3epo - Revision history

OCA at 09:48, 21 February 2024

OCA — Wed, 21 Feb 2024 09:48:57 GMT

←Older revision		Revision as of 09:48, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3epo' size='340' side='right'caption='[[3epo]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3epo' size='340' side='right'caption='[[3epo]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3epo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3epo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EPO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MP5:(4-AMINO~~-2~~-METHYLPYRIMIDIN-5-YL)METHYL+DIHYDROGEN+PHOSPHATE'>MP5</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]] 2.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3epm\|3epm]], [[3epn\|3epn]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MP5:(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL+DIHYDROGEN+PHOSPHATE'>MP5</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=3epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epo OCA], [https://pdbe.org/3epo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3epo RCSB], [https://www.ebi.ac.uk/pdbsum/3epo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3epo 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=3epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epo OCA], [https://pdbe.org/3epo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3epo RCSB], [https://www.ebi.ac.uk/pdbsum/3epo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3epo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~THIC_CAUCR THIC_CAUCR]~~] Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.<ref>PMID:18953358</ref>	+	[https://www.uniprot.org/uniprot/THIC_CAUVC THIC_CAUVC] Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.<ref>PMID:18953358</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3epo ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3epo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase catalyzes a complex rearrangement of 5-aminoimidazole ribonucleotide (AIR) to form HMP-P, the pyrimidine moiety of thiamine phosphate. We determined the three-dimensional structures of HMP-P synthase and its complexes with the product HMP-P and a substrate analog imidazole ribotide. The structure of HMP-P synthase reveals a homodimer in which each protomer comprises three domains: an N-terminal domain with a novel fold, a central (betaalpha)(8) barrel and a disordered C-terminal domain that contains a conserved CX(2)CX(4)C motif, which is suggestive of a [4Fe-4S] cluster. Biochemical studies have confirmed that HMP-P synthase is iron sulfur cluster-dependent, that it is a new member of the radical SAM superfamily and that HMP-P and 5'-deoxyadenosine are products of the reaction. Mossbauer and EPR spectroscopy confirm the presence of one [4Fe-4S] cluster. Structural comparisons reveal that HMP-P synthase is homologous to a group of adenosylcobalamin radical enzymes. This similarity supports an evolutionary relationship between these two superfamilies.
-
-	Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily.,Chatterjee A, Li Y, Zhang Y, Grove TL, Lee M, Krebs C, Booker SJ, Begley TP, Ealick SE Nat Chem Biol. 2008 Dec;4(12):758-65. Epub 2008 Oct 26. PMID:18953358<ref>PMID:18953358</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3epo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Caulobacter vibrioides]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Begley~~, T P~~]]	+	[[Category: Begley TP]]
-	[[Category: Booker~~, S J~~]]	+	[[Category: Booker SJ]]
-	[[Category: Chatterjee, A]]	+	[[Category: Chatterjee A]]
-	[[Category: Ealick~~, S E~~]]	+	[[Category: Ealick SE]]
-	[[Category: Grove~~, T L~~]]	+	[[Category: Grove TL]]
-	[[Category: Krebs, C]]	+	[[Category: Krebs C]]
-	[[Category: Lee, M]]	+	[[Category: Lee M]]
-	[[Category: Li, S]]	+	[[Category: Li S]]
-	[[Category: Zhang, Y]]	+	[[Category: Zhang Y]]
-	~~[[Category: Alpha-beta barrel]]~~	+
-	~~[[Category: Biosynthetic protein]]~~	+
-	~~[[Category: Sam superfamily]]~~	+
-	~~[[Category: Thiamine biosynthesis~~]]	+

OCA at 09:12, 23 February 2022

OCA — Wed, 23 Feb 2022 09:12:47 GMT

←Older revision		Revision as of 09:12, 23 February 2022
Line 3:		Line 3:
	<StructureSection load='3epo' size='340' side='right'caption='[[3epo]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3epo' size='340' side='right'caption='[[3epo]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3epo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3EPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3epo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EPO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MP5:(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL+DIHYDROGEN+PHOSPHATE'>MP5</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MP5:(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL+DIHYDROGEN+PHOSPHATE'>MP5</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3epm\|3epm]], [[3epn\|3epn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3epm\|3epm]], [[3epn\|3epn]]</div></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=3epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epo OCA], [~~http~~://pdbe.org/3epo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3epo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3epo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3epo 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=3epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epo OCA], [https://pdbe.org/3epo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3epo RCSB], [https://www.ebi.ac.uk/pdbsum/3epo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3epo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/THIC_CAUCR THIC_CAUCR]] Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.<ref>PMID:18953358</ref>	+	[[https://www.uniprot.org/uniprot/THIC_CAUCR THIC_CAUCR]] Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.<ref>PMID:18953358</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:48, 7 August 2019

OCA — Wed, 07 Aug 2019 06:48:15 GMT

←Older revision		Revision as of 06:48, 7 August 2019
Line 1:		Line 1:

	==Crystal structure of Caulobacter crescentus ThiC complexed with HMP-P==		==Crystal structure of Caulobacter crescentus ThiC complexed with HMP-P==
-	<StructureSection load='3epo' size='340' side='right' caption='[[3epo]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3epo' size='340' side='right'caption='[[3epo]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3epo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EPO FirstGlance]. <br>		<table><tr><td colspan='2'>[[3epo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EPO FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ep/3epo_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ep/3epo_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]
	[[Category: Booker, S J]]		[[Category: Booker, S J]]

OCA at 09:17, 25 October 2017

OCA — Wed, 25 Oct 2017 09:17:47 GMT

←Older revision		Revision as of 09:17, 25 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of Caulobacter crescentus ThiC complexed with HMP-P==		==Crystal structure of Caulobacter crescentus ThiC complexed with HMP-P==
	<StructureSection load='3epo' size='340' side='right' caption='[[3epo]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3epo' size='340' side='right' caption='[[3epo]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3epo]] is a 2 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3epo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EPO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MP5:(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL+DIHYDROGEN+PHOSPHATE'>MP5</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MP5:(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL+DIHYDROGEN+PHOSPHATE'>MP5</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3epm\|3epm]], [[3epn\|3epn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3epm\|3epm]], [[3epn\|3epn]]</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=3epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epo OCA], [http://pdbe.org/3epo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3epo RCSB], [http://www.ebi.ac.uk/pdbsum/3epo PDBsum]</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=3epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epo OCA], [http://pdbe.org/3epo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3epo RCSB], [http://www.ebi.ac.uk/pdbsum/3epo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3epo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Caulobacter vibrioides]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]
	[[Category: Booker, S J]]		[[Category: Booker, S J]]

OCA at 05:44, 8 February 2016

OCA — Mon, 08 Feb 2016 05:44:29 GMT

←Older revision		Revision as of 05:44, 8 February 2016
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MP5:(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL+DIHYDROGEN+PHOSPHATE'>MP5</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MP5:(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL+DIHYDROGEN+PHOSPHATE'>MP5</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3epm\|3epm]], [[3epn\|3epn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3epm\|3epm]], [[3epn\|3epn]]</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=3epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3epo RCSB], [http://www.ebi.ac.uk/pdbsum/3epo PDBsum]</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=3epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epo OCA], [http://pdbe.org/3epo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3epo RCSB], [http://www.ebi.ac.uk/pdbsum/3epo PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3epo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3epo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:04, 24 December 2014

OCA — Wed, 24 Dec 2014 21:04:24 GMT

←Older revision		Revision as of 21:04, 24 December 2014
Line 7:		Line 7:
	<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=3epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3epo RCSB], [http://www.ebi.ac.uk/pdbsum/3epo PDBsum]</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=3epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3epo RCSB], [http://www.ebi.ac.uk/pdbsum/3epo PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/THIC_CAUCR THIC_CAUCR]] Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.<ref>PMID:18953358</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:48, 26 November 2014

OCA — Wed, 26 Nov 2014 08:48:22 GMT

←Older revision		Revision as of 08:48, 26 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3epo.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Caulobacter crescentus ThiC complexed with HMP-P==
		+	<StructureSection load='3epo' size='340' side='right' caption='[[3epo]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3epo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EPO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MP5:(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL+DIHYDROGEN+PHOSPHATE'>MP5</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3epm\|3epm]], [[3epn\|3epn]]</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=3epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3epo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3epo RCSB], [http://www.ebi.ac.uk/pdbsum/3epo PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ep/3epo_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase catalyzes a complex rearrangement of 5-aminoimidazole ribonucleotide (AIR) to form HMP-P, the pyrimidine moiety of thiamine phosphate. We determined the three-dimensional structures of HMP-P synthase and its complexes with the product HMP-P and a substrate analog imidazole ribotide. The structure of HMP-P synthase reveals a homodimer in which each protomer comprises three domains: an N-terminal domain with a novel fold, a central (betaalpha)(8) barrel and a disordered C-terminal domain that contains a conserved CX(2)CX(4)C motif, which is suggestive of a [4Fe-4S] cluster. Biochemical studies have confirmed that HMP-P synthase is iron sulfur cluster-dependent, that it is a new member of the radical SAM superfamily and that HMP-P and 5'-deoxyadenosine are products of the reaction. Mossbauer and EPR spectroscopy confirm the presence of one [4Fe-4S] cluster. Structural comparisons reveal that HMP-P synthase is homologous to a group of adenosylcobalamin radical enzymes. This similarity supports an evolutionary relationship between these two superfamilies.

-	~~{{STRUCTURE_3epo\| PDB=3epo \| SCENE= }}~~	+	Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily.,Chatterjee A, Li Y, Zhang Y, Grove TL, Lee M, Krebs C, Booker SJ, Begley TP, Ealick SE Nat Chem Biol. 2008 Dec;4(12):758-65. Epub 2008 Oct 26. PMID:18953358<ref>PMID:18953358</ref>

-	~~===Crystal structure~~ of ~~Caulobacter crescentus ThiC complexed with HMP-P===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18953358}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3epo]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3EPO OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018953358<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Caulobacter vibrioides]]		[[Category: Caulobacter vibrioides]]
-	[[Category: Begley, T P.]]	+	[[Category: Begley, T P]]
-	[[Category: Booker, S J.]]	+	[[Category: Booker, S J]]
-	[[Category: Chatterjee, A.]]	+	[[Category: Chatterjee, A]]
-	[[Category: Ealick, S E.]]	+	[[Category: Ealick, S E]]
-	[[Category: Grove, T L.]]	+	[[Category: Grove, T L]]
-	[[Category: Krebs, C.]]	+	[[Category: Krebs, C]]
-	[[Category: Lee, M.]]	+	[[Category: Lee, M]]
-	[[Category: Li, S.]]	+	[[Category: Li, S]]
-	[[Category: Zhang, Y.]]	+	[[Category: Zhang, Y]]
	[[Category: Alpha-beta barrel]]		[[Category: Alpha-beta barrel]]
	[[Category: Biosynthetic protein]]		[[Category: Biosynthetic protein]]
	[[Category: Sam superfamily]]		[[Category: Sam superfamily]]
	[[Category: Thiamine biosynthesis]]		[[Category: Thiamine biosynthesis]]

OCA: Protected "3epo" [edit=sysop:move=sysop]

OCA — Wed, 06 Feb 2013 13:34:03 GMT

Protected "3epo" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:34, 6 February 2013

OCA at 13:34, 6 February 2013

OCA — Wed, 06 Feb 2013 13:34:00 GMT

←Older revision		Revision as of 13:34, 6 February 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3epo.png\|left\|200px]]		[[Image:3epo.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3epo", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3epo\| PDB=3epo \| SCENE= }}		{{STRUCTURE_3epo\| PDB=3epo \| SCENE= }}

	===Crystal structure of Caulobacter crescentus ThiC complexed with HMP-P===		===Crystal structure of Caulobacter crescentus ThiC complexed with HMP-P===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18953358}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18953358 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18953358}}		{{ABSTRACT_PUBMED_18953358}}

	==About this Structure==		==About this Structure==
-	~~3EPO~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPO OCA].	+	[[3epo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Caulobacter_vibrioides Caulobacter vibrioides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPO OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18953358~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018953358</ref><references group="xtra"/>
	[[Category: Caulobacter vibrioides]]		[[Category: Caulobacter vibrioides]]
	[[Category: Begley, T P.]]		[[Category: Begley, T P.]]
Line 38:		Line 26:
	[[Category: Sam superfamily]]		[[Category: Sam superfamily]]
	[[Category: Thiamine biosynthesis]]		[[Category: Thiamine biosynthesis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 19:21:36 2009''

OCA at 17:21, 16 February 2009

OCA — Mon, 16 Feb 2009 17:21:44 GMT

←Older revision		Revision as of 17:21, 16 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
-	Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily., Chatterjee A, Li Y, Zhang Y, Grove TL, Lee M, Krebs C, Booker SJ, Begley TP, Ealick SE, Nat Chem Biol. 2008 Dec;4(12):758-65. Epub 2008 Oct 26. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18953358 18953358]~~	+	<ref group="xtra">PMID:18953358</ref><references group="xtra"/>
	[[Category: Caulobacter vibrioides]]		[[Category: Caulobacter vibrioides]]
	[[Category: Begley, T P.]]		[[Category: Begley, T P.]]
Line 39:		Line 39:
	[[Category: Thiamine biosynthesis]]		[[Category: Thiamine biosynthesis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Nov 27 13~~:54:~~00 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 19:21:36 2009''