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Mascarenhas R, Guha A, Li Z, Ruetz M, An S, Seravalli J, Banerjee R. Cobalt-Sulfur Coordination Chemistry Drives B 12 Loading onto Methionine Synthase. J Am Chem Soc 2023:10.1021/jacs.3c07941. [PMID: 37916782 PMCID: PMC11063128 DOI: 10.1021/jacs.3c07941] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Cobalt-sulfur (Co-S) coordination is labile to both oxidation and reduction chemistry and is rarely seen in nature. Cobalamin (or vitamin B12) is an essential cobalt-containing organometallic cofactor in mammals and is escorted via an intricate network of chaperones to a single cytoplasmic target, methionine synthase. In this study, we report that the human cobalamin trafficking protein, MMADHC, exploits the chemical lability of Co-S coordination for cofactor off-loading onto methionine synthase. Cys-261 on MMADHC serves as the β-axial ligand to cobalamin. Complex formation between MMADHC and methionine synthase is signaled by loss of the lower axial nitrogen ligand, leading to five-coordinate thiolato-cobalamin. Nucleophilic displacement by the vicinal thiolate, Cys-262, completes cofactor transfer to methionine synthase and release of a cysteine disulfide-containing MMADHC. The physiological relevance of this mechanism is supported by clinical variants of MMADHC, which impair cofactor binding and off-loading, explaining the molecular basis of the associated homocystinuria.
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Affiliation(s)
- Romila Mascarenhas
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Arkajit Guha
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zhu Li
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Markus Ruetz
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sojin An
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Javier Seravalli
- Department of Biological Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Vaccaro FA, Faber DA, Andree GA, Born DA, Kang G, Fonseca DR, Jost M, Drennan CL. Structural insight into G-protein chaperone-mediated maturation of a bacterial adenosylcobalamin-dependent mutase. J Biol Chem 2023; 299:105109. [PMID: 37517695 PMCID: PMC10481361 DOI: 10.1016/j.jbc.2023.105109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023] Open
Abstract
G-protein metallochaperones are essential for the proper maturation of numerous metalloenzymes. The G-protein chaperone MMAA in humans (MeaB in bacteria) uses GTP hydrolysis to facilitate the delivery of adenosylcobalamin (AdoCbl) to AdoCbl-dependent methylmalonyl-CoA mutase, an essential metabolic enzyme. This G-protein chaperone also facilitates the removal of damaged cobalamin (Cbl) for repair. Although most chaperones are standalone proteins, isobutyryl-CoA mutase fused (IcmF) has a G-protein domain covalently attached to its target mutase. We previously showed that dimeric MeaB undergoes a 180° rotation to reach a state capable of GTP hydrolysis (an active G-protein state), in which so-called switch III residues of one protomer contact the G-nucleotide of the other protomer. However, it was unclear whether other G-protein chaperones also adopted this conformation. Here, we show that the G-protein domain in a fused system forms a similar active conformation, requiring IcmF oligomerization. IcmF oligomerizes both upon Cbl damage and in the presence of the nonhydrolyzable GTP analog, guanosine-5'-[(β,γ)-methyleno]triphosphate, forming supramolecular complexes observable by mass photometry and EM. Cryo-EM structural analysis reveals that the second protomer of the G-protein intermolecular dimer props open the mutase active site using residues of switch III as a wedge, allowing for AdoCbl insertion or damaged Cbl removal. With the series of structural snapshots now available, we now describe here the molecular basis of G-protein-assisted AdoCbl-dependent mutase maturation, explaining how GTP binding prepares a mutase for cofactor delivery and how GTP hydrolysis allows the mutase to capture the cofactor.
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Affiliation(s)
- Francesca A Vaccaro
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Daphne A Faber
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gisele A Andree
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David A Born
- Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gyunghoon Kang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Dallas R Fonseca
- Amgen Scholar Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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Mascarenhas R, Guha A, Li Z, Ruetz M, An S, Seravalli J, Banerjee R. Cobalt-sulfur coordination chemistry drives B 12 loading onto methionine synthase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550549. [PMID: 37546824 PMCID: PMC10402061 DOI: 10.1101/2023.07.25.550549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Cobalt-sulfur (Co-S) coordination is labile to both oxidation and reduction chemistry and is rarely seen in Nature. Cobalamin (or vitamin B 12 ) is an essential cobalt-containing organometallic cofactor in mammals, and is escorted via an intricate network of chaperones to a single cytoplasmic target, methionine synthase. In this study, we report that the human cobalamin trafficking protein, MMADHC, exploits the chemical lability of Co-S coordination, for cofactor off-loading onto methionine synthase. Cys-261 on MMADHC serves as the β-axial ligand to cobalamin. Complex formation between MMADHC and methionine synthase is signaled by loss of the lower axial nitrogen ligand, leading to five-coordinate thiolato-cobalamin. Nucleophilic displacement by the vicinal thiolate, Cys-262, completes cofactor transfer to methionine synthase and release of a cysteine disulfide-containing MMADHC. The physiological relevance of this mechanism is supported by clinical variants of MMADHC, which impair cofactor binding and off-loading, explaining the molecular basis of the associated homocystinuria.
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Li Z, Mascarenhas R, Twahir UT, Kallon A, Deb A, Yaw M, Penner-Hahn J, Koutmos M, Warncke K, Banerjee R. An Interprotein Co-S Coordination Complex in the B 12-Trafficking Pathway. J Am Chem Soc 2020; 142:16334-16345. [PMID: 32871076 DOI: 10.1021/jacs.0c06590] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The CblC and CblD chaperones are involved in early steps in the cobalamin trafficking pathway. Cobalamin derivatives entering the cytoplasm are converted by CblC to a common cob(II)alamin intermediate via glutathione-dependent alkyltransferase or reductive elimination activities. Cob(II)alamin is subsequently converted to one of two biologically active alkylcobalamins by downstream chaperones. The function of CblD has been elusive although it is known to form a complex with CblC under certain conditions. Here, we report that CblD provides a sulfur ligand to cob(II)alamin bound to CblC, forming an interprotein coordination complex that rapidly oxidizes to thiolato-cob(III)alamin. Cysteine scanning mutagenesis and EPR spectroscopy identified Cys-261 on CblD as the sulfur donor. The unusual interprotein Co-S bond was characterized by X-ray absorption spectroscopy and visualized in the crystal structure of the human CblD thiolato-cob(III)alamin complex. Our study provides insights into how cobalamin coordination chemistry could be utilized for cofactor translocation in the trafficking pathway.
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Affiliation(s)
- Zhu Li
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, United States
| | - Romila Mascarenhas
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, United States
| | - Umar T Twahir
- Department of Physics, Emory University, Atlanta, Georgia 30322-2430, United States
| | - Albert Kallon
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, United States
| | - Aniruddha Deb
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Madeline Yaw
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, United States
| | - James Penner-Hahn
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Markos Koutmos
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, Georgia 30322-2430, United States
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, United States
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Ruetz M, Campanello GC, McDevitt L, Yokom AL, Yadav PK, Watkins D, Rosenblatt DS, Ohi MD, Southworth DR, Banerjee R. Allosteric Regulation of Oligomerization by a B 12 Trafficking G-Protein Is Corrupted in Methylmalonic Aciduria. Cell Chem Biol 2019; 26:960-969.e4. [PMID: 31056463 DOI: 10.1016/j.chembiol.2019.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/07/2019] [Accepted: 03/25/2019] [Indexed: 10/26/2022]
Abstract
Allosteric regulation of methylmalonyl-CoA mutase (MCM) by the G-protein chaperone CblA is transduced via three "switch" elements that gate the movement of the B12 cofactor to and from MCM. Mutations in CblA and MCM cause hereditary methylmalonic aciduria. Unlike the bacterial orthologs used previously to model disease-causing mutations, human MCM and CblA exhibit a complex pattern of regulation that involves interconverting oligomers, which are differentially sensitive to the presence of GTP versus GDP. Patient mutations in the switch III region of CblA perturb the nucleotide-sensitive distribution of the oligomeric complexes with MCM, leading to loss of regulated movement of B12 to and/or from MCM and explain the molecular mechanism of the resulting disease.
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Affiliation(s)
- Markus Ruetz
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Gregory C Campanello
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Liam McDevitt
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Adam L Yokom
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pramod K Yadav
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - David Watkins
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - David S Rosenblatt
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California-San Francisco, San Francisco, CA 94158, USA
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, MI, USA.
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Black WB, King E, Wang Y, Jenic A, Rowley AT, Seki K, Luo R, Li H. Engineering a Coenzyme A Detour To Expand the Product Scope and Enhance the Selectivity of the Ehrlich Pathway. ACS Synth Biol 2018; 7:2758-2764. [PMID: 30433765 DOI: 10.1021/acssynbio.8b00358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Ehrlich pathway is a major route for the renewable production of higher alcohols. However, the product scope of the Ehrlich pathway is restricted, and the product selectivity is suboptimal. Here, we demonstrate that a Coenzyme A (CoA) detour, which involves conversion of the 2-keto acids into acyl-CoAs, expands the biological toolkit of reaction chemistries available in the Ehrlich pathway to include the gamut of CoA-dependent enzymes. As a proof-of-concept, we demonstrated the first biosynthesis of a tertiary branched-alcohol, pivalcohol, at a level of ∼10 mg/L from glucose in Escherichia coli, using a pivalyl-CoA mutase from Xanthobacter autotrophicus. Furthermore, engineering an enzyme in the CoA detour, the Lactobacillus brevis CoA-acylating aldehyde dehydrogenase, allowed stringent product selectivity. Targeted production of 3-methyl-1-butanol (3-MB) in E. coli mediated by the CoA detour showed a 3-MB:side-product (isobutanol) ratio of >20, an increase over the ratios previously achieved using the conventional Ehrlich pathway.
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Campanello GC, Lofgren M, Yokom AL, Southworth DR, Banerjee R. Switch I-dependent allosteric signaling in a G-protein chaperone-B 12 enzyme complex. J Biol Chem 2017; 292:17617-17625. [PMID: 28882898 DOI: 10.1074/jbc.m117.786095] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/14/2017] [Indexed: 11/06/2022] Open
Abstract
G-proteins regulate various processes ranging from DNA replication and protein synthesis to cytoskeletal dynamics and cofactor assimilation and serve as models for uncovering strategies deployed for allosteric signal transduction. MeaB is a multifunctional G-protein chaperone, which gates loading of the active 5'-deoxyadenosylcobalamin cofactor onto methylmalonyl-CoA mutase (MCM) and precludes loading of inactive cofactor forms. MeaB also safeguards MCM, which uses radical chemistry, against inactivation and rescues MCM inactivated during catalytic turnover by using the GTP-binding energy to offload inactive cofactor. The conserved switch I and II signaling motifs used by G-proteins are predicted to mediate allosteric regulation in response to nucleotide binding and hydrolysis in MeaB. Herein, we targeted conserved residues in the MeaB switch I motif to interrogate the function of this loop. Unexpectedly, the switch I mutations had only modest effects on GTP binding and on GTPase activity and did not perturb stability of the MCM-MeaB complex. However, these mutations disrupted multiple MeaB chaperone functions, including cofactor editing, loading, and offloading. Hence, although residues in the switch I motif are not essential for catalysis, they are important for allosteric regulation. Furthermore, single-particle EM analysis revealed, for the first time, the overall architecture of the MCM-MeaB complex, which exhibits a 2:1 stoichiometry. These EM studies also demonstrate that the complex exhibits considerable conformational flexibility. In conclusion, the switch I element does not significantly stabilize the MCM-MeaB complex or influence the affinity of MeaB for GTP but is required for transducing signals between MeaB and MCM.
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Affiliation(s)
- Gregory C Campanello
- From the Departments of Biological Chemistry, University of Michigan Medical Center, and
| | - Michael Lofgren
- From the Departments of Biological Chemistry, University of Michigan Medical Center, and
| | - Adam L Yokom
- From the Departments of Biological Chemistry, University of Michigan Medical Center, and.,the Department of Biological Chemistry and.,the Graduate Program in Chemical Biology, Life Sciences Institute, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Daniel R Southworth
- From the Departments of Biological Chemistry, University of Michigan Medical Center, and.,the Department of Biological Chemistry and
| | - Ruma Banerjee
- From the Departments of Biological Chemistry, University of Michigan Medical Center, and
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