Crystal Structure of Substrate Complexes of Methylmalonyl-CoA Mutase

Mancia, Filippo; Smith, Gavin; Evans, Philip R.

doi:10.1021/bi9903852

Cited by 135 publications

(145 citation statements)

References 15 publications

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“…3B). Comparing the two conformations of the substrate-binding domain to structures of MCM reveals that the closed barrel of chain A resembles the structure of substratebound MCM (27,35), even though no substrate is bound in our holo-IcmF•GDP structure. The open barrel of chain B closely matches the structure of substrate-free MCM (Fig.…”

Section: Insights Into Mcm:g-protein Complexes and Methylmalonic Acidmentioning

confidence: 87%

Visualization of a radical B ₁₂ enzyme with its G-protein chaperone

Jost¹,

Cracan

Hubbard³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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G-protein metallochaperones ensure fidelity during cofactor assembly for a variety of metalloproteins, including adenosylcobalamin (AdoCbl)-dependent methylmalonyl-CoA mutase and hydrogenase, and thus have both medical and biofuel development applications. Here, we present crystal structures of IcmF, a natural fusion protein of AdoCbl-dependent isobutyryl-CoA mutase and its corresponding G-protein chaperone, which reveal the molecular architecture of a G-protein metallochaperone in complex with its target protein.These structures show that conserved G-protein elements become ordered upon target protein association, creating the molecular pathways that both sense and report on the cofactor loading state. Structures determined of both apo-and holo-forms of IcmF depict both open and closed enzyme states, in which the cofactor-binding domain is alternatively positioned for cofactor loading and for catalysis. Notably, the G protein moves as a unit with the cofactorbinding domain, providing a visualization of how a chaperone assists in the sequestering of a precious cofactor inside an enzyme active site.

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Section: Insights Into Mcm:g-protein Complexes and Methylmalonic Acidmentioning

confidence: 87%

Visualization of a radical B ₁₂ enzyme with its G-protein chaperone

Jost¹,

Cracan

Hubbard³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…In the proposed model for human HMG-CoA lyase the side chains of the barrel forming ␤-sheets conform a central cavity, which is similar to the structure of other TIM barrel-like enzymes such as methylmalonyl-CoA mutase (PDB entry 7req) (41). A section of the proposed model (Fig.…”

Section: Localization Of the Mutations Responsible For 3-hydroxy-3-mentioning

confidence: 83%

“…Some of the residues that can be mapped with confidence in the model have been defined previously as essential to the enzyme activity based on mutational studies: His 233 (8,18), which is considered as the active site, Arg 41 , and Asp 42 (13). In the present model, all these amino acids, as well as Leu 263 (18) and Asp 204 (this paper), are located on the COOH-terminal face of the barrel forming ␤-sheets 1, 6, 7, and 8.…”

Section: Discussionmentioning

confidence: 99%

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Structural (βα)8 TIM Barrel Model of 3-Hydroxy-3-methylglutaryl-Coenzyme A Lyase

Casals

Gómez‐Puertas

Pié

et al. 2003

Journal of Biological Chemistry

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This study describes three novel homozygous missense mutations (S75R, S201Y, and D204N) in the 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) lyase gene, which caused 3-hydroxy-3-methylglutaric aciduria in patients from Germany, England, and Argentina. Expression studies in Escherichia coli show that S75R and S201Y substitutions completely abolished the HMG-CoA lyase activity, whereas D204N reduced catalytic efficiency to 6.6% of the wild type. We also propose a threedimensional model for human HMG-CoA lyase containing a (␤␣) 8 (TIM) barrel structure. The model is supported by the similarity with analogous TIM barrel structures of functionally related proteins, by the localization of catalytic amino acids at the active site, and by the coincidence between the shape of the substrate (HMG-CoA) and the predicted inner cavity. The three novel mutations explain the lack of HMG-CoA lyase activity on the basis of the proposed structure: in S75R and S201Y because the new amino acid residues occlude the substrate cavity, and in D204N because the mutation alters the electrochemical environment of the active site. We also report the localization of all missense mutations reported to date and show that these mutations are located in the ␤-sheets around the substrate cavity.3-Hydroxy-3-methylglutaric aciduria (MIM246450) is a rare autosomal recessive metabolic disorder appearing in the 1st year of life. Acute episodes include vomiting, lethargy, hypotonia, and apnea, sometimes evolving to coma (1, 2). Laboratory tests reveal metabolic acidosis with severe hypoketotic hypoglycemia on fasting or during acute illness, hyperammonemia, and abnormal liver function tests. The disease is fatal in about 20% of cases (3) although the symptoms are milder after childhood. Preliminary diagnosis is based on the excretory pattern of organic acids in urine, which include 3-hydroxy-3-methylglutaric, 3-hydroxyisovaleric, 3-methylglutaconic, 3-methylglutaric, and 3-methylcrotonic acids (1, 4).

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“…Our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) calculations using a recently developed optimization algorithm that allows the reaction coordinate to include atoms from both QM and molecular mechanics (MM) layers have permitted for the first time the calculation of the transition state (TS) for the enzyme-catalysed homolysis reaction (Kwiecien et al 2006). Three models, based on the crystal structures of the enzyme in the presence and absence of substrate (Mancia et al 1996(Mancia et al , 1999Mancia & Evans 1998), were employed in this Quantum catalysis in MCM R. Banerjee and others 1335 study. In the absence of substrate, the triosephosphate isomerase (TIM) barrel located above the corrin ring is flared open in a conformation that is referred to as the 'open' or resting state.…”

Section: Computational Analysis Of the Homolysis Reactionmentioning

confidence: 99%

Quantum catalysis in B ₁₂ -dependent methylmalonyl-CoA mutase: experimental and computational insights

Banerjee

Dybała-Defratyka

Paneth

2006

Phil. Trans. R. Soc. B

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B 12 -dependent methylmalonyl-CoA mutase catalyses the interchange of a hydrogen atom and the carbonyl-CoA group on adjacent carbons of methylmalonyl-CoA to give the rearranged product, succinyl-CoA. The first step in this reaction involves the transient generation of cofactor radicals by homolytic rupture of the cobalt-carbon bond to generate the deoxyadenosyl radical and cob(II)alamin. This step exhibits a curious sensitivity to isotopic substitution in the substrate, methylmalonyl-CoA, which has been interpreted as evidence for kinetic coupling. The magnitude of the isotopic discrimination is large and a deuterium isotope effect ranging from 35.6 at 20 8C to 49.9 at 5 8C has been recorded. Arrhenius analysis of the temperature dependence of this isotope effect provides evidence for quantum tunnelling in this hydrogen transfer step. The mechanistic complexity of the observed rate constant for cobalt-carbon bond homolysis together with the spectroscopically silent nature of many of the component steps limits the insights that can be derived by experimental approaches alone. Computational studies using a newly developed geometry optimization scheme that allows determination of the transition state in the full quantum mechanical/molecular mechanical coordinate space have yielded novel insights into the strategy deployed for labilizing the cobalt-carbon bond and poising the resulting deoxyadenosyl radical for subsequent hydrogen atom abstraction.

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Crystal Structure of Substrate Complexes of Methylmalonyl-CoA Mutase

Cited by 135 publications

References 15 publications

Visualization of a radical B ₁₂ enzyme with its G-protein chaperone

Visualization of a radical B ₁₂ enzyme with its G-protein chaperone

Structural (βα)8 TIM Barrel Model of 3-Hydroxy-3-methylglutaryl-Coenzyme A Lyase

Quantum catalysis in B ₁₂ -dependent methylmalonyl-CoA mutase: experimental and computational insights

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Crystal Structure of Substrate Complexes of Methylmalonyl-CoA Mutase

Cited by 135 publications

References 15 publications

Visualization of a radical B 12 enzyme with its G-protein chaperone

Visualization of a radical B 12 enzyme with its G-protein chaperone

Structural (βα)8 TIM Barrel Model of 3-Hydroxy-3-methylglutaryl-Coenzyme A Lyase

Quantum catalysis in B 12 -dependent methylmalonyl-CoA mutase: experimental and computational insights

Contact Info

Product

Resources

About

Visualization of a radical B ₁₂ enzyme with its G-protein chaperone

Visualization of a radical B ₁₂ enzyme with its G-protein chaperone

Quantum catalysis in B ₁₂ -dependent methylmalonyl-CoA mutase: experimental and computational insights