA: New page: '''Unreleased structure''' The entry 7cne is ON HOLD Authors: Murayama, K., Fujisawa, I., Sugimori, D. Description: Crystal Structure of Sphingomyelinase C from Streptomyces griseocarn...

2020-08-05T04:12:30Z

New page: '''Unreleased structure''' The entry 7cne is ON HOLD Authors: Murayama, K., Fujisawa, I., Sugimori, D. Description: Crystal Structure of Sphingomyelinase C from Streptomyces griseocarn...

New page

'''Unreleased structure'''

The entry 7cne is ON HOLD

Authors: Murayama, K., Fujisawa, I., Sugimori, D.

Description: Crystal Structure of Sphingomyelinase C from Streptomyces griseocarneus
[[Category: Unreleased Structures]]
[[Category: Sugimori, D]]
[[Category: Fujisawa, I]]
[[Category: Murayama, K]]