3req
From Proteopedia
(New page: 200px<br /><applet load="3req" size="450" color="white" frame="true" align="right" spinBox="true" caption="3req, resolution 2.7Å" /> '''METHYLMALONYL-COA MUT...) |
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| - | [[Image:3req.jpg|left|200px]]<br /><applet load="3req" size=" | + | [[Image:3req.jpg|left|200px]]<br /><applet load="3req" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="3req, resolution 2.7Å" /> | caption="3req, resolution 2.7Å" /> | ||
'''METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)'''<br /> | '''METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)'''<br /> | ||
==Overview== | ==Overview== | ||
| - | BACKGROUND: Methylmalonyl CoA mutase catalyses the interconversion of | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 3REQ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii] with B12 and ADN as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http:// | + | 3REQ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Propionibacterium_freudenreichii_subsp._shermanii Propionibacterium freudenreichii subsp. shermanii] with <scene name='pdbligand=B12:'>B12</scene> and <scene name='pdbligand=ADN:'>ADN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3REQ OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Propionibacterium freudenreichii subsp. shermanii]] | [[Category: Propionibacterium freudenreichii subsp. shermanii]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Evans, P | + | [[Category: Evans, P R.]] |
[[Category: Mancia, F.]] | [[Category: Mancia, F.]] | ||
[[Category: ADN]] | [[Category: ADN]] | ||
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[[Category: mutase]] | [[Category: mutase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:11:10 2008'' |
Revision as of 17:11, 21 February 2008
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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.
About this Structure
3REQ is a Protein complex structure of sequences from Propionibacterium freudenreichii subsp. shermanii with and as ligands. Active as Methylmalonyl-CoA mutase, with EC number 5.4.99.2 Full crystallographic information is available from OCA.
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:9655823
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