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Ruetz M, Mascarenhas R, Widner F, Kieninger C, Koutmos M, Kräutler B, Banerjee R. A Noble Metal Substitution Leads to B 12 Cofactor Mimicry by a Rhodibalamin. Biochemistry 2024. [PMID: 39012171 DOI: 10.1021/acs.biochem.4c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
In mammals, cobalamin is an essential cofactor that is delivered by a multitude of chaperones in an elaborate trafficking pathway to two client enzymes, methionine synthase and methylmalonyl-CoA mutase (MMUT). Rhodibalamins, the rhodium analogs of cobalamins, have been described as antimetabolites due to their ability to inhibit bacterial growth. In this study, we have examined the reactivity of adenosylrhodibalamin (AdoRhbl) with two key human chaperones, MMACHC (also known as CblC) and adenosyltransferase (MMAB, also known as ATR), and with the human and Mycobacterium tuberculosis MMUT. We demonstrate that while AdoRhbl binds tightly to all four proteins, the Rh-carbon bond is resistant to homolytic (on MMAB and MMUT) as well as heterolytic (on MMACHC) rupture. On the other hand, MMAB catalyzes Rh-carbon bond formation, converting rhodi(I)balamin in the presence of ATP to AdoRhbl. We report the first crystal structure of a rhodibalamin (AdoRhbl) bound to a B12 protein, i.e., MMAB, in the presence of triphosphate, which shows a weakened but intact Rh-carbon bond. The structure provides insights into how MMAB cleaves the corresponding Co-carbon bond in a sacrificial homolytic reaction that purportedly functions as a cofactor sequestration strategy. Collectively, the study demonstrates that while the noble metal substitution of cobalt by rhodium sets up structural mimicry, it compromises chemistry, which could be exploited for targeting human and bacterial B12 chaperones and enzymes.
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2
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Gouda H, Li Z, Ruetz M, Banerjee R. Coordination Chemistry Controls Coenzyme B 12 Synthesis by Human Adenosine Triphosphate:Cob(I)alamin Adenosyltransferase. Inorg Chem 2023; 62:12630-12633. [PMID: 37526260 PMCID: PMC10507449 DOI: 10.1021/acs.inorgchem.3c02163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Cobalamin (or vitamin B12)-dependent enzymes and trafficking chaperones exploit redox-linked coordination chemistry to control the cofactor reactivity during catalysis and translocation. As the cobalt oxidation state decreases from 3+ to 1+, the preferred cobalamin geometry changes from six- to four-coordinate (4-c). In this study, we reveal the sizable thermodynamic gain that accrues for human adenosine triphosphate (ATP):cob(I)alamin adenosyltransferase (or MMAB) by enforcing an unfavorable 4-c cob(II)alamin geometry. MMAB-bound cob(II)alamin is reduced to the supernucleophilic cob(I)alamin intermediate during the synthesis of 5'-deoxyadenosylcobalamin. Herein, we report the first experimentally determined reduction potential for 4-c cob(II)alamin (-325 ± 9 mV), which is 180 mV more positive than for the five-coordinate (5-c) water-liganded species. The redox potential of MMAB-bound cob(II)alamin is within the range of adrenodoxin, which we demonstrate functions as an electron donor. We also show that stabilization of 5-c cob(II)alamin by a subset of MMAB patient variants compromises the reduction by adrenodoxin, explaining the underlying pathogenic mechanism.
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Affiliation(s)
- Harsha Gouda
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 USA
| | - Zhu Li
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 USA
| | - Markus Ruetz
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 USA
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 USA
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3
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Mascarenhas R, Ruetz M, Gouda H, Heitman N, Yaw M, Banerjee R. Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B 12 delivery and repair. Nat Commun 2023; 14:4332. [PMID: 37468522 PMCID: PMC10356863 DOI: 10.1038/s41467-023-40077-4] [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: 04/22/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023] Open
Abstract
G-proteins function as molecular switches to power cofactor translocation and confer fidelity in metal trafficking. The G-protein, MMAA, together with MMAB, an adenosyltransferase, orchestrate cofactor delivery and repair of B12-dependent human methylmalonyl-CoA mutase (MMUT). The mechanism by which the complex assembles and moves a >1300 Da cargo, or fails in disease, are poorly understood. Herein, we report the crystal structure of the human MMUT-MMAA nano-assembly, which reveals a dramatic 180° rotation of the B12 domain, exposing it to solvent. The complex, stabilized by MMAA wedging between two MMUT domains, leads to ordering of the switch I and III loops, revealing the molecular basis of mutase-dependent GTPase activation. The structure explains the biochemical penalties incurred by methylmalonic aciduria-causing mutations that reside at the MMAA-MMUT interfaces we identify here.
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Affiliation(s)
- Romila Mascarenhas
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Markus Ruetz
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Harsha Gouda
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Natalie Heitman
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Madeline Yaw
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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4
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Marques HM. The inorganic chemistry of the cobalt corrinoids - an update. J Inorg Biochem 2023; 242:112154. [PMID: 36871417 DOI: 10.1016/j.jinorgbio.2023.112154] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B12, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B12-dependent enzymes is also given for the reader's convenience.
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Affiliation(s)
- Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
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5
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Mascarenhas R, Ruetz M, Gouda H, Heitman N, Yaw M, Banerjee R. Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B 12 delivery and repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533963. [PMID: 36993209 PMCID: PMC10055420 DOI: 10.1101/2023.03.23.533963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
G-proteins function as molecular switches to power cofactor translocation and confer fidelity in metal trafficking. MMAA, a G-protein motor, together with MMAB, an adenosyltransferase, orchestrate cofactor delivery and repair of B 12 -dependent human methylmalonyl-CoA mutase (MMUT). The mechanism by which the motor assembles and moves a >1300 Da cargo, or fails in disease, are poorly understood. Herein, we report the crystal structure of the human MMUT-MMAA nanomotor assembly, which reveals a dramatic 180° rotation of the B 12 domain, exposing it to solvent. The nanomotor complex, stabilized by MMAA wedging between two MMUT domains, leads to ordering of the switch I and III loops, revealing the molecular basis of mutase-dependent GTPase activation. The structure explains the biochemical penalties incurred by methylmalonic aciduria-causing mutations that reside at the newly identified MMAA-MMUT interfaces.
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6
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Toda MJ, Lodowski P, Mamun AA, Kozlowski PM. Photoproduct formation in coenzyme B 12-dependent CarH via a singlet pathway. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 232:112471. [PMID: 35644067 DOI: 10.1016/j.jphotobiol.2022.112471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/26/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
The CarH photoreceptor exploits of the light-sensing ability of coenzyme B12 ( adenosylcobalamin = AdoCbl) to perform its catalytic function, which includes large-scale structural changes to regulate transcription. In daylight, transcription is activated in CarH via the photo-cleavage of the Co-C5' bond of coenzyme B12. Subsequently, the photoproduct, 4',5'-anhydroadenosine (anhAdo) is formed inducing dissociation of the CarH tetramer from DNA. Several experimental studies have proposed that hydridocoblamin (HCbl) may be formed in process with anhAdo. The photolytic cleavage of the Co-C5' bond of AdoCbl was previously investigated using photochemical techniques and the involvement of both singlet and triplet excited states were explored. Herein, QM/MM calculations were employed to probe (1) the photolytic processes which may involve singlet excited states, (2) the mechanism of anhAdo formation, and (3) whether HCbl is a viable intermediate in CarH. Time-dependent density functional theory (TD-DFT) calculations indicate that the mechanism of photodissociation of the Ado ligand involves the ligand field (LF) portion of the lowest singlet excited state (S1) potential energy surface (PES). This is followed by deactivation to a point on the S0 PES where the Co-C5' bond remains broken. This species corresponds to a singlet diradical intermediate. From this point, the PES for anhAdo formation was explored, using the Co-C5' and Co-C4' bond distances as active coordinates, and a local minimum representing anhAdo and HCbl formation was found. The transition state (TS) for the formation of the Co-H bond of HCbl was located and its identity was confirmed by a single imaginary frequency of i1592 cm-1. Comparisons to experimental studies and the potential role of rotation around the N-glycosidic bond of the Ado ligand were discussed.
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Affiliation(s)
- Megan J Toda
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States
| | - Piotr Lodowski
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Abdullah Al Mamun
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States.
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7
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Ghosh AP, Lodowski P, Kozlowski PM. Aerobic photolysis of methylcobalamin: unraveling the photoreaction mechanism. Phys Chem Chem Phys 2022; 24:6093-6106. [PMID: 35212341 DOI: 10.1039/d1cp02013g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photo-reactivity of cobalamins (Cbls) is influenced by the nature of axial ligands and the cofactor's environment. While the biologically active forms of Cbls with alkyl axial ligands, such as methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), are considered to be photolytically active, in contrast, the non-alkyl Cbls are photostable. In addition to these, the photolytic properties of Cbls can also be modulated in the presence of molecular oxygen, i.e., under aerobic conditions. Herein, the photoreaction of the MeCbl in the presence of oxygen has been explored using density functional theory (DFT) and time-dependent DFT (TD-DFT). The first stage of the aerobic photoreaction is the activation of the Co-C bond and the formation of the ligand field (LF) electronic state through the displacement of axial bonds. Once the photoreaction reaches the LF excited state, three processes can occur: namely the formation of OO-CH3 through the reaction of CH3 with molecular oxygen, de-activation of the {Im⋯[CoII(corrin)]⋯CH3}+ sub-system from the LF electronic state by changing the electronic configuration from (dyz)1(dz2)2 to (dyz)2(dz2)1 and the formation of the deactivation complex (DC) complex via the recombination of OO-CH3 species with the de-excited [CoII(corrin)] system. In the proposed mechanism, the deactivation of the [CoII(corrin)] subsystem may coexist with the formation of OO-CH3, followed by immediate relaxation of the subsystems in the ground state. Moreover, the formation of the OO-CH3 species followed by the formation of the {[CoIII(corrin)]-OO-CH3}+ complex stabilizes the system compared to the reactant complex.
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Affiliation(s)
- Arghya Pratim Ghosh
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
| | - Piotr Lodowski
- Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
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8
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Ghosh AP, Toda MJ, Kozlowski PM. Photolytic properties of B 12-dependent enzymes: A theoretical perspective. VITAMINS AND HORMONES 2022; 119:185-220. [PMID: 35337619 DOI: 10.1016/bs.vh.2022.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The biologically active vitamin B12 derivates, methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), are ubiquitous organometallic cofactors. In addition to their key roles in enzymatic catalysis, B12 cofactors have complex photolytic properties which have been the target of experimental and theoretical studies. With the recent discovery of B12-dependent photoreceptors, there is an increased need to elucidate the underlying photochemical mechanisms of these systems. This book chapter summarizes the photolytic properties of MeCbl- and AdoCbl-dependent enzymes with particular emphasis on the effect of the environment of the cofactor on the excited state processes. These systems include isolated MeCbl and AdoCbl as well as the enzymes, ethanolamine ammonia-lyase (EAL), glutamate mutase (GLM), methionine synthase (MetH), and photoreceptor CarH. Central to determining the photodissociation mechanism of each system is the analysis of the lowest singlet excited state (S1) potential energy surface (PES). Time-dependent density functional theory (TD-DFT), employing BP86/TZVPP, is widely used to construct such PESs. Regardless of the environment, the topology of the S1 PES of AdoCbl or MeCbl is marked by characteristic features, namely the metal-to-ligand charge transfer (MLCT) and ligand field (LF) regions. Conversely, the relative energetics of these electronic states are affected by the environment. Applications and outlooks for Cbl photochemistry are also discussed.
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Affiliation(s)
- Arghya Pratim Ghosh
- Department of Chemistry, University of Louisville, Louisville, KY, United States
| | - Megan J Toda
- Department of Chemistry, University of Louisville, Louisville, KY, United States
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, KY, United States.
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9
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Mascarenhas R, Gouda H, Ruetz M, Banerjee R. Human B 12-dependent enzymes: Methionine synthase and Methylmalonyl-CoA mutase. Methods Enzymol 2022; 668:309-326. [PMID: 35589199 PMCID: PMC9420401 DOI: 10.1016/bs.mie.2021.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Humans have only two known cobalamin or B12-dependent enzymes: cytoplasmic methionine synthase and mitochondrial methylmalonyl-CoA mutase. A complex intracellular B12 trafficking pathway, comprising a multitude of chaperones, process and deliver cobalamin to the two target enzymes. Methionine synthase catalyzes the transfer of a methyl group from N5-methytetrahydrofolate to homocysteine, generating tetrahydrofolate and methionine. Cobalamin serves as an intermediate methyl group carrier and cycles between methylcobalamin and cob(I)alamin. Methylmalonyl-CoA mutase uses the 5'-deoxyadenosylcobalamin form of the cofactor and catalyzes the 1,2 rearrangement of methylmalonyl-CoA to succinyl-CoA. Two chaperones, CblA (or MMAA) and CblB (or MMAB, also known as adenosyltransferase), serve the mutase and ensure that the fidelity of the cofactor loading and unloading processes is maintained. This chapter focuses on assays for purifying and measuring the activities of methionine synthase and methylmalonyl-CoA mutase.
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10
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Mobile loop dynamics in adenosyltransferase control binding and reactivity of coenzyme B 12. Proc Natl Acad Sci U S A 2020; 117:30412-30422. [PMID: 33199623 DOI: 10.1073/pnas.2007332117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cobalamin is a complex organometallic cofactor that is processed and targeted via a network of chaperones to its dependent enzymes. AdoCbl (5'-deoxyadenosylcobalamin) is synthesized from cob(II)alamin in a reductive adenosylation reaction catalyzed by adenosyltransferase (ATR), which also serves as an escort, delivering AdoCbl to methylmalonyl-CoA mutase (MCM). The mechanism by which ATR signals that its cofactor cargo is ready (AdoCbl) or not [cob(II)alamin] for transfer to MCM, is not known. In this study, we have obtained crystallographic snapshots that reveal ligand-induced ordering of the N terminus of Mycobacterium tuberculosis ATR, which organizes a dynamic cobalamin binding site and exerts exquisite control over coordination geometry, reactivity, and solvent accessibility. Cob(II)alamin binds with its dimethylbenzimidazole tail splayed into a side pocket and its corrin ring buried. The cosubstrate, ATP, enforces a four-coordinate cob(II)alamin geometry, facilitating the unfavorable reduction to cob(I)alamin. The binding mode for AdoCbl is notably different from that of cob(II)alamin, with the dimethylbenzimidazole tail tucked under the corrin ring, displacing the N terminus of ATR, which is disordered. In this solvent-exposed conformation, AdoCbl undergoes facile transfer to MCM. The importance of the tail in cofactor handover from ATR to MCM is revealed by the failure of 5'-deoxyadenosylcobinamide, lacking the tail, to transfer. In the absence of MCM, ATR induces a sacrificial cobalt-carbon bond homolysis reaction in an unusual reversal of the heterolytic chemistry that was deployed to make the same bond. The data support an important role for the dimethylbenzimidazole tail in moving the cobalamin cofactor between active sites.
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11
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Ghosh AP, Lodowski P, Bazarganpour A, Leks M, Kozlowski PM. Aerobic photolysis of methylcobalamin: structural and electronic properties of the Cbl-O-O-CH 3 intermediate. Dalton Trans 2020; 49:4114-4124. [PMID: 32142090 DOI: 10.1039/c9dt03740c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Photolysis of methylcobalamin (MeCbl) in the presence of molecular oxygen (O2) has been investigated using density functional theory (DFT) and time-dependent DFT (TD-DFT). The key step involves the formation of the Cbl-O-O-CH3 intermediate as a result of triplet O2 insertion in the Co-C bond in the presence of light. Analysis of low-lying excited states shows that the presence of light is only needed to activate the Co-C bond via the formation of the ligand field (LF) state. The insertion of O2, as well as the change in the spin state, takes place in the ground state. The analysis of the structural and electronic properties of the Cbl-O-O-CH3 intermediate is presented and possible decomposition also discussed.
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Affiliation(s)
- Arghya Pratim Ghosh
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
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12
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Ruetz M, Campanello GC, Purchal M, Shen H, McDevitt L, Gouda H, Wakabayashi S, Zhu J, Rubin EJ, Warncke K, Mootha VK, Koutmos M, Banerjee R. Itaconyl-CoA forms a stable biradical in methylmalonyl-CoA mutase and derails its activity and repair. Science 2019; 366:589-593. [PMID: 31672889 PMCID: PMC7070230 DOI: 10.1126/science.aay0934] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/03/2019] [Indexed: 12/28/2022]
Abstract
Itaconate is an immunometabolite with both anti-inflammatory and bactericidal effects. Its coenzyme A (CoA) derivative, itaconyl-CoA, inhibits B12-dependent methylmalonyl-CoA mutase (MCM) by an unknown mechanism. We demonstrate that itaconyl-CoA is a suicide inactivator of human and Mycobacterium tuberculosis MCM, which forms a markedly air-stable biradical adduct with the 5'-deoxyadenosyl moiety of the B12 coenzyme. Termination of the catalytic cycle in this way impairs communication between MCM and its auxiliary repair proteins. Crystallography and spectroscopy of the inhibited enzyme are consistent with a metal-centered cobalt radical ~6 angstroms away from the tertiary carbon-centered radical and suggest a means of controlling radical trajectories during MCM catalysis. Mycobacterial MCM thus joins enzymes in the glyoxylate shunt and the methylcitrate cycle as targets of itaconate in pathogen propionate metabolism.
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Affiliation(s)
- Markus Ruetz
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gregory C Campanello
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Meredith Purchal
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hongying Shen
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute, Cambridge, MA 02142, USA
| | - Liam McDevitt
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Harsha Gouda
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shoko Wakabayashi
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Cambridge, MA 02115, USA
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Cambridge, MA 02115, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Cambridge, MA 02115, USA
| | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, GA 30322, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute, Cambridge, MA 02142, USA
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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Bito T, Okamoto N, Otsuka K, Yabuta Y, Arima J, Kawano T, Watanabe F. Involvement of Spermidine in the Reduced Lifespan of Caenorhabditis elegans During Vitamin B 12 Deficiency. Metabolites 2019; 9:metabo9090192. [PMID: 31546940 PMCID: PMC6780408 DOI: 10.3390/metabo9090192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/12/2019] [Accepted: 09/18/2019] [Indexed: 11/25/2022] Open
Abstract
Vitamin B12 deficiency leads to various symptoms such as neuropathy, growth retardation, and infertility. Vitamin B12 functions as a coenzyme for two enzymes involved in amino acid metabolisms. However, there is limited information available on whether amino acid disorders caused by vitamin B12 deficiency induce such symptoms. First, free amino acid levels were determined in vitamin B12-deficient Caenorhabditis elegans to clarify the mechanisms underlying the symptoms caused by vitamin B12 deficiency. Various amino acids (valine, leucine, isoleucine, methionine, and cystathionine, among others) metabolized by vitamin B12-dependent enzymes were found to be significantly changed during conditions of B12 deficiency, which indirectly affected certain amino acids metabolized by vitamin B12-independent enzymes. For example, ornithine was significantly increased during vitamin B12 deficiency, which also significantly increased arginase activity. The accumulation of ornithine during vitamin B12 deficiency constitutes the first report. In addition, the biosynthesis of spermidine from ornithine was significantly decreased during vitamin B12 deficiency, likely due to the reduction of S-adenosylmethionine as a substrate for S-adenosylmethionine decarboxylase, which catalyzes the formation of spermidine. Moreover, vitamin B12 deficiency also demonstrated a significant reduction in worm lifespan, which was partially recovered by the addition of spermidine. Collectively, our findings suggest that decreased spermidine is one factor responsible for reduced lifespan in vitamin B12-deficient worms.
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Affiliation(s)
- Tomohiro Bito
- Department of Agricultural, Life and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan.
| | - Naho Okamoto
- The United Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan.
| | - Kenji Otsuka
- Department of Agricultural, Life and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan.
| | - Yukinori Yabuta
- Department of Agricultural, Life and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan.
| | - Jiro Arima
- Department of Agricultural, Life and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan.
| | - Tsuyoshi Kawano
- Department of Agricultural, Life and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan.
| | - Fumio Watanabe
- Department of Agricultural, Life and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan.
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14
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Toda MJ, Lodowski P, Mamun AA, Jaworska M, Kozlowski PM. Photolytic properties of the biologically active forms of vitamin B12. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2018.12.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Kumar N, Bucher D, Kozlowski PM. Mechanistic Implications of Reductive Co–C Bond Cleavage in B12-Dependent Methylmalonyl CoA Mutase. J Phys Chem B 2019; 123:2210-2216. [DOI: 10.1021/acs.jpcb.8b10820] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Neeraj Kumar
- Computational Biology and Bioinformatics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Denis Bucher
- Molecular Modeling & Design at leadXpro Villigen, Canton of Aargau, Switzerland
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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16
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Agarwal S, Dey S, Ghosh B, Biswas M, Dasgupta J. Mechanistic basis of vitamin B12 and cobinamide salvaging by the Vibrio species. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140-151. [DOI: 10.1016/j.bbapap.2018.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/31/2018] [Accepted: 11/16/2018] [Indexed: 12/17/2022]
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17
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Ghosh AP, Mamun AA, Kozlowski PM. How does the mutation in the cap domain of methylcobalamin-dependent methionine synthase influence the photoactivation of the Co–C bond? Phys Chem Chem Phys 2019; 21:20628-20640. [DOI: 10.1039/c9cp01849b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The topology of the S1 PES is modulated by introducing a mutation at the F708 position. The mutation influences the photoactivation of the Co–C bond by decreasing the rate of geminate recombination and altering the rate of radical pair formation.
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18
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Stracey NG, Costa FG, Escalante-Semerena JC, Brunold TC. Spectroscopic Study of the EutT Adenosyltransferase from Listeria monocytogenes: Evidence for the Formation of a Four-Coordinate Cob(II)alamin Intermediate. Biochemistry 2018; 57:5088-5095. [PMID: 30071158 DOI: 10.1021/acs.biochem.8b00743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The EutT enzyme from Listeria monocytogenes ( LmEutT) is a member of the family of ATP:cobalt(I) corrinoid adenosyltransferase (ACAT) enzymes that catalyze the biosynthesis of adenosylcobalamin (AdoCbl) from exogenous Co(II)rrinoids and ATP. Apart from EutT-type ACATs, two evolutionary unrelated types of ACATs have been identified, termed PduO and CobA. Although the three types of ACATs are nonhomologous, they all generate a four-coordinate cob(II)alamin (4C Co(II)Cbl) species to facilitate the formation of a supernucleophilic Co(I)Cbl intermediate capable of attacking the 5'-carbon of cosubstrate ATP. Previous spectroscopic studies of the EutT ACAT from Salmonella enterica ( SeEutT) revealed that this enzyme requires a divalent metal cofactor for the conversion of 5C Co(II)Cbl to a 4C species. Interestingly, LmEutT does not require a divalent metal cofactor for catalytic activity, which exemplifies an interesting phylogenetic divergence among the EutT enzymes. To explore if this disparity in the metal cofactor requirement among EutT enzymes correlates with differences in substrate specificity or the mechanism of Co(II)Cbl reduction, we employed various spectroscopic techniques to probe the interaction of Co(II)Cbl and cob(II)inamide (Co(II)Cbi+) with LmEutT in the absence and presence of cosubstrate ATP. Our data indicate that LmEutT displays a similar substrate specificity as SeEutT and can bind both Co(II)Cbl and Co(II)Cbi+ when complexed with MgATP, though it exclusively converts Co(II)Cbl to a 4C species. Notably, LmEutT is the most effective ACAT studied to date in generating the catalytically relevant 4C Co(II)Cbl species, achieving a >98% 5C → 4C conversion yield on the addition of just over one mol equiv of cosubstrate MgATP.
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Affiliation(s)
- Nuru G Stracey
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Flavia G Costa
- Department of Microbiology , University of Georgia , Athens , Georgia 30602 , United States
| | | | - Thomas C Brunold
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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19
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Bito T, Misaki T, Yabuta Y, Ishikawa T, Kawano T, Watanabe F. Vitamin B 12 deficiency results in severe oxidative stress, leading to memory retention impairment in Caenorhabditis elegans. Redox Biol 2016; 11:21-29. [PMID: 27840283 PMCID: PMC5107735 DOI: 10.1016/j.redox.2016.10.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/21/2016] [Accepted: 10/21/2016] [Indexed: 11/06/2022] Open
Abstract
Oxidative stress is implicated in various human diseases and conditions, such as a neurodegeneration, which is the major symptom of vitamin B12 deficiency, although the underlying disease mechanisms associated with vitamin B12 deficiency are poorly understood. Vitamin B12 deficiency was found to significantly increase cellular H2O2 and NO content in Caenorhabditis elegans and significantly decrease low molecular antioxidant [reduced glutathione (GSH) and L-ascorbic acid] levels and antioxidant enzyme (superoxide dismutase and catalase) activities, indicating that vitamin B12 deficiency induces severe oxidative stress leading to oxidative damage of various cellular components in worms. An NaCl chemotaxis associative learning assay indicated that vitamin B12 deficiency did not affect learning ability but impaired memory retention ability, which decreased to approximately 58% of the control value. When worms were treated with 1 mmol/L GSH, L-ascorbic acid, or vitamin E for three generations during vitamin B12 deficiency, cellular malondialdehyde content as an index of oxidative stress decreased to the control level, but the impairment of memory retention ability was not completely reversed (up to approximately 50%). These results suggest that memory retention impairment formed during vitamin B12 deficiency is partially attributable to oxidative stress.
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Affiliation(s)
- Tomohiro Bito
- The School of Agricultural, Biological and Environmental sciences, Faculty of Agriculture, Tottori University, Tottori 680-8533, Japan
| | - Taihei Misaki
- The School of Agricultural, Biological and Environmental sciences, Faculty of Agriculture, Tottori University, Tottori 680-8533, Japan
| | - Yukinori Yabuta
- The School of Agricultural, Biological and Environmental sciences, Faculty of Agriculture, Tottori University, Tottori 680-8533, Japan
| | - Takahiro Ishikawa
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Shimane 690-8504, Japan
| | - Tsuyoshi Kawano
- The School of Agricultural, Biological and Environmental sciences, Faculty of Agriculture, Tottori University, Tottori 680-8533, Japan
| | - Fumio Watanabe
- The School of Agricultural, Biological and Environmental sciences, Faculty of Agriculture, Tottori University, Tottori 680-8533, Japan.
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20
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Park K, Mera PE, Escalante-Semerena JC, Brunold TC. Resonance Raman spectroscopic study of the interaction between Co(II)rrinoids and the ATP:corrinoid adenosyltransferase PduO from Lactobacillus reuteri. J Biol Inorg Chem 2016; 21:669-81. [PMID: 27383231 PMCID: PMC5118822 DOI: 10.1007/s00775-016-1371-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/14/2016] [Indexed: 12/01/2022]
Abstract
The human-type ATP:corrinoid adenosyltransferase PduO from Lactobacillus reuteri (LrPduO) catalyzes the adenosylation of Co(II)rrinoids to generate adenosylcobalamin (AdoCbl) or adenosylcobinamide (AdoCbi(+)). This process requires the formation of "supernucleophilic" Co(I)rrinoid intermediates in the enzyme active site which are properly positioned to abstract the adeonsyl moiety from co-substrate ATP. Previous magnetic circular dichroism (MCD) spectroscopic and X-ray crystallographic analyses revealed that LrPduO achieves the thermodynamically challenging reduction of Co(II)rrinoids by displacing the axial ligand with a non-coordinating phenylalanine residue to produce a four-coordinate species. However, relatively little is currently known about the interaction between the tetradentate equatorial ligand of Co(II)rrinoids (the corrin ring) and the enzyme active site. To address this issue, we have collected resonance Raman (rR) data of Co(II)rrinoids free in solution and bound to the LrPduO active site. The relevant resonance-enhanced vibrational features of the free Co(II)rrinoids are assigned on the basis of rR intensity calculations using density functional theory to establish a suitable framework for interpreting rR spectral changes that occur upon Co(II)rrinoid binding to the LrPduO/ATP complex in terms of structural perturbations of the corrin ring. To complement our rR data, we have also obtained MCD spectra of Co(II)rrinoids bound to LrPduO complexed with the ATP analogue UTP. Collectively, our results provide compelling evidence that in the LrPduO active site, the corrin ring of Co(II)rrinoids is firmly locked in place by several amino acid side chains so as to facilitate the dissociation of the axial ligand.
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Affiliation(s)
- Kiyoung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Paola E Mera
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, 88003, USA
| | | | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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21
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Garabato BD, Lodowski P, Jaworska M, Kozlowski PM. Mechanism of Co-C photodissociation in adenosylcobalamin. Phys Chem Chem Phys 2016; 18:19070-82. [PMID: 27356617 DOI: 10.1039/c6cp02136k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A mechanism of Co-C bond photodissociation in the base-on form of adenosylcobalamin (AdoCbl) was investigated by time-dependent density functional theory (TD-DFT). The key mechanistic step involves singlet radical pair (RP) generation from the first electronically excited state (S1). To connect TD-DFT calculations with ultra-fast excited state dynamics, the potential energy surface (PES) of the S1 state was constructed using Co-C and Co-NIm axial coordinates. The S1 PES can be characterized by two minima separated by a seam resulting from the crossing of two surfaces, of metal-to-ligand charge transfer (MLCT) character near the minimum, and a shallow ligand field (LF) surface at elongated axial bond distances. Only one possible pathway for photolysis (path A) was identified based on energetic grounds. This pathway is characterized by the first elongation of the Co-C bond, followed by photolysis from an LF state where the axial base is partially detached. A new perspective on the photolysis of AdoCbl is then gained by connecting TD-DFT results with available experimental observations.
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Affiliation(s)
- Brady D Garabato
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40202, USA.
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22
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Kozlowski PM, Garabato BD, Lodowski P, Jaworska M. Photolytic properties of cobalamins: a theoretical perspective. Dalton Trans 2016; 45:4457-70. [PMID: 26865262 DOI: 10.1039/c5dt04286k] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This Perspective Article highlights recent theoretical developments, and summarizes the current understanding of the photolytic properties of cobalamins from a computational point of view. The primary focus is on two alkyl cobalamins, methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), as well as two non-alkyl cobalamins, cyanocobalamin (CNCbl) and hydroxocobalamin (HOCbl). Photolysis of alkyl cobalamins involves low-lying singlet excited states where photodissociation of the Co-C bond leads to formation of singlet-born alkyl/cob(ii)alamin radical pairs (RPs). Potential energy surfaces (PESs) associated with cobalamin low-lying excited states as functions of both axial bonds, provide the most reliable tool for initial analysis of their photochemical and photophysical properties. Due to the complexity, and size limitations associated with the cobalamins, the primary method for calculating ground state properties is density functional theory (DFT), while time-dependent DFT (TD-DFT) is used for electronically excited states. For alkyl cobalamins, energy pathways on the lowest singlet surface, connecting metal-to-ligand charge transfer (MLCT) and ligand field (LF) minima, can be associated with photo-homolysis of the Co-C bond observed experimentally. Additionally, energy pathways between minima and seams associated with crossing of S1/S0 surfaces, are the most efficient for internal conversion (IC) to the ground state. Depending on the specific cobalamin, such IC may involve simultaneous elongation of both axial bonds (CNCbl), or detachment of axial base followed by corrin ring distortion (MeCbl). The possibility of intersystem crossing, and the formation of triplet RPs is also discussed based on Landau-Zener theory.
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Affiliation(s)
- Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
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23
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Kitanishi K, Cracan V, Banerjee R. Engineered and Native Coenzyme B12-dependent Isovaleryl-CoA/Pivalyl-CoA Mutase. J Biol Chem 2015; 290:20466-76. [PMID: 26134562 DOI: 10.1074/jbc.m115.646299] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Indexed: 11/06/2022] Open
Abstract
Adenosylcobalamin-dependent isomerases catalyze carbon skeleton rearrangements using radical chemistry. We have recently demonstrated that an isobutyryl-CoA mutase variant, IcmF, a member of this enzyme family that catalyzes the interconversion of isobutyryl-CoA and n-butyryl-CoA also catalyzes the interconversion between isovaleryl-CoA and pivalyl-CoA, albeit with low efficiency and high susceptibility to inactivation. Given the biotechnological potential of the isovaleryl-CoA/pivalyl-CoA mutase (PCM) reaction, we initially attempted to engineer IcmF to be a more proficient PCM by targeting two active site residues predicted based on sequence alignments and crystal structures, to be key to substrate selectivity. Of the eight mutants tested, the F598A mutation was the most robust, resulting in an ∼17-fold increase in the catalytic efficiency of the PCM activity and a concomitant ∼240-fold decrease in the isobutyryl-CoA mutase activity compared with wild-type IcmF. Hence, mutation of a single residue in IcmF tuned substrate specificity yielding an ∼4000-fold increase in the specificity for an unnatural substrate. However, the F598A mutant was even more susceptible to inactivation than wild-type IcmF. To circumvent this limitation, we used bioinformatics analysis to identify an authentic PCM in genomic databases. Cloning and expression of the putative AdoCbl-dependent PCM with an α2β2 heterotetrameric organization similar to that of isobutyryl-CoA mutase and a recently characterized archaeal methylmalonyl-CoA mutase, allowed demonstration of its robust PCM activity. To simplify kinetic analysis and handling, a variant PCM-F was generated in which the αβ subunits were fused into a single polypeptide via a short 11-amino acid linker. The fusion protein, PCM-F, retained high PCM activity and like PCM, was resistant to inactivation. Neither PCM nor PCM-F displayed detectable isobutyryl-CoA mutase activity, demonstrating that PCM represents a novel 5'-deoxyadenosylcobalamin-dependent acyl-CoA mutase. The newly discovered PCM and the derivative PCM-F, have potential applications in bioremediation of pivalic acid found in sludge, in stereospecific synthesis of C5 carboxylic acids and alcohols, and in the production of potential commodity and specialty chemicals.
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Affiliation(s)
- Kenichi Kitanishi
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Valentin Cracan
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
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24
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Gherasim C, Ruetz M, Li Z, Hudolin S, Banerjee R. Pathogenic mutations differentially affect the catalytic activities of the human B12-processing chaperone CblC and increase futile redox cycling. J Biol Chem 2015; 290:11393-402. [PMID: 25809485 DOI: 10.1074/jbc.m115.637132] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 11/06/2022] Open
Abstract
Human CblC catalyzes the elimination of the upper axial ligand in cobalamin or B12 derivatives entering the cell from circulation. This processing step is critical for assimilation of dietary cobalamin into the active cofactor forms that support the B12-dependent enzymes, methionine synthase and methylmalonyl-CoA mutase. Using a modified nitroreductase scaffold tailored to bind cobalamin and glutathione, CblC exhibits versatility in the mechanism by which it removes cyano versus alkyl ligands in cobalamin. In this study, we have characterized the effects of two pathogenic missense mutations at the same residue, R161G and R161Q, which are associated with early and late onset of the CblC disorder, respectively. We find that the R161Q and R161G CblC mutants display lower protein stability and decreased dealkylation but not decyanation activity, suggesting that cyanocobalamin might be therapeutically useful for patients carrying mutations at Arg-161. The mutant proteins also exhibit impaired glutathione binding. In the presence of physiologically relevant glutathione concentrations, stabilization of the cob(II)alamin derivative is observed, which occurs at the expense of increased oxidation of glutathione. Futile redox cycling, which is suppressed in wild-type human CblC, explains the reported increase in oxidative stress levels associated with the CblC disorder.
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Affiliation(s)
- Carmen Gherasim
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Markus Ruetz
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Zhu Li
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Stephanie Hudolin
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
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25
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Synthesis, solution and crystal structure of the coenzyme B(12) analogue Co(β)-2'-fluoro-2',5'-dideoxyadenosylcobalamin. J Inorg Biochem 2015; 148:62-8. [PMID: 25726330 DOI: 10.1016/j.jinorgbio.2015.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/06/2015] [Accepted: 02/07/2015] [Indexed: 11/23/2022]
Abstract
Crystal structure analyses have helped to decipher the mode of binding of coenzyme B12 (AdoCbl) in the active site of AdoCbl-dependent enzymes. However, the question of how such enzymes perform their radical reactions is still incompletely answered. A pioneering study by Gruber and Kratky of AdoCbl-dependent glutamate mutase (GLM) laid out a path for the movement of the catalytically active 5'-deoxyadenosyl radical, in which H-bonds between the protein and the 2'- and 3'-OH groups of the protein bound AdoCbl would play a decisive role. Studies with correspondingly modified coenzyme B12-analogues are of interest to gain insights into cofactor binding and enzyme mechanism. Here we report the preparation of Coβ-2'-fluoro-2',5'-dideoxyadenosylcobalamin (2'FAdoCbl), which lacks the 2'-OH group critical for the interaction in enzymes. 2'FAdoCbl was prepared by alkylation of cob(I)alamin, obtained from the electrochemical reduction of aquocobalamin. Spectroscopic data and a single crystal X-ray analysis of 2'FAdoCbl established its structure, which was very similar to that one of coenzyme B12. 2'FAdoCbl is a (19)F NMR active mimic of coenzyme B12 that may help to gain insights into binding interactions of coenzyme B12 with AdoCbl-dependent enzymes, proteins of B12 transport and of AdoCbl-biosynthesis, as well as with B12-riboswitches.
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26
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Pallares IG, Moore TC, Escalante-Semerena JC, Brunold TC. Spectroscopic studies of the Salmonella enterica adenosyltransferase enzyme SeCobA: molecular-level insight into the mechanism of substrate Cob(II)alamin activation. Biochemistry 2014; 53:7969-82. [PMID: 25423616 PMCID: PMC4278676 DOI: 10.1021/bi5011877] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CobA from Salmonella enterica (SeCobA) is a member of the family of ATP:Co(I)rrinoid adenosyltransferase (ACAT) enzymes that participate in the biosynthesis of adenosylcobalamin by catalyzing the transfer of the adenosyl group from an ATP molecule to a reactive Co(I)rrinoid species transiently generated in the enzyme active site. This reaction is thermodynamically challenging, as the reduction potential of the Co(II)rrinoid precursor in solution is far more negative than that of available reducing agents in the cell (e.g., flavodoxin), precluding nonenzymic reduction to the Co(I) oxidation state. However, in the active sites of ACATs, the Co(II)/Co(I) redox potential is increased by >250 mV via the formation of a unique four-coordinate (4c) Co(II)rrinoid species. In the case of the SeCobA ACAT, crystallographic and kinetic studies have revealed that the phenylalanine 91 (F91) and tryptophan 93 (W93) residues are critical for in vivo activity, presumably by blocking access to the lower axial ligand site of the Co(II)rrinoid substrate. To further assess the importance of the F91 and W93 residues with respect to enzymatic function, we have characterized various SeCobA active-site variants using electronic absorption, magnetic circular dichroism, and electron paramagnetic resonance spectroscopies. Our data provide unprecedented insight into the mechanism by which SeCobA converts the Co(II)rrinoid substrate to 4c species, with the hydrophobicity, size, and ability to participate in offset π-stacking interactions of key active-site residues all being critical for activity. The structural changes that occur upon Co(II)rrinoid binding also appear to be crucial for properly orienting the transiently generated Co(I) "supernucleophile" for rapid reaction with cosubstrate ATP.
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Affiliation(s)
- Ivan G Pallares
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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27
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Lodowski P, Jaworska M, Andruniów T, Garabato BD, Kozlowski PM. Mechanism of Co–C Bond Photolysis in the Base-On Form of Methylcobalamin. J Phys Chem A 2014; 118:11718-34. [DOI: 10.1021/jp508513p] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piotr Lodowski
- Department
of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Department
of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland
| | - Tadeusz Andruniów
- Institute
of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland
| | - Brady D. Garabato
- Department
of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Pawel M. Kozlowski
- Department
of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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28
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Bito T, Yabuta Y, Ichiyanagi T, Kawano T, Watanabe F. A dodecylamine derivative of cyanocobalamin potently inhibits the activities of cobalamin-dependent methylmalonyl-CoA mutase and methionine synthase of Caenorhabditis elegans. FEBS Open Bio 2014; 4:722-9. [PMID: 25161880 PMCID: PMC4141197 DOI: 10.1016/j.fob.2014.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/21/2014] [Accepted: 07/28/2014] [Indexed: 11/18/2022] Open
Abstract
CN-Cbl dodecylamine, a derivative of cyanocobalamin, was absorbed by C. elegans. CN-Cbl dodecylamine decreased activities of cobalamin-dependent enzymes. CN-Cbl dodecylamine induced cobalamin deficiency in C. elegans. CN-Cbl dodecylamine acts as an inhibitor of cobalamin-dependent enzymes.
In this study, we showed that cyanocobalamin dodecylamine, a ribose 5′-carbamate derivative of cyanocobalamin, was absorbed and accumulated to significant levels by Caenorhabditis elegans and was not further metabolized. The levels of methylmalonic acid and homocysteine, which serve as indicators of cobalamin deficiency, were significantly increased in C. elegans treated with the dodecylamine derivative, indicating severe cobalamin deficiency. Kinetic studies show that the affinity of the cyanocobalamin dodecylamine derivative was greater for two cobalamin-dependent enzymes, methylmalonyl-CoA mutase and methionine synthase, compared with their respective coenzymes, suggesting that the dodecylamine derivative inactivated these enzymes. The dodecylamine derivative did not affect the levels of mRNAs encoding these enzymes or those of other proteins involved in intercellular cobalamin metabolism, including methylmalonyl-CoA mutase (mmcm-1), methylmalonic acidemia cobalamin A complementation group (mmaa-1), methylmalonic aciduria cblC type (cblc-1), and methionine synthase reductase (mtrr-1). In contrast, the level of the mRNAs encoding cob(I)alamin adenosyltransferase (mmab-1) was increased significantly and identical to that of cobalamin-deficient C. elegans. These results indicate that the cyanocobalamin-dodecylamine derivative acts as a potent inhibitor of cobalamin-dependent enzymes and induces severe cobalamin deficiency in C. elegans.
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Key Words
- AdoCbl, 5′-deoxyadenosylcobalamin
- C. elegans, Caenorhabditis elegans
- CH3-Cbl, methylcobalamin
- CN-Cbl, cyanocobalamin
- Caenorhabditis elegans
- Cbl, cobalamin
- Cyanocobalamin
- Hcy, homocysteine
- IF, intrinsic factor
- MCM, methylmalonyl-CoA mutase
- MMA, methylmalonic acid
- MMAA, methylmalonic acidemia cobalamin A complementation group
- MMAB, cob(I)alamin adenosyltransferase
- MMACHC, methylmalonic aciduria cblC type
- MS, methionine synthase
- MSR, methionine synthase reductase
- Methionine synthase
- Methylmalonic acid
- Methylmalonyl-CoA mutase
- NGM, nematode growth medium
- Vitamin B12
- qPCR, quantitative PCR analysis
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Affiliation(s)
| | | | | | | | - Fumio Watanabe
- Corresponding author. Address: The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-minami, Tottori 680-8553, Japan. Tel./fax: +81 857 31 5412.
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29
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Liu H, Kornobis K, Lodowski P, Jaworska M, Kozlowski PM. TD-DFT insight into photodissociation of the Co-C bond in coenzyme B12. Front Chem 2014; 1:41. [PMID: 24790969 PMCID: PMC3982521 DOI: 10.3389/fchem.2013.00041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/24/2013] [Indexed: 11/30/2022] Open
Abstract
Coenzyme B12 (AdoCbl) is one of the most biologically active forms of vitamin B12, and continues to be a topic of active research interest. The mechanism of Co-C bond cleavage in AdoCbl, and the corresponding enzymatic reactions are however, not well understood at the molecular level. In this work, time-dependent density functional theory (TD-DFT) has been applied to investigate the photodissociation of coenzyme B12. To reduce computational cost, while retaining the major spectroscopic features of AdoCbl, a truncated model based on ribosylcobalamin (RibCbl) was used to simulate Co-C photodissociation. Equilibrium geometries of RibCbl were obtained by optimization at the DFT/BP86/TZVP level of theory, and low-lying excited states were calculated by TD-DFT using the same functional and basis set. The calculated singlet states, and absorption spectra were simulated in both the gas phase, and water, using the polarizable continuum model (PCM). Both spectra were in reasonable agreement with experimental data, and potential energy curves based on vertical excitations were plotted to explore the nature of Co-C bond dissociation. It was found that a repulsive 3(σCo−C → σ*Co−C) triplet state became dissociative at large Co-C bond distance, similar to a previous observation for methylcobalamin (MeCbl). Furthermore, potential energy surfaces (PESs) obtained as a function of both Co-CRib and Co-NIm distances, identify the S1 state as a key intermediate generated during photoexcitation of RibCbl, attributed to a mixture of a metal-to-ligand charge transfer (MLCT) and a σ bonding-ligand charge transfer (SBLCT) states.
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Affiliation(s)
- Hui Liu
- Department of Chemistry, University of Louisville Louisville, KY, USA
| | - Karina Kornobis
- Department of Chemistry, University of Louisville Louisville, KY, USA
| | - Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia Katowice, Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia Katowice, Poland
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville Louisville, KY, USA
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30
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Makins C, Pickering AV, Mariani C, Wolthers KR. Mutagenesis of a conserved glutamate reveals the contribution of electrostatic energy to adenosylcobalamin co-C bond homolysis in ornithine 4,5-aminomutase and methylmalonyl-CoA mutase. Biochemistry 2013; 52:878-88. [PMID: 23311430 DOI: 10.1021/bi3012719] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Binding of substrate to ornithine 4,5-aminomutase (OAM) and methylmalonyl-CoA mutase (MCM) leads to the formation of an electrostatic interaction between a conserved glutamate side chain and the adenosyl ribose of the adenosylcobalamin (AdoCbl) cofactor. The contribution of this residue (Glu338 in OAM from Clostridium sticklandii and Glu392 in human MCM) to AdoCbl Co-C bond labilization and catalysis was evaluated by substituting the residue with a glutamine, aspartate, or alanine. The OAM variants, E338Q, E338D, and E338A, showed 90-, 380-, and 670-fold reductions in catalytic turnover and 20-, 60-, and 220-fold reductions in k(cat)/K(m), respectively. Likewise, the MCM variants, E392Q, E392D, and E392A, showed 16-, 330-, and 12-fold reductions in k(cat), respectively. Binding of substrate to OAM is unaffected by the single-amino acid mutation as stopped-flow absorbance spectroscopy showed that the rates of external aldimine formation in the OAM variants were similar to that of the native enzyme. The decrease in the level of catalysis is instead linked to impaired Co-C bond rupture, as UV-visible spectroscopy did not show detectable AdoCbl homolysis upon binding of the physiological substrate, d-ornithine. AdoCbl homolysis was also not detected in the MCM mutants, as it was for the native enzyme. We conclude from these results that a gradual weakening of the electrostatic energy between the protein and the ribose leads to a progressive increase in the activation energy barrier for Co-C bond homolysis, thereby pointing to a key role for the conserved polar glutamate residue in controlling the initial generation of radical species.
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Affiliation(s)
- Caitlyn Makins
- Department of Chemistry, University of British Columbia, 3333 University Way, Kelowna, BC, Canada
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31
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Kornobis K, Kumar N, Lodowski P, Jaworska M, Piecuch P, Lutz JJ, Wong BM, Kozlowski PM. Electronic structure of the S1state in methylcobalamin: Insight from CASSCF/MC-XQDPT2, EOM-CCSD, and TD-DFT calculations. J Comput Chem 2013; 34:987-1004. [DOI: 10.1002/jcc.23204] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 10/25/2012] [Accepted: 11/19/2012] [Indexed: 11/12/2022]
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32
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33
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Cracan V, Banerjee R. Novel B(12)-dependent acyl-CoA mutases and their biotechnological potential. Biochemistry 2012; 51:6039-46. [PMID: 22803641 DOI: 10.1021/bi300827v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recent spate of discoveries of novel acyl-CoA mutases has engendered a growing appreciation for the diversity of 5'-deoxyadenosylcobalamin-dependent rearrangement reactions. The prototype of the reaction catalyzed by these enzymes is the 1,2 interchange of a hydrogen atom with a thioester group leading to a change in the degree of carbon skeleton branching. These enzymes are predicted to share common architectural elements: a Rossman fold and a triose phosphate isomerase (TIM)-barrel domain for binding cofactor and substrate, respectively. Within this family, methylmalonyl-CoA mutase (MCM) is the best studied and is the only member found in organisms ranging from bacteria to man. MCM interconverts (2R)-methylmalonyl-CoA and succinyl-CoA. The more recently discovered family members include isobutyryl-CoA mutase (ICM), which interconverts isobutyryl-CoA and n-butyryl-CoA; ethylmalonyl-CoA mutase, which interconverts (2R)-ethylmalonyl-CoA and (2S)-methylsuccinyl-CoA; and 2-hydroxyisobutyryl-CoA mutase, which interconverts 2-hydroxyisobutyryl-CoA and (3S)-hydroxybutyryl-CoA. A variant in which the two subunits of ICM are fused to a G-protein chaperone, IcmF, has been described recently. In addition to its ICM activity, IcmF also catalyzes the interconversion of isovaleryl-CoA and pivalyl-CoA. This review focuses on the involvement of acyl-CoA mutases in central carbon and secondary bacterial metabolism and on their biotechnological potential for applications ranging from bioremediation to stereospecific synthesis of C2-C5 carboxylic acids and alcohols, and for production of potential commodity and specialty chemicals.
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Affiliation(s)
- Valentin Cracan
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109-0600, USA
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34
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Kozlowski PM, Kumar M, Piecuch P, Li W, Bauman NP, Hansen JA, Lodowski P, Jaworska M. The Cobalt–Methyl Bond Dissociation in Methylcobalamin: New Benchmark Analysis Based on Density Functional Theory and Completely Renormalized Coupled-Cluster Calculations. J Chem Theory Comput 2012; 8:1870-94. [DOI: 10.1021/ct300170y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pawel M. Kozlowski
- Department of Chemistry, University
of Louisville,
2320 South Brook St., Louisville, Kentucky 40292, United States
| | - Manoj Kumar
- Department of Chemistry, University
of Louisville,
2320 South Brook St., Louisville, Kentucky 40292, United States
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Wei Li
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Nicholas P. Bauman
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Jared A. Hansen
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Piotr Lodowski
- Institute
of Chemistry, University of Silesia, Szkolna
9, PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Institute
of Chemistry, University of Silesia, Szkolna
9, PL-40 006 Katowice, Poland
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35
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Park K, Mera PE, Escalante-Semerena JC, Brunold TC. Spectroscopic characterization of active-site variants of the PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri: insights into the mechanism of four-coordinate Co(II)corrinoid formation. Inorg Chem 2012; 51:4482-94. [PMID: 22480351 DOI: 10.1021/ic202096x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The PduO-type adenosine 5'-triphosphate (ATP):corrinoid adenosyltransferase from Lactobacillus reuteri (LrPduO) catalyzes the transfer of the adenosyl-group of ATP to Co(1+)cobalamin (Cbl) and Co(1+)cobinamide (Cbi) substrates to synthesize adenosylcobalamin (AdoCbl) and adenosylcobinamide (AdoCbi(+)), respectively. Previous studies revealed that to overcome the thermodynamically challenging Co(2+) → Co(1+) reduction, the enzyme drastically weakens the axial ligand-Co(2+) bond so as to generate effectively four-coordinate (4c) Co(2+)corrinoid species. To explore how LrPduO generates these unusual 4c species, we have used magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) spectroscopic techniques. The effects of active-site amino acid substitutions on the relative yield of formation of 4c Co(2+)corrinoid species were examined by performing eight single-amino acid substitutions at seven residues that are involved in ATP-binding, an intersubunit salt bridge, and the hydrophobic region surrounding the bound corrin ring. A quantitative analysis of our MCD and EPR spectra indicates that the entire hydrophobic pocket below the corrin ring, and not just residue F112, is critical for the removal of the axial ligand from the cobalt center of the Co(2+)corrinoids. Our data also show that a higher level of coordination among several LrPduO amino acid residues is required to exclude the dimethylbenzimidazole moiety of Co(II)Cbl from the active site than to remove the water molecule from Co(II)Cbi(+). Thus, the hydrophilic interactions around and above the corrin ring are more critical to form 4c Co(II)Cbl than 4c Co(II)Cbi(+). Finally, when ATP analogues were used as cosubstrate, only "unactivated" five-coordinate (5c) Co(II)Cbl was observed, disclosing an unexpectedly large role of the ATP-induced active-site conformational changes with respect to the formation of 4c Co(II)Cbl. Collectively, our results indicate that the level of control exerted by LrPduO over the timing for the formation of the 4c Co(2+)corrinoid intermediates is even more exquisite than previously anticipated.
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Affiliation(s)
- Kiyoung Park
- University of Wisconsin-Madison, Department of Chemistry, Madison, Wisconsin 53706, USA
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36
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Bucher D, Sandala GM, Durbeej B, Radom L, Smith DM. The Elusive 5′-Deoxyadenosyl Radical in Coenzyme-B12-Mediated Reactions. J Am Chem Soc 2012; 134:1591-9. [DOI: 10.1021/ja207809b] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Denis Bucher
- School of Chemistry and ARC Centre of Excellence
for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - Gregory M. Sandala
- School of Chemistry and ARC Centre of Excellence
for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
- Division of Organic
Chemistry and Biochemistry, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - Bo Durbeej
- Division of Computational
Physics, IFM Theory and Modelling, Linköping University, SE-581 83 Linköping, Sweden
| | - Leo Radom
- School of Chemistry and ARC Centre of Excellence
for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - David M. Smith
- Division of Organic
Chemistry and Biochemistry, Ruđer Bošković Institute, 10002 Zagreb, Croatia
- Computer-Chemie-Centrum, University of Erlangen-Nürnberg, 91052 Erlangen, Germany
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37
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Bonanata JN, Signorelli S, Coitiño EL. Increasing complexity models for describing the generation of substrate radicals at the active site of ethanolamine ammonia-lyase/B12. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.07.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Lodowski P, Jaworska M, Kornobis K, Andruniów T, Kozlowski PM. Electronic and Structural Properties of Low-lying Excited States of Vitamin B12. J Phys Chem B 2011; 115:13304-19. [DOI: 10.1021/jp200911y] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland
| | - Karina Kornobis
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Tadeusz Andruniów
- Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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39
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Conrad KS, Brunold TC. Spectroscopic and computational studies of glutathionylcobalamin: nature of Co-S bonding and comparison to Co-C bonding in coenzyme B12. Inorg Chem 2011; 50:8755-66. [PMID: 21859072 DOI: 10.1021/ic200428r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Glutathionylcobalamin (GSCbl) is a unique, biologically relevant cobalamin featuring an axial Co-S bond that distinguishes it from the enzymatically active forms of vitamin B(12), which possess axial Co-C bonds. GSCbl has been proposed to serve as an intermediate in cobalamin processing and, more recently, as a therapeutic for neurological disorders associated with oxidative stress. In this study, GSCbl and its close relative cysteinylcobalamin (CysCbl) were investigated using electronic absorption, circular dichroism, magnetic circular dichroism, and resonance Raman spectroscopies. The spectroscopic data were analyzed in the framework of density functional theory (DFT) and time-dependent DFT computations to generate experimentally validated electronic structure descriptions. Although the change in the upper axial ligand from an alkyl to a thiol group represents a major perturbation in terms of the size, basicity, and polarizability of the coordinating atom, our spectroscopic and computational results reveal striking similarities in electronic structure between methylcobalamin (MeCbl) and GSCbl, especially with regard to the σ donation from the alkyl/thiol ligand and the extent of mixing between the cobalt 3d and the ligand frontier orbitals. A detailed comparison of Co-C and Co-S bonding in MeCbl and GSCbl, respectively, is presented, and the implications of our results with respect to the proposed biological roles of GSCbl are discussed.
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Affiliation(s)
- Karen S Conrad
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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40
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Hirao H. Which DFT Functional Performs Well in the Calculation of Methylcobalamin? Comparison of the B3LYP and BP86 Functionals and Evaluation of the Impact of Empirical Dispersion Correction. J Phys Chem A 2011; 115:9308-13. [DOI: 10.1021/jp2052807] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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41
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Alfonso-Prieto M, Biarnés X, Kumar M, Rovira C, Kozlowski PM. Reductive cleavage mechanism of Co-C bond in cobalamin-dependent methionine synthase. J Phys Chem B 2011; 114:12965-71. [PMID: 20853870 DOI: 10.1021/jp1043738] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The key step in the catalytic cycle of methionine synthase (MetH) is the transfer of a methyl group from the methylcobalamin (MeCbl) cofactor to homocysteine (Hcy). This mechanism has been traditionally viewed as an S(N)2-type reaction, but a different mechanism based on one-electron reduction of the cofactor (reductive cleavage) has been recently proposed. In this work, we analyze whether this mechanism is plausible from a theoretical point of view. By means of a combination of gas-phase as well as hybrid QM/MM calculations, we show that cleavage of the Co-C bond in a MeCbl···Hcy complex (Hcy = methylthiolate substrate (Me-S(-)), a structural mimic of deprotonated homocysteine) proceeds via a [Co(III)(corrin(*-))]-Me···*S-Me diradical configuration, involving electron transfer (ET) from a π*(corrin)-type state to a σ*(Co-C) one, and the methyl transfer displays an energy barrier ≤8.5 kcal/mol. This value is comparable to the one previously computed for the alternative S(N)2 reaction pathway (10.5 kcal/mol). However, the ET-based reductive cleavage pathway does not impose specific geometrical and distance constraints with respect to substrate and cofactor, as does the S(N)2 pathway. This might be advantageous from the enzymatic point of view because in that case, a methyl group can be transferred efficiently at longer distances.
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Affiliation(s)
- Mercedes Alfonso-Prieto
- Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
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42
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Kuta J, Wuerges J, Randaccio L, Kozlowski PM. Axial bonding in alkylcobalamins: DFT analysis of the inverse versus normal trans influence. J Phys Chem A 2010; 113:11604-12. [PMID: 19848426 DOI: 10.1021/jp901397p] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional theory has been applied to study the origin of the inverse and normal trans influence in alkylcobalamins. In order to cover the X-ray structural data available for alkylcobalamins with a variety of axial substituents, geometries of 28 related corrin-containing models have been optimized and analyzed. The BP86/6-31G(d) level of theory was applied which showed good reliability in reproducing the axial bond lengths. Comparison of experimental and calculated data allowed to conclude that the inverse trans influence is not a general feature of cobalamins, as it appeared from the experimental data analysis alone. Inverse trans influence is observed for the series of R groups with increasing bulk and electron donating ability. For the series of R groups having similar medium bulk, but differing significantly in the electron donating ability, normal trans influence was found. Finally, it was determined, that the axial bond lengths correlate well but differently in the two series of R groups with the orbital energies of the six molecular orbitals essential in axial interligand bonding.
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Affiliation(s)
- Jadwiga Kuta
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA
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43
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Jones AR, Woodward JR, Scrutton NS. Continuous wave photolysis magnetic field effect investigations with free and protein-bound alkylcobalamins. J Am Chem Soc 2010; 131:17246-53. [PMID: 19899795 DOI: 10.1021/ja9059238] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The activation of the Co-C bond in adenosylcobalamin-dependent enzymes generates a singlet-born Co(II)-adenosyl radical pair. Two of the salient questions regarding this process are: (1) What is the origin of the considerable homolysis rate enhancement achieved by this class of enzyme? (2) Are the reaction dynamics of the resultant radical pair sensitive to the application of external magnetic fields? Here, we present continuous wave photolysis magnetic field effect (MFE) data that reveal the ethanolamine ammonia lyase (EAL) active site to be an ideal microreactor in which to observe enhanced magnetic field sensitivity in the adenosylcobalamin radical pair. The observed field dependence is in excellent agreement with that calculated from published hyperfine couplings for the constituent radicals, and the magnitude of the MFE (<18%) is almost identical to that observed in a solvent containing 67% glycerol. Similar augmentation is not observed, however, in the equivalent experiments with EAL-bound methylcobalamin, where all field sensitivity observed in the free cofactor is washed out completely. Parallels are drawn between the latter case and the loss of field sensitivity in the EAL holoenzyme upon substrate binding (Jones et al. J. Am. Chem. Soc. 2007, 129, 15718-15727). Both are attributed to the rapid removal of the alkyl radical immediately after homolysis, such that there is inadequate radical pair recombination for the observation of field effects. Taken together, these results support the notion that rapid radical quenching, through the coupling of homolysis and hydrogen abstraction steps, and subsequent radical pair stabilization make a contribution to the observed rate acceleration of Co-C bond homolysis in adenosylcobalamin-dependent enzymes.
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Affiliation(s)
- Alex R Jones
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester M1 7DN, United Kingdom
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44
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Bhattacharya D, Maji S, Pal K, Sarkar S. Oxygen−Cobalt Chemistry Using a Porphyrinogen Platform. Inorg Chem 2009; 48:6362-70. [DOI: 10.1021/ic802102k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Suman Maji
- Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Kuntal Pal
- Indian Institute of Technology Kanpur, Kanpur 208016, India
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45
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Zhang Y, Gladyshev VN. Comparative Genomics of Trace Elements: Emerging Dynamic View of Trace Element Utilization and Function. Chem Rev 2009; 109:4828-61. [DOI: 10.1021/cr800557s] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yan Zhang
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Vadim N. Gladyshev
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0664
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46
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Insights into the mechanisms of adenosylcobalamin (coenzyme B12)-dependent enzymes from rapid chemical quench experiments. Biochem Soc Trans 2009; 37:336-42. [PMID: 19290858 DOI: 10.1042/bst0370336] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that use free radicals to catalyse unusual and chemically difficult rearrangements involving 1,2-migrations of hydrogen atoms. A key mechanistic feature of these enzymes is the transfer of the migrating hydrogen atom between substrate, coenzyme and product. The present review summarizes recent experiments from my laboratory that have used rapid chemical quench techniques to identify intermediates in the reaction and probe the mechanism of hydrogen transfer through a variety of pre-steady-state kinetic isotope effect measurements.
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47
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Sarangi R, Dey M, Ragsdale SW. Geometric and electronic structures of the Ni(I) and methyl-Ni(III) intermediates of methyl-coenzyme M reductase. Biochemistry 2009; 48:3146-56. [PMID: 19243132 PMCID: PMC2667316 DOI: 10.1021/bi900087w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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Methyl-coenzyme M reductase (MCR) catalyzes the terminal step in the formation of biological methane from methyl-coenzyme M (Me-SCoM) and coenzyme B (CoBSH). The active site in MCR contains a Ni−F430 cofactor, which can exist in different oxidation states. The catalytic mechanism of methane formation has remained elusive despite intense spectroscopic and theoretical investigations. On the basis of spectroscopic and crystallographic data, the first step of the mechanism is proposed to involve a nucleophilic attack of the NiI active state (MCRred1) on Me-SCoM to form a NiIII−methyl intermediate, while computational studies indicate that the first step involves the attack of NiI on the sulfur of Me-SCoM, forming a CH3• radical and a NiII−thiolate species. In this study, a combination of Ni K-edge X-ray absorption spectroscopic (XAS) studies and density functional theory (DFT) calculations have been performed on the NiI (MCRred1), NiII (MCRred1−silent), and NiIII−methyl (MCRMe) states of MCR to elucidate the geometric and electronic structures of the different redox states. Ni K-edge EXAFS data are used to reveal a five-coordinate active site with an open upper axial coordination site in MCRred1. Ni K-pre-edge and EXAFS data and time-dependent DFT calculations unambiguously demonstrate the presence of a long Ni−C bond (∼2.04 Å) in the NiIII−methyl state of MCR. The formation and stability of this species support mechanism I, and the Ni−C bond length suggests a homolytic cleavage of the NiIII−methyl bond in the subsequent catalytic step. The XAS data provide insight into the role of the unique F430 cofactor in tuning the stability of the different redox states of MCR.
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Affiliation(s)
- Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
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48
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Lodowski P, Jaworska M, Andruniów T, Kumar M, Kozlowski PM. Photodissociation of Co−C Bond in Methyl- and Ethylcobalamin: An Insight from TD-DFT Calculations. J Phys Chem B 2009; 113:6898-909. [DOI: 10.1021/jp810223h] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland; Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland; and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Maria Jaworska
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland; Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland; and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Tadeusz Andruniów
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland; Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland; and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Manoj Kumar
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland; Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland; and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Pawel M. Kozlowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia, Szkolna 9, PL-40 006 Katowice, Poland; Institute of Physical and Theoretical Chemistry, Department of Chemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland; and Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
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49
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Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN. Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics 2009; 10:78. [PMID: 19208259 PMCID: PMC2667541 DOI: 10.1186/1471-2164-10-78] [Citation(s) in RCA: 182] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2008] [Accepted: 02/10/2009] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Nickel (Ni) and cobalt (Co) are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitamin B12. Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. RESULTS We carried out comparative genomic analyses to examine occurrence and evolutionary dynamics of the use of Ni and Co at the level of (i) transport systems, and (ii) metalloproteomes. Our data show that both metals are widely used in bacteria and archaea. Cbi/NikMNQO is the most common prokaryotic Ni/Co transporter, while Ni-dependent urease and Ni-Fe hydrogenase, and B12-dependent methionine synthase (MetH), ribonucleotide reductase and methylmalonyl-CoA mutase are the most widespread metalloproteins for Ni and Co, respectively. Occurrence of other metalloenzymes showed a mosaic distribution and a new B12-dependent protein family was predicted. Deltaproteobacteria and Methanosarcina generally have larger Ni- and Co-dependent proteomes. On the other hand, utilization of these two metals is limited in eukaryotes, and very few of these organisms utilize both of them. The Ni-utilizing eukaryotes are mostly fungi (except saccharomycotina) and plants, whereas most B12-utilizing organisms are animals. The NiCoT transporter family is the most widespread eukaryotic Ni transporter, and eukaryotic urease and MetH are the most common Ni- and B12-dependent enzymes, respectively. Finally, investigation of environmental and other conditions and identity of organisms that show dependence on Ni or Co revealed that host-associated organisms (particularly obligate intracellular parasites and endosymbionts) have a tendency for loss of Ni/Co utilization. CONCLUSION Our data provide information on the evolutionary dynamics of Ni and Co utilization and highlight widespread use of these metals in the three domains of life, yet only a limited number of user proteins.
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Affiliation(s)
- Yan Zhang
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, NE 68588-0664, USA.
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Andruniów T, Jaworska M, Lodowski P, Zgierski MZ, Dreos R, Randaccio L, Kozlowski PM. Time-dependent density functional theory study of cobalt corrinoids: Electronically excited states of coenzyme B[sub 12]. J Chem Phys 2009. [DOI: 10.1063/1.3190326] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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