6a34 - Revision history

OCA at 09:16, 22 November 2023

OCA — Wed, 22 Nov 2023 09:16:04 GMT

←Older revision		Revision as of 09:16, 22 November 2023
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	<StructureSection load='6a34' size='340' side='right'caption='[[6a34]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6a34' size='340' side='right'caption='[[6a34]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a34]] is a 2 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=6A34 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6A34 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a34]] is a 2 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=6A34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A34 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HEZ:HEXANE~~-1,~~6-DIOL'>HEZ</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]] 2.3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PH0702 ([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=HEZ:HEXANE-1,6-DIOL'>HEZ</scene></td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/S-methyl-5-thioribose~~-1~~-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23]~~ </~~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=6a34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a34 OCA], [https://pdbe.org/6a34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a34 RCSB], [https://www.ebi.ac.uk/pdbsum/6a34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a34 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=6a34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a34 OCA], [~~http~~://pdbe.org/6a34 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6a34 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6a34 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6a34 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MTNA_PYRHO MTNA_PYRHO]] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).[HAMAP-Rule:MF_01678]	+	[https://www.uniprot.org/uniprot/MTNA_PYRHO MTNA_PYRHO] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).[HAMAP-Rule:MF_01678]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pyrococcus horikoshii]]	+	[[Category: Pyrococcus horikoshii OT3]]
-	~~[[Category: S-methyl-5-thioribose-1-phosphate isomerase~~]]	+	[[Category: Gogoi P]]
-	[[Category: Gogoi, P]]	+	[[Category: Kanaujia SP]]
-	[[Category: Kanaujia~~, S P~~]]	+	[[Category: Mordina P]]
-	[[Category: Mordina, P]]	+
-	~~[[Category: Cis-phosphoenolate intermediate]]~~	+
-	~~[[Category: Hydride transfer]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Methionine salvage pathway]]~~	+
-	~~[[Category: Ph0702~~]]	+

OCA at 21:25, 28 October 2020

OCA — Wed, 28 Oct 2020 21:25:51 GMT

←Older revision		Revision as of 21:25, 28 October 2020
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	==Crystal structure of 5-methylthioribose 1-phosphate isomerase from Pyrococcus horikoshii OT3 - Form I==		==Crystal structure of 5-methylthioribose 1-phosphate isomerase from Pyrococcus horikoshii OT3 - Form I==
-	<StructureSection load='6a34' size='340' side='right' caption='[[6a34]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='6a34' size='340' side='right'caption='[[6a34]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a34]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A34 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6A34 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a34]] is a 2 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=6A34 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6A34 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0702 ([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/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </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=6a34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a34 OCA], [http://pdbe.org/6a34 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a34 RCSB], [http://www.ebi.ac.uk/pdbsum/6a34 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a34 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=6a34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a34 OCA], [http://pdbe.org/6a34 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a34 RCSB], [http://www.ebi.ac.uk/pdbsum/6a34 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a34 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pyrococcus horikoshii]]
	[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]		[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]
	[[Category: Gogoi, P]]		[[Category: Gogoi, P]]

OCA at 06:41, 12 December 2018

OCA — Wed, 12 Dec 2018 06:41:22 GMT

←Older revision		Revision as of 06:41, 12 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6a34 is ~~ON HOLD~~	+	==Crystal structure of 5-methylthioribose 1-phosphate isomerase from Pyrococcus horikoshii OT3 - Form I==
		+	<StructureSection load='6a34' size='340' side='right' caption='[[6a34]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6a34]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A34 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A34 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </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=6a34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a34 OCA], [http://pdbe.org/6a34 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a34 RCSB], [http://www.ebi.ac.uk/pdbsum/6a34 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a34 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MTNA_PYRHO MTNA_PYRHO]] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).[HAMAP-Rule:MF_01678]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	5-Methylthioribose 1-phosphate isomerase (M1Pi) is a crucial enzyme involved in the universally conserved methionine salvage pathway (MSP) where it is known to catalyze the conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P) via a mechanism which remains unspecified till date. Furthermore, although M1Pi has a discrete function, it surprisingly shares high structural similarity with two functionally non-related proteins such as ribose-1,5-bisphosphate isomerase (R15Pi) and the regulatory subunits of eukaryotic translation initiation factor 2B (eIF2B). To identify the distinct structural features that lead to divergent functional obligations of M1Pi as well as to understand the mechanism of enzyme catalysis, the crystal structure of M1Pi from a hyperthermophilic archaeon Pyrococcus horikoshii OT3 was determined. A meticulous structural investigation of the dimeric M1Pi revealed the presence of an N-terminal extension and a hydrophobic patch absent in R15Pi and the regulatory alpha-subunit of eIF2B. Furthermore, unlike R15Pi in which a kink formation is observed in one of the helices, the domain movement of M1Pi is distinguished by a forward shift in a loop covering the active-site pocket. All these structural attributes contribute towards a hydrophobic microenvironment in the vicinity of the active site of the enzyme making it favorable for the reaction mechanism to commence. Thus, a hydrophobic active-site microenvironment in addition to the availability of optimal amino-acid residues surrounding the catalytic residues in M1Pi led us to propose its probable reaction mechanism via a cis-phosphoenolate intermediate formation.

-	~~Authors~~:	+	Structural insights into the catalytic mechanism of 5-methylthioribose 1-phosphate isomerase.,Gogoi P, Mordina P, Kanaujia SP J Struct Biol. 2018 Nov 22. pii: S1047-8477(18)30290-9. doi:, 10.1016/j.jsb.2018.11.007. PMID:30471343<ref>PMID:30471343</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6a34" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]
		+	[[Category: Gogoi, P]]
		+	[[Category: Kanaujia, S P]]
		+	[[Category: Mordina, P]]
		+	[[Category: Cis-phosphoenolate intermediate]]
		+	[[Category: Hydride transfer]]
		+	[[Category: Isomerase]]
		+	[[Category: Methionine salvage pathway]]
		+	[[Category: Ph0702]]

OCA: Protected "6a34" [edit=sysop:move=sysop]

OCA — Wed, 20 Jun 2018 03:57:06 GMT

Protected "6a34" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:57, 20 June 2018

OCA: New page: '''Unreleased structure''' The entry 6a34 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 20 Jun 2018 03:57:04 GMT

New page: '''Unreleased structure''' The entry 6a34 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6a34 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]