1
|
Watkins M, Wang H, Burnim A, Ando N. Conformational switching and flexibility in cobalamin-dependent methionine synthase studied by small-angle X-ray scattering and cryoelectron microscopy. Proc Natl Acad Sci U S A 2023; 120:e2302531120. [PMID: 37339208 PMCID: PMC10293825 DOI: 10.1073/pnas.2302531120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Cobalamin-dependent methionine synthase (MetH) catalyzes the synthesis of methionine from homocysteine and 5-methyltetrahydrofolate (CH3-H4folate) using the unique chemistry of its cofactor. In doing so, MetH links the cycling of S-adenosylmethionine with the folate cycle in one-carbon metabolism. Extensive biochemical and structural studies on Escherichia coli MetH have shown that this flexible, multidomain enzyme adopts two major conformations to prevent a futile cycle of methionine production and consumption. However, as MetH is highly dynamic as well as both a photosensitive and oxygen-sensitive metalloenzyme, it poses special challenges for structural studies, and existing structures have necessarily come from a "divide and conquer" approach. In this study, we investigate E. coli MetH and a thermophilic homolog from Thermus filiformis using small-angle X-ray scattering (SAXS), single-particle cryoelectron microscopy (cryo-EM), and extensive analysis of the AlphaFold2 database to present a structural description of the full-length MetH in its entirety. Using SAXS, we describe a common resting-state conformation shared by both active and inactive oxidation states of MetH and the roles of CH3-H4folate and flavodoxin in initiating turnover and reactivation. By combining SAXS with a 3.6-Å cryo-EM structure of the T. filiformis MetH, we show that the resting-state conformation consists of a stable arrangement of the catalytic domains that is linked to a highly mobile reactivation domain. Finally, by combining AlphaFold2-guided sequence analysis and our experimental findings, we propose a general model for functional switching in MetH.
Collapse
Affiliation(s)
- Maxwell B. Watkins
- Department of Chemistry, Princeton University, Princeton, NJ08544
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Haoyue Wang
- Field of Biophysics, Cornell University, Ithaca, NY14853
| | - Audrey Burnim
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ08544
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
- Field of Biophysics, Cornell University, Ithaca, NY14853
| |
Collapse
|
2
|
Watkins MB, Wang H, Burnim A, Ando N. Conformational switching and flexibility in cobalamin-dependent methionine synthase studied by small-angle X-ray scattering and cryo-electron microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.11.528079. [PMID: 36798380 PMCID: PMC9934640 DOI: 10.1101/2023.02.11.528079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Cobalamin-dependent methionine synthase (MetH) catalyzes the synthesis of methionine from homocysteine and 5-methyltetrahydrofolate (CH 3 -H 4 folate) using the unique chemistry of its cofactor. In doing so, MetH links the cycling of S -adenosylmethionine with the folate cycle in one-carbon metabolism. Extensive biochemical and structural studies on Escherichia coli MetH have shown that this flexible, multi-domain enzyme adopts two major conformations to prevent a futile cycle of methionine production and consumption. However, as MetH is highly dynamic as well as both a photosensitive and oxygen-sensitive metalloenzyme, it poses special challenges for structural studies, and existing structures have necessarily come from a "divide and conquer" approach. In this study, we investigate E. coli MetH and a thermophilic homolog from Thermus filiformis using small-angle X-ray scattering (SAXS), single-particle cryo-electron microscopy (cryo-EM), and extensive analysis of the AlphaFold2 database to present the first structural description of MetH in its entirety. Using SAXS, we describe a common resting-state conformation shared by both active and inactive oxidation states of MetH and the roles of CH 3 -H 4 folate and flavodoxin in initiating turnover and reactivation. By combining SAXS with a 3.6-Å cryo-EM structure of the T. filiformis MetH, we show that the resting-state conformation consists of a stable arrangement of the catalytic domains that is linked to a highly mobile reactivation domain. Finally, by combining AlphaFold2-guided sequence analysis and our experimental findings, we propose a general model for functional switching in MetH.
Collapse
Affiliation(s)
- Maxwell B. Watkins
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Haoyue Wang
- Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
| | - Audrey Burnim
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA,Field of Biophysics, Cornell University, Ithaca, NY 14853, USA,Correspondence should be addressed to
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Bridwell-Rabb J, Li B, Drennan CL. Cobalamin-Dependent Radical S-Adenosylmethionine Enzymes: Capitalizing on Old Motifs for New Functions. ACS BIO & MED CHEM AU 2022; 2:173-186. [PMID: 35726326 PMCID: PMC9204698 DOI: 10.1021/acsbiomedchemau.1c00051] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 01/21/2023]
Abstract
The members of the radical S-adenosylmethionine (SAM) enzyme superfamily are responsible for catalyzing a diverse set of reactions in a multitude of biosynthetic pathways. Many members of this superfamily accomplish their transformations using the catalytic power of a 5'-deoxyadenosyl radical (5'-dAdo•), but there are also enzymes within this superfamily that bind auxiliary cofactors and extend the catalytic repertoire of SAM. In particular, the cobalamin (Cbl)-dependent class synergistically uses Cbl to facilitate challenging methylation and radical rearrangement reactions. Despite identification of this class by Sofia et al. 20 years ago, the low sequence identity between members has led to difficulty in predicting function of uncharacterized members, pinpointing catalytic residues, and elucidating reaction mechanisms. Here, we capitalize on the three recent structures of Cbl-dependent radical SAM enzymes that use common cofactors to facilitate ring contraction as well as radical-based and non-radical-based methylation reactions. With these three structures as a framework, we describe how the Cbl-dependent radical SAM enzymes repurpose the traditional SAM- and Cbl-binding motifs to form an active site where both Cbl and SAM can participate in catalysis. In addition, we describe how, in some cases, the classic SAM- and Cbl-binding motifs support the diverse functionality of this enzyme class, and finally, we define new motifs that are characteristic of Cbl-dependent radical SAM enzymes.
Collapse
Affiliation(s)
- Jennifer Bridwell-Rabb
- Department
of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109, United States,
| | - Bin Li
- Department
of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109, United States
| | - Catherine L. Drennan
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States,Department
of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States,Howard
Hughes Medical Institute, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
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.
Collapse
|
8
|
Padmanabhan S, Jost M, Drennan CL, Elías-Arnanz M. A New Facet of Vitamin B 12: Gene Regulation by Cobalamin-Based Photoreceptors. Annu Rev Biochem 2017; 86:485-514. [PMID: 28654327 PMCID: PMC7153952 DOI: 10.1146/annurev-biochem-061516-044500] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Living organisms sense and respond to light, a crucial environmental factor, using photoreceptors, which rely on bound chromophores such as retinal, flavins, or linear tetrapyrroles for light sensing. The discovery of photoreceptors that sense light using 5'-deoxyadenosylcobalamin, a form of vitamin B12 that is best known as an enzyme cofactor, has expanded the number of known photoreceptor families and unveiled a new biological role of this vitamin. The prototype of these B12-dependent photoreceptors, the transcriptional repressor CarH, is widespread in bacteria and mediates light-dependent gene regulation in a photoprotective cellular response. CarH activity as a transcription factor relies on the modulation of its oligomeric state by 5'-deoxyadenosylcobalamin and light. This review surveys current knowledge about these B12-dependent photoreceptors, their distribution and mode of action, and the structural and photochemical basis of how they orchestrate signal transduction and control gene expression.
Collapse
Affiliation(s)
- S Padmanabhan
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain;
| | - Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158-2140;
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética, Unidad Asociada al Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain;
| |
Collapse
|
9
|
Jost M, Fernández-Zapata J, Polanco MC, Ortiz-Guerrero JM, Chen PYT, Kang G, Padmanabhan S, Elías-Arnanz M, Drennan CL. Structural basis for gene regulation by a B12-dependent photoreceptor. Nature 2015; 526:536-41. [PMID: 26416754 PMCID: PMC4634937 DOI: 10.1038/nature14950] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/14/2015] [Indexed: 12/29/2022]
Abstract
Photoreceptor proteins enable organisms to sense and respond to light. The newly discovered CarH-type photoreceptors use a vitamin B12 derivative, adenosylcobalamin, as the light-sensing chromophore to mediate light-dependent gene regulation. Here, we present crystal structures of Thermus thermophilus CarH in all three relevant states: in the dark, both free and bound to operator DNA, and after light exposure. These structures provide a visualization of how adenosylcobalamin mediates CarH tetramer formation in the dark, how this tetramer binds to the promoter −35 element to repress transcription, and how light exposure leads to a large-scale conformational change that activates transcription. In addition to the remarkable functional repurposing of adenosylcobalamin from an enzyme cofactor to a light sensor, we find that nature also repurposed two independent protein modules in assembling CarH. These results expand the biological role of vitamin B12 and provide fundamental insight into a new mode of light-dependent gene regulation.
Collapse
Affiliation(s)
- Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Jésus Fernández-Zapata
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - María Carmen Polanco
- Department of Genetics and Microbiology, Area of Genetics (Unidad Asociada al Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas), Faculty of Biology, Universidad de Murcia, Murcia 30100, Spain
| | - Juan Manuel Ortiz-Guerrero
- Department of Genetics and Microbiology, Area of Genetics (Unidad Asociada al Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas), Faculty of Biology, Universidad de Murcia, Murcia 30100, Spain
| | - Percival Yang-Ting Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Gyunghoon Kang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Montserrat Elías-Arnanz
- Department of Genetics and Microbiology, Area of Genetics (Unidad Asociada al Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas), Faculty of Biology, Universidad de Murcia, Murcia 30100, Spain
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.,Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
10
|
Jost M, Simpson JH, Drennan CL. The Transcription Factor CarH Safeguards Use of Adenosylcobalamin as a Light Sensor by Altering the Photolysis Products. Biochemistry 2015; 54:3231-4. [PMID: 25966286 PMCID: PMC4455981 DOI: 10.1021/acs.biochem.5b00416] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The newly discovered light-dependent
transcription factor CarH
uses adenosylcobalamin as a light sensor to regulate expression of
protective genes in bacteria upon exposure to sunlight. This use of
adenosylcobalamin is a clever adaptation of a classic enzyme cofactor,
taking advantage of its photolabile Co–C bond. However, it
is also puzzling in that photolysis of adenosylcobalamin generates
the 5′-deoxyadenosyl radical that could damage DNA. Here, using
liquid chromatography and spectroscopic techniques, we demonstrate
that CarH suppresses release of the 5′-deoxyadenosyl radical
and instead effects conversion to a nonreactive 4′,5′-anhydroadenosine.
In this manner, CarH safeguards use of adenosylcobalamin in light-dependent
gene regulation.
Collapse
Affiliation(s)
- Marco Jost
- †Department of Chemistry and ‡Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeffrey H Simpson
- †Department of Chemistry and ‡Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Catherine L Drennan
- †Department of Chemistry and ‡Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
11
|
Lodowski P, Jaworska M, Andruniów T, Garabato BD, Kozlowski PM. Mechanism of the S1 excited state internal conversion in vitamin B12. Phys Chem Chem Phys 2014; 16:18675-9. [DOI: 10.1039/c4cp02465f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To explain the photostability of vitamin B12, internal conversion of the S1 state was investigated using TD-DFT.
Collapse
Affiliation(s)
- Piotr Lodowski
- Department of Theoretical Chemistry
- Institute of Chemistry
- University of Silesia
- PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry
- Institute of Chemistry
- University of Silesia
- PL-40 006 Katowice, Poland
| | - Tadeusz Andruniów
- Institute of Physical and Theoretical Chemistry
- Department of Chemistry
- Wroclaw University of Technology
- 50-370 Wroclaw, Poland
| | | | | |
Collapse
|
12
|
Knör G, Monkowius U. Photosensitization and photocatalysis in bioinorganic, bio-organometallic and biomimetic systems. ADVANCES IN INORGANIC CHEMISTRY 2011. [DOI: 10.1016/b978-0-12-385904-4.00005-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
13
|
Abstract
This chapter reviews the literature on cobalamin- and corrinoid-containing enzymes. These enzymes fall into two broad classes, those using methylcobalamin or related methylcorrinoids as prosthetic groups and catalyzing methyl transfer reactions, and those using adenosylcobalamin as the prosthetic group and catalyzing the generation of substrate radicals that in turn undergo rearrangements and/or eliminations.
Collapse
Affiliation(s)
- Rowena G Matthews
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor MI 48109-2216, USA
| |
Collapse
|
14
|
Liptak MD, Fleischhacker AS, Matthews RG, Brunold TC. Probing the role of the histidine 759 ligand in cobalamin-dependent methionine synthase. Biochemistry 2007; 46:8024-35. [PMID: 17567043 PMCID: PMC3113539 DOI: 10.1021/bi700341y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cobalamin-dependent methionine synthase (MetH) of Escherichia coli is a 136 kDa, modular enzyme that undergoes large conformational changes as it uses a cobalamin cofactor as a donor or acceptor in three separate methyl transfer reactions. At different points during the reaction cycle, the coordination to the cobalt of the cobalamin changes; most notably, the imidazole side chain of His759 that coordinates to the cobalamin in the "His-on" state can dissociate to produce a "His-off" state. Here, two distinct species of the cob(II)alamin-bound His759Gly variant have been identified and separated. Limited proteolysis with trypsin was employed to demonstrate that the two species differ in protein conformation. Magnetic circular dichroism and electron paramagnetic resonance spectroscopies were used to show that the two species also differ with respect to the axial coordination to the central cobalt ion of the cobalamin cofactor. One form appears to be in a conformation poised for reductive methylation with adenosylmethionine; this form was readily reduced to cob(I)alamin and subsequently methylated [albeit yielding a unique, five-coordinate methylcob(III)alamin species]. Our spectroscopic data revealed that this form contains a five-coordinate cob(II)alamin species, with a water molecule as an axial ligand to the cobalt. The other form appears to be in a catalytic conformation and could not be reduced to cob(I)alamin under any of the conditions tested, which precluded conversion to the methylcob(III)alamin state. This form was found to possess an effectively four-coordinate cob(II)alamin species that has neither water nor histidine coordinated to the cobalt center. The formation of this four-coordinate cob(II)alamin "dead-end" species in the His759Gly variant illustrates the importance of the His759 residue in governing the equilibria between the different conformations of MetH.
Collapse
Affiliation(s)
- Matthew D. Liptak
- Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706
| | | | - Rowena G. Matthews
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Life Sciences Institute, Department of Biological Chemistry, and Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109
| | - Thomas C. Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706
- To whom correspondence should be addressed: 1101 University Ave., Madison, WI 53706, phone: (608) 265-9056, fax: (608) 262-6143,
| |
Collapse
|
15
|
Szaciłowski K, Macyk W, Drzewiecka-Matuszek A, Brindell M, Stochel G. Bioinorganic photochemistry: frontiers and mechanisms. Chem Rev 2005; 105:2647-94. [PMID: 15941225 DOI: 10.1021/cr030707e] [Citation(s) in RCA: 561] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
16
|
Shiang JJ, Walker LA, Anderson NA, Cole AG, Sension RJ. Time-Resolved Spectroscopic Studies of B12 Coenzymes: The Photolysis of Methylcobalamin Is Wavelength Dependent. J Phys Chem B 1999. [DOI: 10.1021/jp992358r] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph J. Shiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Larry A. Walker
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Neil A. Anderson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Allwyn G. Cole
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Roseanne J. Sension
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| |
Collapse
|
17
|
Brasch NE, Hsu TL, Doll KM, Finke RG. Synthesis and characterization of isolable thiolatocobalamin complexes relevant to coenzyme B12-dependent ribonucleoside triphosphate reductase. J Inorg Biochem 1999; 76:197-209. [PMID: 10605837 DOI: 10.1016/s0162-0134(99)00128-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The syntheses, isolation and characterization of cyclohexylthiolatocobalamin (C6H11SCbl), glutathionylcobalamin (GluSCbl), and cysteinylcobalamin (CysSCbl) are reported in 75, 55, and 65% yield, respectively. Characterization was achieved using elemental analyses, L-SIMS (liquid secondary ion mass spectrometry), UV-visible spectroscopy and, for the more stable C6H11SCbl and GluSCbl, our recently established 1H NMR method (which emphasizes the readily interpreted aromatic region of the cobalamin's 1H NMR spectrum). Preliminary evidence is presented for clean homolysis of the RS-Co bond in C6H11SCbl, GluSCbl, and CysSCbl to give RS. and .Co(II)Cbl radical pairs analogous to those that are intermediates in ribonucleoside triphosphate reductase (RTPR). A summary is provided which emphasizes the seven variables identified to date, underlying the successful syntheses and isolation of thiolatocobalamins, variables which make the one-step syntheses of RSCbls considerably more complex than they initially appear. Also briefly discussed are the analogous protein-S-Cbl complexes that are seen as side-products in RTPR, and the probability that such side-products are formed when HOCbl.HX is used as a possible 'active-site inhibitor' complex with B12-dependent enzymes.
Collapse
Affiliation(s)
- N E Brasch
- Department of Chemistry, Colorado State University, Fort Collins 80523, USA
| | | | | | | |
Collapse
|
18
|
Walker LA, Jarrett JT, Anderson NA, Pullen SH, Matthews RG, Sension RJ. Time-Resolved Spectroscopic Studies of B12 Coenzymes: The Identification of a Metastable Cob(III)alamin Photoproduct in the Photolysis of Methylcobalamin. J Am Chem Soc 1998. [DOI: 10.1021/ja974024q] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Larry A. Walker
- Contribution from the Department of Chemistry, Department of Biological Chemistry, and Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Joseph T. Jarrett
- Contribution from the Department of Chemistry, Department of Biological Chemistry, and Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Neil A. Anderson
- Contribution from the Department of Chemistry, Department of Biological Chemistry, and Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Stuart H. Pullen
- Contribution from the Department of Chemistry, Department of Biological Chemistry, and Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Rowena G. Matthews
- Contribution from the Department of Chemistry, Department of Biological Chemistry, and Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Roseanne J. Sension
- Contribution from the Department of Chemistry, Department of Biological Chemistry, and Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109-1055
| |
Collapse
|
19
|
|
20
|
Abstract
The cobalamins are B12 cofactors with a reactive cobalt-carbon bond at their core and support the activity of two mammalian enzymes that are both medically important. The reactive organometallic bond of the cofactor can be cleaved either homolytically or heterolytically, but what determines how the enzymes control the fate of this bond?
Collapse
Affiliation(s)
- R Banerjee
- Biochemistry Department University of Nebraska Lincoln, NE 68588-0664, USA
| |
Collapse
|
21
|
Abstract
Two X-ray structures of cobalamin (B12) bound to proteins have now been determined. These structures reveal that the B12 cofactor undergoes a major conformational change on binding to the apoenzymes of methionine synthase and methylmalonyl-coenzyme A mutase: The dimethylbenzimidazole ligand to the cobalt is displaced by a histidine residue from the protein. Two methyltransferases from archaebacteria that catalyze methylation of mercaptoethanesulfonate (coenzyme M) during methanogenesis have also been shown to contain histidine-ligated cobamides. In corrinoid iron-sulfur methyltransferases from acetogenic and methanogenic organisms, benzimidazole is dissociated from cobalt, but without replacement by histidine. Thus, dimethylbenzimidazole displacement appears to be an emerging theme in cobamide-containing methyltransferases. In methionine synthase, the best studied of the methyltransferases, the histidine ligand appears to be required for competent methyl transfer between methyl-tetrahydrofolate and homocysteine but dissociates for reductive reactivation of the inactive oxidized enzyme. Replacement of dimethylbenzimidazole by histidine may allow switching between the catalytic and activation cycles. The best-characterized B12-dependent mutases that catalyze carbon skeleton rearrangement, for which methylmalonyl-coenzyme A mutase is the prototype, also bind cobalamin cofactors with histidine as the cobalt ligand, although other cobalamin-dependent mutases do not appear to utilize histidine ligation. It is intriguing to find that mutases, which catalyze homolytic rather than heterolytic cleavage of the carbon-cobalt bond, can use this structural motif. In methylmalonylCoA mutase a significant feature, which may be important in facilitating homolytic cleavage, is the long cobalt-nitrogen bond linking histidine to the co-factor. The intermediate radical species generated in catalysis are sequestered in the relatively hydrophilic core of an alpha/beta barrel domain of the mutase.
Collapse
Affiliation(s)
- M L Ludwig
- Biophysics Research Division, University of Michigan, Ann Arbor 48109-1055, USA
| | | |
Collapse
|