3req - Revision history

OCA at 10:11, 13 August 2026

2026-08-13T10:11:08Z

← Older revision		Revision as of 10:11, 13 August 2026
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	<table><tr><td colspan='2'>[[3req]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3REQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3req]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3REQ 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]] 2.7Å</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]] 2.7Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN~~</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12~~</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</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=3req FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3req OCA], [https://pdbe.org/3req PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3req RCSB], [https://www.ebi.ac.uk/pdbsum/3req PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3req 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=3req FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3req OCA], [https://pdbe.org/3req PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3req RCSB], [https://www.ebi.ac.uk/pdbsum/3req PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3req ProSAT]</span></td></tr>
	</table>		</table>
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/re/3req_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/re/3req_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 06:49, 9 August 2023

2023-08-09T06:49:11Z

← Older revision		Revision as of 06:49, 9 August 2023
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	==METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)==		==METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)==
	<StructureSection load='3req' size='340' side='right' caption='[[3req]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3req' size='340' side='right'caption='[[3req]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3req]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"propionibacterium_shermanii"_van_niel_1928 "propionibacterium~~ shermanii~~" van niel 1928~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3REQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3req]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3REQ FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ADN:ADENOSINE'>ADN</scene~~>, ~~<scene name='pdbligand=B12:COBALAMIN'>B12</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]] 2.7Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>MUTA, MUTB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1752~~ "~~Propionibacterium shermanii~~" ~~van Niel 1928])</td~~><~~/tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Methylmalonyl-CoA_mutase Methylmalonyl-CoA mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.2 5.4.99.2]~~ </~~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=3req FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3req OCA], [https://pdbe.org/3req PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3req RCSB], [https://www.ebi.ac.uk/pdbsum/3req PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3req ProSAT]</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=3req FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3req OCA], [~~http~~://pdbe.org/3req PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3req RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3req PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/MUTB_PROFR MUTB_PROFR~~]] Catalyzes the isomerization of succinyl-CoA to methylmalonyl-CoA during synthesis of propionate from tricarboxylic acid-cycle intermediates. [[http://www.uniprot.org/uniprot/MUTA_PROFR MUTA_PROFR]~~] Catalyzes the isomerization of succinyl-CoA to methylmalonyl-CoA during synthesis of propionate from tricarboxylic acid-cycle intermediates.		[https://www.uniprot.org/uniprot/MUTB_PROFR MUTB_PROFR] Catalyzes the isomerization of succinyl-CoA to methylmalonyl-CoA during synthesis of propionate from tricarboxylic acid-cycle intermediates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/re/3req_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/re/3req_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>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Propionibacterium shermanii van niel 1928~~]]		[[Category: Large Structures]]
	[[Category: ~~Methylmalonyl-CoA mutase~~]]		[[Category: Propionibacterium freudenreichii subsp. shermanii]]
	[[Category: Evans~~, P R~~]]		[[Category: Evans PR]]
	[[Category: Mancia, F]]		[[Category: Mancia F]]
	~~[[Category: Intramolecular transferase]]~~
	~~[[Category: Isomerase]]~~
	~~[[Category: Mutase~~]]

OCA at 03:25, 7 February 2016

2016-02-07T03:25:29Z

← Older revision		Revision as of 03:25, 7 February 2016
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	<StructureSection load='3req' size='340' side='right' caption='[[3req]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3req' size='340' side='right' caption='[[3req]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3req]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp.~~ shermanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3REQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3req]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"propionibacterium_shermanii"_van_niel_1928 "propionibacterium shermanii" van niel 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3REQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MUTA, MUTB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1752 Propionibacterium ~~freudenreichii subsp.~~ shermanii])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MUTA, MUTB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1752 "Propionibacterium shermanii" van Niel 1928])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylmalonyl-CoA_mutase Methylmalonyl-CoA mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.2 5.4.99.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylmalonyl-CoA_mutase Methylmalonyl-CoA mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.2 5.4.99.2] </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=3req FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3req OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3req RCSB], [http://www.ebi.ac.uk/pdbsum/3req 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=3req FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3req OCA], [http://pdbe.org/3req PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3req RCSB], [http://www.ebi.ac.uk/pdbsum/3req PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<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=3req ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 3req" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Propionibacterium shermanii van niel 1928]]
	[[Category: Methylmalonyl-CoA mutase]]		[[Category: Methylmalonyl-CoA mutase]]
	~~[[Category: Propionibacterium freudenreichii subsp. shermanii]]~~
	[[Category: Evans, P R]]		[[Category: Evans, P R]]
	[[Category: Mancia, F]]		[[Category: Mancia, F]]

OCA at 07:28, 24 December 2014

2014-12-24T07:28:47Z

← Older revision		Revision as of 07:28, 24 December 2014
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	<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=3req FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3req OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3req RCSB], [http://www.ebi.ac.uk/pdbsum/3req 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=3req FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3req OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3req RCSB], [http://www.ebi.ac.uk/pdbsum/3req PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/MUTB_PROFR MUTB_PROFR]] Catalyzes the isomerization of succinyl-CoA to methylmalonyl-CoA during synthesis of propionate from tricarboxylic acid-cycle intermediates. [[http://www.uniprot.org/uniprot/MUTA_PROFR MUTA_PROFR]] Catalyzes the isomerization of succinyl-CoA to methylmalonyl-CoA during synthesis of propionate from tricarboxylic acid-cycle intermediates.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:01, 9 December 2014

2014-12-09T12:01:05Z

← Older revision		Revision as of 12:01, 9 December 2014
Line 1:		Line 1:
	[[Image:~~3req~~.~~png~~\|~~left~~\|~~200px~~]]		==METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)==
			<StructureSection load='3req' size='340' side='right' caption='[[3req]], [[Resolution\|resolution]] 2.70Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3req]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3REQ FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MUTA, MUTB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1752 Propionibacterium freudenreichii subsp. shermanii])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylmalonyl-CoA_mutase Methylmalonyl-CoA mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.99.2 5.4.99.2] </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=3req FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3req OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3req RCSB], [http://www.ebi.ac.uk/pdbsum/3req 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/re/3req_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 ==
			BACKGROUND: Methylmalonyl CoA mutase catalyses the interconversion of succinyl CoA and methylmalonyl CoA via a free radical mechanism. The enzyme belongs to a family of enzymes that catalyse intramolecular rearrangement reactions in which a group and a hydrogen atom on adjacent carbons are exchanged. These enzymes use the cofactor adenosylcobalamin (coenzyme B12) which breaks to form an adenosyl radical, thus initiating the reaction. Determination of the structure of substrate-free methylmalonyl CoA mutase was initiated to provide further insight into the mechanism of radical formation. RESULTS: We report here two structures of methylmalonyl CoA mutase from Propionibacterium shermanii. The first structure is of the enzyme in a nonproductive complex with CoA at 2.5 A resolution. This structure serves as a model for the substrate-free conformation of the enzyme, as it is very similar to the second much poorer 2.7 A resolution structure derived from a truly substrate-free crystal. The true substrate-free structure also shows the adenosyl group bound to the cobalt atom. Comparison of this structure with that of the previously reported complex of the enzyme with a substrate analogue shows that major conformational changes occur upon substrate binding. The substrate-binding site of the enzyme is located within a (beta alpha)8 TIM-barrel domain. In the absence of substrate, this TIM-barrel domain is split apart and the active site is accessible to solvent. When substrate binds, the barrel closes up with the substrate along its axis and the active site becomes completely buried. CONCLUSIONS: The closure of the active-site cavity upon substrate binding displaces the adenosyl group of the cofactor from the central cobalt atom into the active-site cavity. This triggers the formation of the free radical that initiates the rearrangement reaction. The TIM-barrel domain is substantially different from all others yet reported: in its unliganded form it is broken open, exposing the small hydrophilic sidechains which fill the centre. The typical barrel structure is only formed when substrate is bound.

	~~{{STRUCTURE_3req\| PDB=3req \| SCENE= }}~~		Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism.,Mancia F, Evans PR Structure. 1998 Jun 15;6(6):711-20. PMID:9655823<ref>PMID:9655823</ref>

	~~===METHYLMALONYL-COA MUTASE~~, ~~SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_9655823}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[3req]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Propionibacterium_freudenreichii_subsp~~.~~_shermanii Propionibacterium freudenreichii subsp. shermanii]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:009655823<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Methylmalonyl-CoA mutase]]		[[Category: Methylmalonyl-CoA mutase]]
	[[Category: Propionibacterium freudenreichii subsp. shermanii]]		[[Category: Propionibacterium freudenreichii subsp. shermanii]]
	[[Category: Evans, P R.]]		[[Category: Evans, P R]]
	[[Category: Mancia, F.]]		[[Category: Mancia, F]]
	[[Category: Intramolecular transferase]]		[[Category: Intramolecular transferase]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Mutase]]		[[Category: Mutase]]

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

2012-10-24T06:22:17Z

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

← Older revision	Revision as of 06:22, 24 October 2012
(No difference)

OCA at 06:22, 24 October 2012

2012-10-24T06:22:16Z

← Older revision		Revision as of 06:22, 24 October 2012
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	[[Image:3req.png\|left\|200px]]		[[Image:3req.png\|left\|200px]]

	~~<!--~~
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	~~or leave the SCENE parameter empty for the default display.~~
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	{{STRUCTURE_3req\| PDB=3req \| SCENE= }}		{{STRUCTURE_3req\| PDB=3req \| SCENE= }}

	===METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)===		===METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_9655823}}, adds the Publication Abstract to the page~~
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	{{ABSTRACT_PUBMED_9655823}}		{{ABSTRACT_PUBMED_9655823}}

	==About this Structure==		==About this Structure==
	~~3REQ~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA].		[[3req]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~9655823~~</ref><references group="xtra"/>		<ref group="xtra">PMID:009655823</ref><references group="xtra"/>
	[[Category: Methylmalonyl-CoA mutase]]		[[Category: Methylmalonyl-CoA mutase]]
	[[Category: Propionibacterium freudenreichii subsp. shermanii]]		[[Category: Propionibacterium freudenreichii subsp. shermanii]]
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	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Mutase]]		[[Category: Mutase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 10:46:45 2009''~~

OCA at 08:46, 16 February 2009

2009-02-16T08:46:46Z

← Older revision		Revision as of 08:46, 16 February 2009
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	==About this Structure==		==About this Structure==
	3REQ is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA].		3REQ is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA].

	==Reference==		==Reference==
	~~Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism., Mancia F, Evans PR, Structure. 1998 Jun 15;6(6):711-20.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9655823 9655823]~~		<ref group="xtra">PMID:9655823</ref><references group="xtra"/>
	[[Category: Methylmalonyl-CoA mutase]]		[[Category: Methylmalonyl-CoA mutase]]
	[[Category: Propionibacterium freudenreichii subsp. shermanii]]		[[Category: Propionibacterium freudenreichii subsp. shermanii]]
	~~[[Category: Protein complex]]~~
	[[Category: Evans, P R.]]		[[Category: Evans, P R.]]
	[[Category: Mancia, F.]]		[[Category: Mancia, F.]]
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	[[Category: Mutase]]		[[Category: Mutase]]

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OCA at 10:05, 3 July 2008

2008-07-03T10:05:13Z

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	{{STRUCTURE_3req\| PDB=3req \| SCENE= }}		{{STRUCTURE_3req\| PDB=3req \| SCENE= }}

	~~'''~~METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)~~'''~~		===METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)===


	~~==Overview==~~		<!--
	~~BACKGROUND: Methylmalonyl CoA mutase catalyses the interconversion of succinyl CoA and methylmalonyl CoA via a free radical mechanism.~~ The enzyme belongs to a family of enzymes that catalyse intramolecular rearrangement reactions in which a group and a hydrogen atom on adjacent carbons are exchanged. These enzymes use the cofactor adenosylcobalamin (coenzyme B12) which breaks to form an adenosyl radical, ~~thus initiating the reaction. Determination of~~ the ~~structure of substrate-free methylmalonyl CoA mutase was initiated~~ to ~~provide further insight into~~ the mechanism of radical formation. RESULTS: We report here two structures of methylmalonyl CoA mutase from Propionibacterium shermanii. The first structure is of the enzyme in a nonproductive complex with CoA at 2.5 A resolution. This structure serves as a model for the substrate-free conformation of the enzyme, as it ~~is very similar to the second much poorer 2.7 A resolution structure derived from a truly substrate-free crystal~~. ~~The true substrate-free structure also shows the adenosyl group bound to the cobalt atom~~. Comparison of this structure with that of the previously reported complex of the enzyme with a substrate analogue shows that major conformational changes occur upon substrate binding. The substrate-binding site of the enzyme is located within a (beta alpha)~~8 TIM-barrel domain. In the absence of substrate~~, ~~this TIM-barrel domain~~ is ~~split apart and~~ the ~~active site is accessible to solvent~~. ~~When substrate binds, the barrel closes up with the substrate along its axis and the active site becomes completely buried. CONCLUSIONS: The closure of the active~~-~~site cavity upon substrate binding displaces the adenosyl group of the cofactor from the central cobalt atom into the active~~-site cavity. This triggers the formation of the free radical that initiates the rearrangement reaction. The TIM-barrel domain is substantially different from all others yet reported: in its unliganded form it is broken open, exposing the small hydrophilic sidechains which fill the centre. The typical barrel structure is only formed when substrate is bound.		The line below this paragraph, {{ABSTRACT_PUBMED_9655823}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 9655823 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_9655823}}

	==About this Structure==		==About this Structure==
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	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Mutase]]		[[Category: Mutase]]
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OCA at 19:12, 4 May 2008

2008-05-04T19:12:05Z

← Older revision		Revision as of 19:12, 4 May 2008
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	~~{{Structure~~		<!--
	~~\|PDB= 3req \|SIZE=350\|CAPTION= <scene name='initialview01'>3req</scene>~~, ~~resolution 2~~.~~7Å~~		The line below this paragraph, containing "STRUCTURE_3req", creates the "Structure Box" on the page.
	~~\|SITE=~~		You may change the PDB parameter (which sets the PDB file loaded into the applet)
	~~\|LIGAND= <~~scene ~~name='pdbligand=ADN:ADENOSINE'>ADN</scene>~~, ~~<scene name='pdbligand=B12:COBALAMIN'>B12</scene>~~		or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
	~~\|ACTIVITY= <span class='plainlinks'>[http://en~~.~~wikipedia.org/wiki/Methylmalonyl-CoA_mutase Methylmalonyl~~-~~CoA mutase], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=5.4.99.2 5.4.99.2] </span~~>		or leave the SCENE parameter empty for the default display.
	\|~~GENE~~= ~~MUTA, MUTB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1752 Propionibacterium freudenreichii subsp. shermanii])~~		-->
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	}}

	'''METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)'''		'''METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)'''
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	[[Category: Evans, P R.]]		[[Category: Evans, P R.]]
	[[Category: Mancia, F.]]		[[Category: Mancia, F.]]
	[[Category: ~~complex (isomerase/deoxyadenosine)]]~~		[[Category: Intramolecular transferase]]
	~~[[Category: intramolecular~~ transferase]]		[[Category: Isomerase]]
	[[Category: ~~isomerase~~]]		[[Category: Mutase]]
	[[Category: ~~mutase~~]]		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:12:03 2008''

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