5yg9 - Revision history

OCA at 19:25, 29 May 2024

OCA — Wed, 29 May 2024 19:25:51 GMT

←Older revision		Revision as of 19:25, 29 May 2024
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	<table><tr><td colspan='2'>[[5yg9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YG9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5yg9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YG9 FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.8Å</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]] 2.8Å</td></tr>
-	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RI2:1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE'>RI2</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RI2:1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE'>RI2</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=5yg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg9 OCA], [https://pdbe.org/5yg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yg9 RCSB], [https://www.ebi.ac.uk/pdbsum/5yg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg9 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=5yg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg9 OCA], [https://pdbe.org/5yg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yg9 RCSB], [https://www.ebi.ac.uk/pdbsum/5yg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg9 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:29, 22 November 2023

OCA — Wed, 22 Nov 2023 08:29:20 GMT

←Older revision		Revision as of 08:29, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5yg9' size='340' side='right'caption='[[5yg9]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5yg9' size='340' side='right'caption='[[5yg9]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yg9]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii~~ Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YG9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yg9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YG9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RI2:1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE'>RI2</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]] 2.8Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0208 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RI2:1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE'>RI2</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose_1,5-bisphosphate_isomerase Ribose 1,5-bisphosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.29 5.3.1.29] </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=5yg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg9 OCA], [https://pdbe.org/5yg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yg9 RCSB], [https://www.ebi.ac.uk/pdbsum/5yg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg9 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=5yg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg9 OCA], [~~http~~://pdbe.org/5yg9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yg9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yg9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg9 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/R15PI_PYRHO R15PI_PYRHO]] Catalyzes the isomerization of ribose 1,5-bisphosphate (R15P) to ribulose 1,5-bisphosphate (RuBP), the CO(2) acceptor and substrate for RubisCO. Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and RubisCO (By similarity).	+	[https://www.uniprot.org/uniprot/R15PI_PYRHO R15PI_PYRHO] Catalyzes the isomerization of ribose 1,5-bisphosphate (R15P) to ribulose 1,5-bisphosphate (RuBP), the CO(2) acceptor and substrate for RubisCO. Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and RubisCO (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pyrococcus horikoshii]]	+	[[Category: Pyrococcus horikoshii OT3]]
-	~~[[Category: Ribose 1,5-bisphosphate isomerase~~]]	+	[[Category: Gogoi P]]
-	[[Category: Gogoi, P]]	+	[[Category: Kanaujia SP]]
-	[[Category: Kanaujia~~, S P]]~~	+
-	~~[[Category: 5-bisphosphate]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Nmp degradation pathway]]~~	+
-	~~[[Category: Ribose-1]]~~	+
-	~~[[Category: Rossmann-like fold~~]]	+

OCA at 09:18, 21 October 2020

OCA — Wed, 21 Oct 2020 09:18:58 GMT

←Older revision		Revision as of 09:18, 21 October 2020
Line 1:		Line 1:

	==Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate, AMP and GMP==		==Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate, AMP and GMP==
-	<StructureSection load='5yg9' size='340' side='right' caption='[[5yg9]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5yg9' size='340' side='right'caption='[[5yg9]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yg9]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG9 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YG9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yg9]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YG9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RI2:1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE'>RI2</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RI2:1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE'>RI2</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0208 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose_1,5-bisphosphate_isomerase Ribose 1,5-bisphosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.29 5.3.1.29] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose_1,5-bisphosphate_isomerase Ribose 1,5-bisphosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.29 5.3.1.29] </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=5yg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg9 OCA], [http://pdbe.org/5yg9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yg9 RCSB], [http://www.ebi.ac.uk/pdbsum/5yg9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg9 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=5yg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg9 OCA], [http://pdbe.org/5yg9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yg9 RCSB], [http://www.ebi.ac.uk/pdbsum/5yg9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pyrococcus horikoshii]]
	[[Category: Ribose 1,5-bisphosphate isomerase]]		[[Category: Ribose 1,5-bisphosphate isomerase]]
	[[Category: Gogoi, P]]		[[Category: Gogoi, P]]

OCA at 06:31, 15 February 2018

OCA — Thu, 15 Feb 2018 06:31:17 GMT

←Older revision		Revision as of 06:31, 15 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yg9 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of ribose-1,5-bisphosphate isomerase mutant C135S from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate, AMP and GMP==
		+	<StructureSection load='5yg9' size='340' side='right' caption='[[5yg9]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yg9]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YG9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YG9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RI2:1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE'>RI2</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose_1,5-bisphosphate_isomerase Ribose 1,5-bisphosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.29 5.3.1.29] </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=5yg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yg9 OCA], [http://pdbe.org/5yg9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yg9 RCSB], [http://www.ebi.ac.uk/pdbsum/5yg9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yg9 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/R15PI_PYRHO R15PI_PYRHO]] Catalyzes the isomerization of ribose 1,5-bisphosphate (R15P) to ribulose 1,5-bisphosphate (RuBP), the CO(2) acceptor and substrate for RubisCO. Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and RubisCO (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The homologues of the regulatory subunits of eukaryotic translation initiation factor 2B (eIF2B) are assumed to be present in archaea. Likewise, an ORF, PH0208 in Pyrococcus horikoshii OT3 have been proposed to encode one of the homologues of regulatory subunits of eIF2B. However, PH0208 protein also shares sequence similarity with a functionally non-related enzyme, ribose-1,5-bisphosphate isomerase (R15Pi), involved in conversion of ribose-1,5-bisphosphate (R15P) to ribulose-1,5-bisphosphate (RuBP) in an AMP-dependent manner. Herein, we have determined the crystal structure of PH0208 protein in order to decipher its true function. Although structurally similar to the regulatory subunits of eIF2B, the ability to bind R15P and RuBP suggests that PH0208 would function as R15Pi. Additionally, this study for the first time reports the binding sites of AMP and GMP in R15Pi. The AMP binding site in PH0208 protein clarified the role of AMP in providing structural stability to R15Pi. The binding of GMP to the 'AMP binding site' in addition to its own binding site indicates that GMP might also execute a similar function, though with less specificity. Furthermore, we have utilized the resemblance between PH0208 and the regulatory subunits of eIF2B to propose a model for the regulatory mechanism of eIF2B in eukaryotes.

-	~~Authors~~:	+	A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3.,Gogoi P, Kanaujia SP Sci Rep. 2018 Jan 30;8(1):1891. doi: 10.1038/s41598-018-20418-w. PMID:29382938<ref>PMID:29382938</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yg9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ribose 1,5-bisphosphate isomerase]]
		+	[[Category: Gogoi, P]]
		+	[[Category: Kanaujia, S P]]
		+	[[Category: 5-bisphosphate]]
		+	[[Category: Isomerase]]
		+	[[Category: Nmp degradation pathway]]
		+	[[Category: Ribose-1]]
		+	[[Category: Rossmann-like fold]]

OCA at 06:23, 22 November 2017

OCA — Wed, 22 Nov 2017 06:23:34 GMT

←Older revision		Revision as of 06:23, 22 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yg9 is ON HOLD	+	The entry 5yg9 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5yg9" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:32:05 GMT

Protected "5yg9" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:32, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5yg9 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 16:32:04 GMT

New page: '''Unreleased structure''' The entry 5yg9 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yg9 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]