7c8i - Revision history

OCA at 15:59, 29 November 2023

2023-11-29T15:59:15Z

←Older revision		Revision as of 15:59, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7c8i]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C8I FirstGlance]. <br>		<table><tr><td colspan='2'>[[7c8i]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C8I 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=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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]] 2.5Å</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=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=7c8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c8i OCA], [https://pdbe.org/7c8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c8i RCSB], [https://www.ebi.ac.uk/pdbsum/7c8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c8i 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=7c8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c8i OCA], [https://pdbe.org/7c8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c8i RCSB], [https://www.ebi.ac.uk/pdbsum/7c8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c8i ProSAT]</span></td></tr>
	</table>		</table>

OCA at 20:37, 12 April 2023

2023-04-12T20:37:45Z

←Older revision		Revision as of 20:37, 12 April 2023
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	==Ambient temperature structure of Bifidobacgterium longum phosphoketolase with thiamine diphosphate and phosphoenol pyuruvate==		==Ambient temperature structure of Bifidobacgterium longum phosphoketolase with thiamine diphosphate and phosphoenol pyuruvate==
-	<StructureSection load='7c8i' size='340' side='right'caption='[[7c8i]]' scene=''>	+	<StructureSection load='7c8i' size='340' side='right'caption='[[7c8i]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C8I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7c8i]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C8I FirstGlance]. <br>
-	</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=7c8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c8i OCA], [https://pdbe.org/7c8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c8i RCSB], [https://www.ebi.ac.uk/pdbsum/7c8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c8i 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=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=7c8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c8i OCA], [https://pdbe.org/7c8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c8i RCSB], [https://www.ebi.ac.uk/pdbsum/7c8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c8i ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q6R2Q7_BIFLN Q6R2Q7_BIFLN]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phosphoketolase and transketolase are thiamine diphosphate-dependent enzymes and play a central role in the primary metabolism of bifidobacteria: the bifid shunt. The enzymes both catalyze phosphorolytic cleavage of xylulose 5-phosphate or fructose 6-phosphate in the first reaction step, but possess different substrate specificity in the second reaction step, where phosphoketolase and transketolase utilize inorganic phosphate (P(i)) and D-ribose 5-phosphate, respectively, as the acceptor substrate. Structures of Bifidobacterium longum phosphoketolase holoenzyme and its complex with a putative inhibitor, phosphoenolpyruvate, were determined at 2.5 A resolution by serial femtosecond crystallography using an X-ray free-electron laser. In the complex structure, phosphoenolpyruvate was present at the entrance to the active-site pocket and plugged the channel to thiamine diphosphate. The phosphate-group position of phosphoenolpyruvate coincided well with those of xylulose 5-phosphate and fructose 6-phosphate in the structures of their complexes with transketolase. The most striking structural change was observed in a loop consisting of Gln546-Asp547-His548-Asn549 (the QN-loop) at the entrance to the active-site pocket. Contrary to the conformation of the QN-loop that partially covers the entrance to the active-site pocket (;closed form') in the known crystal structures, including the phosphoketolase holoenzyme and its complexes with reaction intermediates, the QN-loop in the current ambient structures showed a more compact conformation with a widened entrance to the active-site pocket (;open form'). In the phosphoketolase reaction, the ;open form' QN-loop may play a role in providing the binding site for xylulose 5-phosphate or fructose 6-phosphate in the first step, and the ;closed form' QN-loop may help confer specificity for P(i) in the second step.
		+
		+	Ambient temperature structure of phosphoketolase from Bifidobacterium longum determined by serial femtosecond X-ray crystallography.,Nakata K, Kashiwagi T, Kunishima N, Naitow H, Matsuura Y, Miyano H, Mizukoshi T, Tono K, Yabashi M, Nango E, Iwata S Acta Crystallogr D Struct Biol. 2023 Apr 1;79(Pt 4):290-303. doi: , 10.1107/S2059798323001638. Epub 2023 Mar 28. PMID:36974963<ref>PMID:36974963</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7c8i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bifidobacterium longum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Iwata S]]		[[Category: Iwata S]]

OCA at 14:34, 2 June 2021

2021-06-02T14:34:27Z

←Older revision		Revision as of 14:34, 2 June 2021
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-	'''Unreleased structure'''

-	~~The entry 7c8i is ON HOLD until Jun 01 2022~~	+	==Ambient temperature structure of Bifidobacgterium longum phosphoketolase with thiamine diphosphate and phosphoenol pyuruvate==
-		+	<StructureSection load='7c8i' size='340' side='right'caption='[[7c8i]]' scene=''>
-	~~Authors: Nakata, K., Kashiwagi, T., Nango, E., Miyano, H., Mizukoshi, T., Iwata, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C8I FirstGlance]. <br>
-	~~Description:~~ Ambient temperature structure of Bifidobacgterium longum phosphoketolase with thiamine diphosphate and phosphoenol pyuruvate	+	</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=7c8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c8i OCA], [https://pdbe.org/7c8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c8i RCSB], [https://www.ebi.ac.uk/pdbsum/7c8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c8i ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Mizukoshi~~, T]]	+	__TOC__
-	[[Category: ~~Nango, E~~]]	+	</StructureSection>
-	[[Category: Iwata, S]]	+	[[Category: Large Structures]]
-	[[Category: Kashiwagi, T]]	+	[[Category: Iwata S]]
-	[[Category: Miyano, H]]	+	[[Category: Kashiwagi T]]
-	[[Category: Nakata, K]]	+	[[Category: Miyano H]]
		+	[[Category: Mizukoshi T]]
		+	[[Category: Nakata K]]
		+	[[Category: Nango E]]

OCA at 08:58, 17 June 2020

2020-06-17T08:58:46Z

←Older revision		Revision as of 08:58, 17 June 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7c8i is ON HOLD	+	The entry 7c8i is ON HOLD until Jun 01 2022

	Authors: Nakata, K., Kashiwagi, T., Nango, E., Miyano, H., Mizukoshi, T., Iwata, S.		Authors: Nakata, K., Kashiwagi, T., Nango, E., Miyano, H., Mizukoshi, T., Iwata, S.

OCA: Protected "7c8i" [edit=sysop:move=sysop]

2020-06-10T05:18:15Z

Protected "7c8i" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:18, 10 June 2020

OCA: New page: '''Unreleased structure''' The entry 7c8i is ON HOLD Authors: Nakata, K., Kashiwagi, T., Nango, E., Miyano, H., Mizukoshi, T., Iwata, S. Description: Ambient temperature structure of B...

2020-06-10T05:18:13Z

New page: '''Unreleased structure''' The entry 7c8i is ON HOLD Authors: Nakata, K., Kashiwagi, T., Nango, E., Miyano, H., Mizukoshi, T., Iwata, S. Description: Ambient temperature structure of B...

New page

'''Unreleased structure'''

The entry 7c8i is ON HOLD

Authors: Nakata, K., Kashiwagi, T., Nango, E., Miyano, H., Mizukoshi, T., Iwata, S.

Description: Ambient temperature structure of Bifidobacgterium longum phosphoketolase with thiamine diphosphate and phosphoenol pyuruvate
[[Category: Unreleased Structures]]
[[Category: Mizukoshi, T]]
[[Category: Nango, E]]
[[Category: Iwata, S]]
[[Category: Kashiwagi, T]]
[[Category: Miyano, H]]
[[Category: Nakata, K]]