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| | <StructureSection load='5req' size='340' side='right'caption='[[5req]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='5req' size='340' side='right'caption='[[5req]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5req]] is a 4 chain structure with sequence from [https://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=5REQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5REQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5req]] is a 4 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=5REQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5REQ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MCD:METHYLMALONYL(CARBADETHIA)-COENZYME+A'>MCD</scene>, <scene name='pdbligand=SCD:SUCCINYL(CARBADETHIA)-COENZYME+A'>SCD</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]] 2.2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MUTB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1752 "Propionibacterium shermanii" van Niel 1928]), MUTA ([https://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=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MCD:METHYLMALONYL(CARBADETHIA)-COENZYME+A'>MCD</scene>, <scene name='pdbligand=SCD:SUCCINYL(CARBADETHIA)-COENZYME+A'>SCD</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methylmalonyl-CoA_mutase Methylmalonyl-CoA mutase], with EC number [https://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=5req FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5req OCA], [https://pdbe.org/5req PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5req RCSB], [https://www.ebi.ac.uk/pdbsum/5req PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5req 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=5req FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5req OCA], [https://pdbe.org/5req PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5req RCSB], [https://www.ebi.ac.uk/pdbsum/5req PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5req ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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. [[https://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]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Propionibacterium shermanii van niel 1928]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Methylmalonyl-CoA mutase]] | + | [[Category: Propionibacterium freudenreichii subsp. shermanii]] |
| - | [[Category: Evans, P R]] | + | [[Category: Evans PR]] |
| - | [[Category: Thomae, N H]] | + | [[Category: Thomae NH]] |
| - | [[Category: Intramolecular transferase]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Mutase]]
| + | |
| Structural highlights
Function
MUTB_PROFR Catalyzes the isomerization of succinyl-CoA to methylmalonyl-CoA during synthesis of propionate from tricarboxylic acid-cycle intermediates.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The adenosylcobalamin-dependent methylmalonyl-CoA mutase catalyzes the reversible rearrangement of methylmalonyl-CoA into succinyl-CoA by a free-radical mechanism. The recently solved X-ray crystal structure of methylmalonyl-CoA mutase from Propionibacterium shermanii has shown that tyrosine 89 is an active-site residue involved in substrate binding. The role of tyrosine 89, a conserved residue among methylmalonyl-CoA mutases, has been investigated by using site-directed mutagenesis to replace this residue with phenylalanine. The crystal structure of the Tyr89Phe mutant was determined to 2.2 A resolution and was found to be essentially superimposable on that of wild-type. Mutant and wild-type enzyme have very similar KM values, but kcat for the Tyr89Phe mutant is 580-fold lower than for wild-type. The rate of release of tritium from 5'-[3H]adenosylcobalamin during the enzymatic reaction and its rate of appearance in substrate and product were measured. The tritium released was found to partition unequally between methylmalonyl-CoA and succinyl-CoA, in a ratio of 40:60 when the reaction was initiated by addition of methylmalonyl-CoA and in a ratio of 10:90 when the reaction was initiated by addition of succinyl-CoA. The overall release of tritium was four times faster when succinyl-CoA was used as substrate. The tritium isotope effect on the enzyme catalyzed hydrogen transfer, measured with methylmalonyl-CoA as a substrate, was kH/kT = 30, which is within the expected range for a full primary kinetic tritium isotope effect. The different partitioning of tritium, dependent upon which substrate was used, and the normal value for the kinetic tritium isotope effect contrast markedly with the behavior of wild-type mutase. It appears that the loss of a single interaction involving the hydroxyl group of tyrosine 89 both affects the stability of radical intermediates and decreases the rate of interconversion of the substrate- and product-derived radicals.
Stabilization of radical intermediates by an active-site tyrosine residue in methylmalonyl-CoA mutase.,Thoma NH, Meier TW, Evans PR, Leadlay PF Biochemistry. 1998 Oct 13;37(41):14386-93. PMID:9772164[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Thoma NH, Meier TW, Evans PR, Leadlay PF. Stabilization of radical intermediates by an active-site tyrosine residue in methylmalonyl-CoA mutase. Biochemistry. 1998 Oct 13;37(41):14386-93. PMID:9772164 doi:10.1021/bi981375o
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