6lu2 - Revision history

OCA at 06:01, 22 April 2020

2020-04-22T06:01:53Z

←Older revision		Revision as of 06:01, 22 April 2020
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	<StructureSection load='6lu2' size='340' side='right'caption='[[6lu2]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6lu2' size='340' side='right'caption='[[6lu2]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lu2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LU2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6LU2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lu2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_16089 Dsm 16089]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LU2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LU2 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=6lu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lu2 OCA], [http://pdbe.org/6lu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lu2 RCSB], [http://www.ebi.ac.uk/pdbsum/6lu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lu2 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=6lu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lu2 OCA], [http://pdbe.org/6lu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lu2 RCSB], [http://www.ebi.ac.uk/pdbsum/6lu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lu2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dsm 16089]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Akiyama, T]]		[[Category: Akiyama, T]]

OCA at 10:09, 27 March 2020

2020-03-27T10:09:36Z

←Older revision		Revision as of 10:09, 27 March 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6lu2 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of a substrate binding protein from Microbacterium hydrocarbonoxydans==
		+	<StructureSection load='6lu2' size='340' side='right'caption='[[6lu2]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6lu2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6LU2 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=6lu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lu2 OCA], [http://pdbe.org/6lu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lu2 RCSB], [http://www.ebi.ac.uk/pdbsum/6lu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lu2 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Microbacterium hydrocarbonoxydans was isolated, using hydrazide compounds as its sole carbon source. The key enzyme that metabolizes these compounds was identified as hydrazidase, and the operon containing the gene coding for the enzyme, was revealed by genome sequencing. The operon also contained genes coding for an ATP-binding cassette transporter (ABC transporter), which was expected to transport the hydrazide compounds. Substrate binding protein (SBP), a component subunit of the transporter, plays an important role in recognizing the correct substrates for transport. Therefore, to elucidate the mechanism of recognition of the unnatural hydrazide compounds, we determined the crystal structures of the SBP, obtained from M. hydrocarbonoxydans (Mh-SBP), complexed with and without the hydrazide compound, at 2.2 A and 1.75 A resolutions, respectively. The overall structures of Mh-SBP were similar to those of the SBP in oligopeptide transporters such as OppA. On comparison, the liganded and unliganded structures of Mh-SBP showed an open - close conformation change. Interestingly, the binding mode of the compound to Mh-SBP was almost identical to that of the compound to hydrazidase, suggesting that the ABC transporter served transporting these compounds. Furthermore, based on the hydrazide complex structure, paraben, the other putative substrate of the protein, was successfully used with Mh-SBP to obtain the paraben complex structure.

-	~~Authors: Shimamura~~, K., ~~Akiyama~~, T., Yokoyama, K., Takenoya, M., Ito, S., Sasaki, Y., Yajima, S.	+	Structural basis of substrate recognition by the substrate binding protein (SBP) of a hydrazide transporter, obtained from Microbacterium hydrocarbonoxydans.,Shimamura K, Akiyama T, Yokoyama K, Takenoya M, Ito S, Sasaki Y, Yajima S Biochem Biophys Res Commun. 2020 Mar 3. pii: S0006-291X(20)30435-6. doi:, 10.1016/j.bbrc.2020.02.146. PMID:32143826<ref>PMID:32143826</ref>

-	~~Description: Crystal structure of~~ a ~~substrate binding protein from Microbacterium hydrocarbonoxydans~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Takenoya, M~~]]	+	<div class="pdbe-citations 6lu2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Akiyama, T]]		[[Category: Akiyama, T]]
-	[[Category: ~~Shimamura~~, K]]	+	[[Category: Ito, S]]
	[[Category: Sasaki, Y]]		[[Category: Sasaki, Y]]
-	[[Category: ~~Yokoyama~~, K]]	+	[[Category: Shimamura, K]]
		+	[[Category: Takenoya, M]]
	[[Category: Yajima, S]]		[[Category: Yajima, S]]
-	[[Category: ~~Ito~~, S]]	+	[[Category: Yokoyama, K]]
		+	[[Category: Complex]]
		+	[[Category: Transport protein]]

OCA: Protected "6lu2" [edit=sysop:move=sysop]

2020-02-05T06:05:26Z

Protected "6lu2" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:05, 5 February 2020

OCA: New page: '''Unreleased structure''' The entry 6lu2 is ON HOLD until Paper Publication Authors: Shimamura, K., Akiyama, T., Yokoyama, K., Takenoya, M., Ito, S., Sasaki, Y., Yajima, S. Descriptio...

2020-02-05T06:05:25Z

New page: '''Unreleased structure''' The entry 6lu2 is ON HOLD until Paper Publication Authors: Shimamura, K., Akiyama, T., Yokoyama, K., Takenoya, M., Ito, S., Sasaki, Y., Yajima, S. Descriptio...

New page

'''Unreleased structure'''

The entry 6lu2 is ON HOLD until Paper Publication

Authors: Shimamura, K., Akiyama, T., Yokoyama, K., Takenoya, M., Ito, S., Sasaki, Y., Yajima, S.

Description: Crystal structure of a substrate binding protein from Microbacterium hydrocarbonoxydans
[[Category: Unreleased Structures]]
[[Category: Takenoya, M]]
[[Category: Akiyama, T]]
[[Category: Shimamura, K]]
[[Category: Sasaki, Y]]
[[Category: Yokoyama, K]]
[[Category: Yajima, S]]
[[Category: Ito, S]]