1
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Elmendorf LD, Brunold TC. Electronic structure studies of free and enzyme-bound B 12 species by magnetic circular dichroism and complementary spectroscopic techniques. Methods Enzymol 2022; 669:333-365. [PMID: 35644179 DOI: 10.1016/bs.mie.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Electronic absorption (Abs) and circular dichroism (CD) spectroscopic techniques have been used successfully for over half a century in studies of free and enzyme-bound B12 species. More recently, magnetic circular dichroism (MCD) spectroscopy and other complementary techniques have provided an increasingly detailed understanding of the electronic structure of cobalamins. While CD spectroscopy measures the difference in the absorption of left- and right-circularly polarized light, MCD spectroscopy adds the application of a magnetic field parallel to the direction of light propagation. Transitions that are formally forbidden according to the Abs and CD selection rules, such as ligand field (or d→d) transitions, can gain MCD intensity through spin-orbit coupling. As such, MCD spectroscopy provides a uniquely sensitive probe of the different binding modes, Co oxidation states, and axial ligand environments of B12 species in enzyme active sites, and thus the distinct reactivities displayed by these species. This chapter summarizes representative MCD studies of free and enzyme-bound B12 species, including those present in adenosyltransferases, isomerases, and reductive dehalogenases. Complementary spectroscopic and computational data are also presented and discussed where appropriate.
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Affiliation(s)
- Laura D Elmendorf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States.
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2
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Forny P, Plessl T, Frei C, Bürer C, Froese DS, Baumgartner MR. Spectrum and characterization of bi-allelic variants in MMAB causing cblB-type methylmalonic aciduria. Hum Genet 2021; 141:1253-1267. [PMID: 34796408 PMCID: PMC9262797 DOI: 10.1007/s00439-021-02398-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/03/2021] [Indexed: 12/31/2022]
Abstract
Pathogenic variants in MMAB cause cblB-type methylmalonic aciduria, an autosomal-recessive disorder of propionate metabolism. MMAB encodes ATP:cobalamin adenosyltransferase, using ATP and cob(I)alamin to create 5’-deoxyadenosylcobalamin (AdoCbl), the cofactor of methylmalonyl-CoA mutase (MMUT). We identified bi-allelic disease-causing variants in MMAB in 97 individuals with cblB-type methylmalonic aciduria, including 33 different and 16 novel variants. Missense changes accounted for the most frequent pathogenic alleles (p.(Arg186Trp), N = 57; p.(Arg191Trp), N = 19); while c.700C > T (p.(Arg234*)) was the most frequently identified truncating variant (N = 14). In fibroblasts from 76 affected individuals, the ratio of propionate incorporation in the presence and absence of hydroxocobalamin (PI ratio) was associated to clinical cobalamin responsiveness and later disease onset. We found p.(Arg234*) to be associated with cobalamin responsiveness in vitro, and clinically with later onset; p.(Arg186Trp) and p.(Arg191Trp) showed no clear cobalamin responsiveness and early onset. Mapping these and novel variants onto the MMAB structure revealed their potential to affect ATP and AdoCbl binding. Follow-up biochemical characterization of recombinant MMAB identified its three active sites to be equivalent for ATP binding, determined by fluorescence spectroscopy (Kd = 21 µM) and isothermal calorimetry (Kd = 14 µM), but function as two non-equivalent AdoCbl binding sites (Kd1 = 0.55 μM; Kd2 = 8.4 μM). Ejection of AdoCbl was activated by ATP (Ka = 24 µM), which was sensitized by the presence of MMUT (Ka = 13 µM). This study expands the landscape of pathogenic MMAB variants, provides association of in vitro and clinical responsiveness, and facilitates insight into MMAB function, enabling better disease understanding.
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Affiliation(s)
- Patrick Forny
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032, Zurich, Switzerland
| | - Tanja Plessl
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032, Zurich, Switzerland
| | - Caroline Frei
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032, Zurich, Switzerland
| | - Celine Bürer
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032, Zurich, Switzerland
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032, Zurich, Switzerland.
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032, Zurich, Switzerland.
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3
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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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4
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Kieninger C, Wurst K, Podewitz M, Stanley M, Deery E, Lawrence AD, Liedl KR, Warren MJ, Kräutler B. Replacement of the Cobalt Center of Vitamin B
12
by Nickel: Nibalamin and Nibyric Acid Prepared from Metal‐Free B
12
Ligands Hydrogenobalamin and Hydrogenobyric Acid. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Christoph Kieninger
- Institute of Organic Chemistry University of Innsbruck 6020 Innsbruck Austria
- Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
| | - Klaus Wurst
- Institute of General Inorganic and Theoretical Chemistry University of Innsbruck 6020 Innsbruck Austria
| | - Maren Podewitz
- Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
- Institute of General Inorganic and Theoretical Chemistry University of Innsbruck 6020 Innsbruck Austria
| | - Maria Stanley
- School of Biosciences University of Kent Canterbury CT2 7NJ UK
| | - Evelyne Deery
- School of Biosciences University of Kent Canterbury CT2 7NJ UK
| | | | - Klaus R. Liedl
- Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
- Institute of General Inorganic and Theoretical Chemistry University of Innsbruck 6020 Innsbruck Austria
| | - Martin J. Warren
- School of Biosciences University of Kent Canterbury CT2 7NJ UK
- Quadram Institute Bioscience Norwich Science Park Norwich NR4 7UQ UK
| | - Bernhard Kräutler
- Institute of Organic Chemistry University of Innsbruck 6020 Innsbruck Austria
- Center for Molecular Biosciences (CMBI) University of Innsbruck 6020 Innsbruck Austria
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5
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Kieninger C, Wurst K, Podewitz M, Stanley M, Deery E, Lawrence AD, Liedl KR, Warren MJ, Kräutler B. Replacement of the Cobalt Center of Vitamin B 12 by Nickel: Nibalamin and Nibyric Acid Prepared from Metal-Free B 12 Ligands Hydrogenobalamin and Hydrogenobyric Acid. Angew Chem Int Ed Engl 2020; 59:20129-20136. [PMID: 32686888 PMCID: PMC7693184 DOI: 10.1002/anie.202008407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Indexed: 12/18/2022]
Abstract
The (formal) replacement of Co in cobalamin (Cbl) by NiII generates nibalamin (Nibl), a new transition-metal analogue of vitamin B12 . Described here is Nibl, synthesized by incorporation of a NiII ion into the metal-free B12 ligand hydrogenobalamin (Hbl), itself prepared from hydrogenobyric acid (Hby). The related NiII corrin nibyric acid (Niby) was similarly synthesized from Hby, the metal-free cobyric acid ligand. The solution structures of Hbl, and Niby and Nibl, were characterized by spectroscopic studies. Hbl features two inner protons bound at N2 and N4 of the corrin ligand, as discovered in Hby. X-ray analysis of Niby shows the structural adaptation of the corrin ligand to NiII ions and the coordination behavior of NiII . The diamagnetic Niby and Nibl, and corresponding isoelectronic CoI corrins, were deduced to be isostructural. Nibl is a structural mimic of four-coordinate base-off Cbls, as verified by its ability to act as a strong inhibitor of bacterial adenosyltransferase.
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Affiliation(s)
- Christoph Kieninger
- Institute of Organic ChemistryUniversity of Innsbruck6020InnsbruckAustria
- Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
| | - Klaus Wurst
- Institute of GeneralInorganic and Theoretical ChemistryUniversity of Innsbruck6020InnsbruckAustria
| | - Maren Podewitz
- Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
- Institute of GeneralInorganic and Theoretical ChemistryUniversity of Innsbruck6020InnsbruckAustria
| | - Maria Stanley
- School of BiosciencesUniversity of KentCanterburyCT2 7NJUK
| | - Evelyne Deery
- School of BiosciencesUniversity of KentCanterburyCT2 7NJUK
| | | | - Klaus R. Liedl
- Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
- Institute of GeneralInorganic and Theoretical ChemistryUniversity of Innsbruck6020InnsbruckAustria
| | - Martin J. Warren
- School of BiosciencesUniversity of KentCanterburyCT2 7NJUK
- Quadram Institute BioscienceNorwich Science ParkNorwichNR4 7UQUK
| | - Bernhard Kräutler
- Institute of Organic ChemistryUniversity of Innsbruck6020InnsbruckAustria
- Center for Molecular Biosciences (CMBI)University of Innsbruck6020InnsbruckAustria
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6
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Kieninger C, Deery E, Lawrence AD, Podewitz M, Wurst K, Nemoto-Smith E, Widner FJ, Baker JA, Jockusch S, Kreutz CR, Liedl KR, Gruber K, Warren MJ, Kräutler B. The Hydrogenobyric Acid Structure Reveals the Corrin Ligand as an Entatic State Module Empowering B 12 Cofactors for Catalysis. Angew Chem Int Ed Engl 2019; 58:10756-10760. [PMID: 31115943 PMCID: PMC6771967 DOI: 10.1002/anie.201904713] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Indexed: 11/09/2022]
Abstract
The B12 cofactors instill a natural curiosity regarding the primordial selection and evolution of their corrin ligand. Surprisingly, this important natural macrocycle has evaded molecular scrutiny, and its specific role in predisposing the incarcerated cobalt ion for organometallic catalysis has remained obscure. Herein, we report the biosynthesis of the cobalt-free B12 corrin moiety, hydrogenobyric acid (Hby), a compound crafted through pathway redesign. Detailed insights from single-crystal X-ray and solution structures of Hby have revealed a distorted helical cavity, redefining the pattern for binding cobalt ions. Consequently, the corrin ligand coordinates cobalt ions in desymmetrized "entatic" states, thereby promoting the activation of B12 -cofactors for their challenging chemical transitions. The availability of Hby also provides a route to the synthesis of transition metal analogues of B12 .
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Affiliation(s)
- Christoph Kieninger
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
| | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | | | - Maren Podewitz
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Klaus Wurst
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Emi Nemoto-Smith
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Florian J Widner
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
| | - Joseph A Baker
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | | | - Christoph R Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Karl Gruber
- Institute for Molecular Biosciences, University of Graz, Austria
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020, Innsbruck, Austria
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7
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Kieninger C, Deery E, Lawrence AD, Podewitz M, Wurst K, Nemoto‐Smith E, Widner FJ, Baker JA, Jockusch S, Kreutz CR, Liedl KR, Gruber K, Warren MJ, Kräutler B. Die Hydrogenobyrsäure‐Struktur enthüllt den Corrin‐Liganden als entatisches Zustandsmodul zur Steigerung der Katalyseaktivität von B
12
‐Cofaktoren. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Christoph Kieninger
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of Innsbruck 6020 Innsbruck Österreich
| | - Evelyne Deery
- School of BiosciencesUniversity of Kent Canterbury CT2 7NJ Großbritannien
| | - Andrew D. Lawrence
- School of BiosciencesUniversity of Kent Canterbury CT2 7NJ Großbritannien
| | - Maren Podewitz
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck 6020 Innsbruck Österreich
| | - Klaus Wurst
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck 6020 Innsbruck Österreich
| | - Emi Nemoto‐Smith
- School of BiosciencesUniversity of Kent Canterbury CT2 7NJ Großbritannien
| | - Florian J. Widner
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of Innsbruck 6020 Innsbruck Österreich
| | - Joseph A. Baker
- School of BiosciencesUniversity of Kent Canterbury CT2 7NJ Großbritannien
| | | | - Christoph R. Kreutz
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of Innsbruck 6020 Innsbruck Österreich
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences (CMBI)University of Innsbruck 6020 Innsbruck Österreich
| | - Karl Gruber
- Institute for Molecular BiosciencesUniversity of Graz Österreich
| | - Martin J. Warren
- School of BiosciencesUniversity of Kent Canterbury CT2 7NJ Großbritannien
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular BiosciencesUniversity of Innsbruck 6020 Innsbruck Österreich
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8
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Campanello GC, Ruetz M, Dodge GJ, Gouda H, Gupta A, Twahir UT, Killian MM, Watkins D, Rosenblatt DS, Brunold TC, Warncke K, Smith JL, Banerjee R. Sacrificial Cobalt-Carbon Bond Homolysis in Coenzyme B 12 as a Cofactor Conservation Strategy. J Am Chem Soc 2018; 140:13205-13208. [PMID: 30282455 DOI: 10.1021/jacs.8b08659] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A sophisticated intracellular trafficking pathway in humans is used to tailor vitamin B12 into its active cofactor forms, and to deliver it to two known B12-dependent enzymes. Herein, we report an unexpected strategy for cellular retention of B12, an essential and reactive cofactor. If methylmalonyl-CoA mutase is unavailable to accept the coenzyme B12 product of adenosyltransferase, the latter catalyzes homolytic scission of the cobalt-carbon bond in an unconventional reversal of the nucleophilic displacement reaction that was used to make it. The resulting homolysis product binds more tightly to adenosyltransferase than does coenzyme B12, facilitating cofactor retention. We have trapped, and characterized spectroscopically, an intermediate in which the cobalt-carbon bond is weakened prior to being broken. The physiological relevance of this sacrificial catalytic activity for cofactor retention is supported by the significantly lower coenzyme B12 concentration in patients with dysfunctional methylmalonyl-CoA mutase but normal adenosyltransferase activity.
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Affiliation(s)
- Gregory C Campanello
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109-0600 , United States
| | - Markus Ruetz
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109-0600 , United States
| | - Greg J Dodge
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109-0600 , United States.,Life Sciences Institute, University of Michigan , Ann Arbor , Michigan 48109-0600 , United States
| | - Harsha Gouda
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109-0600 , United States.,Indian Institute of Science Education and Research , Pune 411008 , India
| | - Aditi Gupta
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109-0600 , United States
| | - Umar T Twahir
- Department of Physics , Emory University , Atlanta , Georgia 30322-2430 , United States
| | - Michelle M Killian
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - David Watkins
- Department of Human Genetics , McGill University , Montreal , Quebec H3A 1B1 , Canada
| | - David S Rosenblatt
- Department of Human Genetics , McGill University , Montreal , Quebec H3A 1B1 , Canada
| | - Thomas C Brunold
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Kurt Warncke
- Department of Physics , Emory University , Atlanta , Georgia 30322-2430 , United States
| | - Janet L Smith
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109-0600 , United States.,Life Sciences Institute, University of Michigan , Ann Arbor , Michigan 48109-0600 , United States
| | - Ruma Banerjee
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109-0600 , United States
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9
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Gagnon DM, Stich TA, Mehta AP, Abdelwahed SH, Begley TP, Britt RD. An Aminoimidazole Radical Intermediate in the Anaerobic Biosynthesis of the 5,6-Dimethylbenzimidazole Ligand to Vitamin B12. J Am Chem Soc 2018; 140:12798-12807. [PMID: 30208703 DOI: 10.1021/jacs.8b05686] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Organisms that perform the de novo biosynthesis of cobalamin (vitamin B12) do so via unique pathways depending on the presence of oxygen in the environment. The anaerobic biosynthesis pathway of 5,6-dimethylbenzimidazole, the so-called "lower ligand" to the cobalt center, has been recently identified. This process begins with the conversion of 5-aminoimidazole ribotide (AIR) to 5-hydroxybenzimidazole (HBI) by the radical S-adenosyl-l-methionine (SAM) enzyme BzaF, also known as HBI synthase. In this work we report the characterization of a radical intermediate in the reaction of BzaF using electron paramagnetic resonance spectroscopy. Using various isotopologues of AIR, we extracted hyperfine parameters for a number of nuclei, allowing us to propose plausible chemical compositions and structures for this intermediate. Specifically, we find that an aminoimidazole radical is formed in close proximity to a fragment of the ribose ring. These findings induce the revision of past proposed mechanisms and illustrate the ability of radical SAM enzymes to tightly control the radical chemistry that they engender.
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Affiliation(s)
- Derek M Gagnon
- Department of Chemistry , University of California , Davis , California 95616 , United States
| | - Troy A Stich
- Department of Chemistry , University of California , Davis , California 95616 , United States
| | - Angad P Mehta
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Sameh H Abdelwahed
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Tadhg P Begley
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - R David Britt
- Department of Chemistry , University of California , Davis , California 95616 , United States
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10
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Pavlova A, Parks JM, Gumbart JC. Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations. J Chem Theory Comput 2018; 14:784-798. [PMID: 29334459 DOI: 10.1021/acs.jctc.7b01236] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co3+, Co2+, and Co1+, and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.
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Affiliation(s)
- Anna Pavlova
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States.,School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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11
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Plegaria JS, Sutter M, Ferlez B, Aussignargues C, Niklas J, Poluektov OG, Fromwiller C, TerAvest M, Utschig LM, Tiede DM, Kerfeld CA. Structural and Functional Characterization of a Short-Chain Flavodoxin Associated with a Noncanonical 1,2-Propanediol Utilization Bacterial Microcompartment. Biochemistry 2017; 56:5679-5690. [PMID: 28956602 DOI: 10.1021/acs.biochem.7b00682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles that encapsulate enzymes involved in CO2 fixation (carboxysomes) or carbon catabolism (metabolosomes). Metabolosomes share a common core of enzymes and a distinct signature enzyme for substrate degradation that defines the function of the BMC (e.g., propanediol or ethanolamine utilization BMCs, or glycyl-radical enzyme microcompartments). Loci encoding metabolosomes also typically contain genes for proteins that support organelle function, such as regulation, transport of substrate, and cofactor (e.g., vitamin B12) synthesis and recycling. Flavoproteins are frequently among these ancillary gene products, suggesting that these redox active proteins play an undetermined function in many metabolosomes. Here, we report the first characterization of a BMC-associated flavodoxin (Fld1C), a small flavoprotein, derived from the noncanonical 1,2-propanediol utilization BMC locus (PDU1C) of Lactobacillus reuteri. The 2.0 Å X-ray structure of Fld1C displays the α/β flavodoxin fold, which noncovalently binds a single flavin mononucleotide molecule. Fld1C is a short-chain flavodoxin with redox potentials of -240 ± 3 mV oxidized/semiquinone and -344 ± 1 mV semiquinone/hydroquinone versus the standard hydrogen electrode at pH 7.5. It can participate in an electron transfer reaction with a photoreductant to form a stable semiquinone species. Collectively, our structural and functional results suggest that PDU1C BMCs encapsulate Fld1C to store and transfer electrons for the reactivation and/or recycling of the B12 cofactor utilized by the signature enzyme.
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Affiliation(s)
- Jefferson S Plegaria
- MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Bryan Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States
| | - Clément Aussignargues
- MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States
| | - Jens Niklas
- Solar Energy Conversion Group, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Oleg G Poluektov
- Solar Energy Conversion Group, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Ciara Fromwiller
- MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States
| | - Michaela TerAvest
- Department of Biochemistry & Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
| | - Lisa M Utschig
- Solar Energy Conversion Group, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - David M Tiede
- Solar Energy Conversion Group, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,Department of Biochemistry & Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States.,Berkeley Synthetic Biology Institute , Berkeley, California 94720, United States
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12
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Electronic and structural properties of Cob(I)alamin: Ramifications for B 12 -dependent processes. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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13
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Li Z, Kitanishi K, Twahir UT, Cracan V, Chapman D, Warncke K, Banerjee R. Cofactor Editing by the G-protein Metallochaperone Domain Regulates the Radical B 12 Enzyme IcmF. J Biol Chem 2017; 292:3977-3987. [PMID: 28130442 DOI: 10.1074/jbc.m117.775957] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Indexed: 11/06/2022] Open
Abstract
IcmF is a 5'-deoxyadenosylcobalamin (AdoCbl)-dependent enzyme that catalyzes the carbon skeleton rearrangement of isobutyryl-CoA to butyryl-CoA. It is a bifunctional protein resulting from the fusion of a G-protein chaperone with GTPase activity and the cofactor- and substrate-binding mutase domains with isomerase activity. IcmF is prone to inactivation during catalytic turnover, thus setting up its dependence on a cofactor repair system. Herein, we demonstrate that the GTPase activity of IcmF powers the ejection of the inactive cob(II)alamin cofactor and requires the presence of an acceptor protein, adenosyltransferase, for receiving it. Adenosyltransferase in turn converts cob(II)alamin to AdoCbl in the presence of ATP and a reductant. The repaired cofactor is then reloaded onto IcmF in a GTPase-gated step. The mechanistic details of cofactor loading and offloading from the AdoCbl-dependent IcmF are distinct from those of the better characterized and homologous methylmalonyl-CoA mutase/G-protein chaperone system.
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Affiliation(s)
- Zhu Li
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600 and
| | - Kenichi Kitanishi
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600 and
| | - Umar T Twahir
- the Department of Physics, Emory University, Atlanta, Georgia 30322-2430
| | - Valentin Cracan
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600 and
| | - Derrell Chapman
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600 and
| | - Kurt Warncke
- the Department of Physics, Emory University, Atlanta, Georgia 30322-2430
| | - Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600 and
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Pallares IG, Moore TC, Escalante-Semerena JC, Brunold TC. Spectroscopic Studies of the EutT Adenosyltransferase from Salmonella enterica: Evidence of a Tetrahedrally Coordinated Divalent Transition Metal Cofactor with Cysteine Ligation. Biochemistry 2017; 56:364-375. [PMID: 28045498 DOI: 10.1021/acs.biochem.6b00750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The EutT enzyme from Salmonella enterica, a member of the family of ATP:cobalt(I) corrinoid adenosyltransferase (ACAT) enzymes, requires a divalent transition metal ion for catalysis, with Fe(II) yielding the highest activity. EutT contains a unique cysteine-rich HX11CCX2C(83) motif (where H and the last C occupy the 67th and 83rd positions, respectively, in the amino acid sequence) not found in other ACATs and employs an unprecedented mechanism for the formation of adenosylcobalamin. Recent kinetic and spectroscopic studies of this enzyme revealed that residues in the HX11CCX2C(83) motif are required for the tight binding of the divalent metal ion and are critical for the formation of a four-coordinate (4c) cob(II)alamin [Co(II)Cbl] intermediate in the catalytic cycle. However, it remained unknown which, if any, of the residues in the HX11CCX2C(83) motif bind the divalent metal ion. To address this issue, we have characterized Co(II)-substituted wild-type EutT (EutTWT/Co) by using electronic absorption, electron paramagnetic resonance, and magnetic circular dichroism (MCD) spectroscopies. Our results indicate that the reduced catalytic activity of EutTWT/Co relative to that of the Fe(II)-containing enzyme arises from the incomplete incorporation of Co(II) ions and, thus, a decrease in the relative population of 4c Co(II)Cbl. Our MCD data for EutTWT/Co also reveal that the Co(II) ions reside in a distorted tetrahedral coordination environment with direct cysteine sulfur ligation. Additional spectroscopic studies of EutT/Co variants possessing a single alanine substitution of either His67, His75, Cys79, Cys80, or Cys83 indicate that Cys80 coordinates to the Co(II) ion, while the additional residues are important for maintaining the structural integrity and/or high affinity of the metal binding site.
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Affiliation(s)
- Ivan G Pallares
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Theodore C Moore
- 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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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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16
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Widner FJ, Lawrence AD, Deery E, Heldt D, Frank S, Gruber K, Wurst K, Warren MJ, Kräutler B. Total Synthesis, Structure, and Biological Activity of Adenosylrhodibalamin, the Non-Natural Rhodium Homologue of Coenzyme B12. Angew Chem Int Ed Engl 2016; 55:11281-6. [PMID: 27355790 PMCID: PMC5103170 DOI: 10.1002/anie.201603738] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Indexed: 12/12/2022]
Abstract
B12 is unique among the vitamins as it is biosynthesized only by certain prokaryotes. The complexity of its synthesis relates to its distinctive cobalt corrin structure, which is essential for B12 biochemistry and renders coenzyme B12 (AdoCbl) so intriguingly suitable for enzymatic radical reactions. However, why is cobalt so fit for its role in B12 -dependent enzymes? To address this question, we considered the substitution of cobalt in AdoCbl with rhodium to generate the rhodium analogue 5'-deoxy-5'-adenosylrhodibalamin (AdoRbl). AdoRbl was prepared by de novo total synthesis involving both biological and chemical steps. AdoRbl was found to be inactive in vivo in microbial bioassays for methionine synthase and acted as an in vitro inhibitor of an AdoCbl-dependent diol dehydratase. Solution NMR studies of AdoRbl revealed a structure similar to that of AdoCbl. However, the crystal structure of AdoRbl revealed a conspicuously better fit of the corrin ligand for Rh(III) than for Co(III) , challenging the current views concerning the evolution of corrins.
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Affiliation(s)
- Florian J Widner
- Institut für Organische Chemie und Centrum für Molekulare Biowissenschaften (CMBI), Universität Innsbruck, 6020, Innsbruck, Austria.,Plant and Microbial Biology Department, University of California, Berkeley, CA, USA
| | | | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Dana Heldt
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Stefanie Frank
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Karl Gruber
- Institut für Molekulare Biowissenschaften, Universität Graz, Austria
| | - Klaus Wurst
- Institut für Allgemeine, Anorganische und Theoretische Chemie, Universität Innsbruck, Austria
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| | - Bernhard Kräutler
- Institut für Organische Chemie und Centrum für Molekulare Biowissenschaften (CMBI), Universität Innsbruck, 6020, Innsbruck, Austria.
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17
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Widner FJ, Lawrence AD, Deery E, Heldt D, Frank S, Gruber K, Wurst K, Warren MJ, Kräutler B. Totalsynthese, Struktur und biologische Aktivität von Adenosylrhodibalamin, dem unnatürlichen Rhodiumhomologen von Coenzym B12. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603738] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Florian J. Widner
- Institut für Organische Chemie und Centrum für Molekulare Biowissenschaften (CMBI); Universität Innsbruck; 6020 Innsbruck Österreich
- Plant and Microbial Biology Department; University of California; Berkeley USA
| | - Andrew D. Lawrence
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Evelyne Deery
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Dana Heldt
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Stefanie Frank
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Karl Gruber
- Institut für Molekulare Biowissenschaften; Universität Graz; Österreich
| | - Klaus Wurst
- Institut für Allgemeine, Anorganische und Theoretische Chemie; Universität Innsbruck; Österreich
| | - Martin J. Warren
- School of Biosciences; University of Kent; Canterbury CT2 7NJ Großbritannien
| | - Bernhard Kräutler
- Institut für Organische Chemie und Centrum für Molekulare Biowissenschaften (CMBI); Universität Innsbruck; 6020 Innsbruck Österreich
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18
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Pallares IG, Moore TC, Escalante-Semerena JC, Brunold TC. Spectroscopic Studies of the EutT Adenosyltransferase from Salmonella enterica: Mechanism of Four-Coordinate Co(II)Cbl Formation. J Am Chem Soc 2016; 138:3694-704. [PMID: 26886077 DOI: 10.1021/jacs.5b11708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
EutT from Salmonella enterica is a member of a class of enzymes termed ATP:Co(I)rrinoid adenosyltransferases (ACATs), implicated in the biosynthesis of adenosylcobalamin (AdoCbl). In the presence of cosubstrate ATP, ACATs raise the Co(II)/Co(I) reduction potential of their cob(II)alamin [Co(II)Cbl] substrate by >250 mV via the formation of a unique four-coordinate (4c) Co(II)Cbl species, thereby facilitating the formation of a "supernucleophilic" cob(I)alamin intermediate required for the formation of the AdoCbl product. Previous kinetic studies of EutT revealed the importance of a HX11CCX2C(83) motif for catalytic activity and have led to the proposal that residues in this motif serve as the binding site for a divalent transition metal cofactor [e.g., Fe(II) or Zn(II)]. This motif is absent in other ACAT families, suggesting that EutT employs a distinct mechanism for AdoCbl formation. To assess how metal ion binding to the HX11CCX2C(83) motif affects the relative yield of 4c Co(II)Cbl generated in the EutT active site, we have characterized several enzyme variants by using electronic absorption, magnetic circular dichroism, and electron paramagnetic resonance spectroscopies. Our results indicate that Fe(II) or Zn(II) binding to the HX11CCX2C(83) motif of EutT is required for promoting the formation of 4c Co(II)Cbl. Intriguingly, our spectroscopic data also reveal the presence of an equilibrium between five-coordinate "base-on" and "base-off" Co(II)Cbl species bound to the EutT active site at low ATP concentrations, which shifts in favor of "base-off" Co(II)Cbl in the presence of excess ATP, suggesting that the base-off species serves as a precursor to 4c Co(II)Cbl.
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Affiliation(s)
- Ivan G Pallares
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Theodore C Moore
- 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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Park K, Mera PE, Moore TC, Escalante-Semerena JC, Brunold TC. Unprecedented Mechanism Employed by the Salmonella entericaEutT ATP:Co Irrinoid Adenosyltransferase Precludes Adenosylation of Incomplete Co IIrrinoids. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Park K, Mera PE, Moore TC, Escalante-Semerena JC, Brunold TC. Unprecedented Mechanism Employed by the Salmonella enterica EutT ATP:Co(I)rrinoid Adenosyltransferase Precludes Adenosylation of Incomplete Co(II)rrinoids. Angew Chem Int Ed Engl 2015; 54:7158-61. [PMID: 25914129 DOI: 10.1002/anie.201501930] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Indexed: 11/08/2022]
Abstract
Three distinct families of ATP:corrinoid adenosyltransferases (ACATs) exist that are capable of converting vitamin B12 derivatives into coenzyme B12 by catalyzing the thermodynamically challenging reduction of Co(II) rrinoids to form "supernucleophilic" Co(I) intermediates. While the structures and mechanisms of two of the ACAT families have been studied extensively, little is known about the EutT enzymes beyond the fact that they exhibit a unique requirement for a divalent metal cofactor for enzymatic activity. In this study we have obtained compelling evidence that EutT converts cob(II)alamin into an effectively four-coordinate Co(II) species so as to facilitate Co(II)→Co(I) reduction. Intriguingly, EutT fails to promote axial ligand dissociation from the substrate analogue cob(II)inamide, a natural precursor of cob(II)alamin. This unique substrate specificity of EutT has important physiological implications.
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Affiliation(s)
- Kiyoung Park
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 (USA).,Present address: Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon (Republic of Korea)
| | - Paola E Mera
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 (USA).,Present address: Department of Developmental Biology, Stanford University, Stanford, CA 94305 (USA)
| | - Theodore C Moore
- Department of Microbiology, University of Georgia-Athens, Athens, GA 30602 (USA)
| | | | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 (USA).
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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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Dereven'kov IA, Salnikov DS, Makarov SV, Boss GR, Koifman OI. Kinetics and mechanism of oxidation of super-reduced cobalamin and cobinamide species by thiosulfate, sulfite and dithionite. Dalton Trans 2014; 42:15307-16. [PMID: 23999614 DOI: 10.1039/c3dt51714d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We studied the kinetics of reactions of cob(I)alamin and cob(I)inamide with thiosulfate, sulfite, and dithionite by UV-Visible (UV-Vis) and stopped-flow spectroscopy. We found that the two Co(I) species were oxidized by these sulfur-containing compounds to Co(II) forms: oxidation by excess thiosulfate leads to penta-coordinate complexes and oxidation by excess sulfite or dithionite leads to hexa-coordinate Co(II)-SO2(-) complexes. The net scheme involves transfer of three electrons in the case of oxidation by thiosulfate and one electron for oxidation by sulfite and dithionite. On the basis of kinetic data, the nature of the reactive oxidants was suggested, i.e., HS2O3(-) (for oxidation by thiosulfate), S2O5(2-), HSO3(-), and aquated SO2 (for oxidation by sulfite), and S2O4(2-) and SO2(-) (for oxidation by dithionite). No difference was observed in kinetics with cob(i)alamin or cob(i)inamide as reductants.
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Affiliation(s)
- Ilia A Dereven'kov
- State University of Chemistry and Technology, Sheremetevskiy str. 7, 153000 Ivanovo, Russia.
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Moore TC, Newmister SA, Rayment I, Escalante-Semerena JC. Structural insights into the mechanism of four-coordinate Cob(II)alamin formation in the active site of the Salmonella enterica ATP:Co(I)rrinoid adenosyltransferase enzyme: critical role of residues Phe91 and Trp93. Biochemistry 2012; 51:9647-57. [PMID: 23148601 DOI: 10.1021/bi301378d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ATP:co(I)rrinoid adenosyltransferases (ACATs) are enzymes that catalyze the formation of adenosylcobalamin (AdoCbl, coenzyme B(12)) from cobalamin and ATP. There are three families of ACATs, namely, CobA, EutT, and PduO. In Salmonella enterica, CobA is the housekeeping enzyme that is required for de novo AdoCbl synthesis and for salvaging incomplete precursors and cobalamin from the environment. Here, we report the crystal structure of CobA in complex with ATP, four-coordinate cobalamin, and five-coordinate cobalamin. This provides the first crystallographic evidence of the existence of cob(II)alamin in the active site of CobA. The structure suggests a mechanism in which the enzyme adopts a closed conformation and two residues, Phe91 and Trp93, displace 5,6-dimethylbenzimidazole, the lower nucleotide ligand base of cobalamin, to generate a transient four-coordinate cobalamin, which is critical in the formation of the AdoCbl Co-C bond. In vivo and in vitro mutational analyses of Phe91 and Trp93 emphasize the important role of bulky hydrophobic side chains in the active site. The proposed manner in which CobA increases the redox potential of the cob(II)alamin/cob(I)alamin couple to facilitate formation of the Co-C bond appears to be analogous to that utilized by the PduO-type ACATs, where in both cases the polar coordination of the lower ligand to the cobalt ion is eliminated by placing that face of the corrin ring adjacent to a cluster of bulky hydrophobic side chains.
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Affiliation(s)
- Theodore C Moore
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
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Co+–H interaction inspired alternate coordination geometries of biologically important cob(I)alamin: possible structural and mechanistic consequences for methyltransferases. J Biol Inorg Chem 2012; 17:1107-21. [DOI: 10.1007/s00775-012-0924-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 07/03/2012] [Indexed: 10/28/2022]
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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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Abstract
The density functional calculations suggest that the expansion of the corrin macrocycle's N(4) core by 0.06-0.10 Å leads to an appreciable lowering of 100-150 mV vs. saturated calomel electrode in the reduction potentials of two biologically important B(12) cofactors namely methylcobalamin and adenosylcobalamin respectively. This redox tuning of B(12) cofactors may encourage the electron transfer-based activation mechanism for B(12)-dependent enzymes.
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Affiliation(s)
- Manoj Kumar
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA
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Plymale NT, Dassanayake RS, Hassanin HA, Brasch NE. Kinetic and Mechanistic Studies on the Reactions of the Reduced Vitamin B12 Complex Cob(I)alamin with Nitrite and Nitrate. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201100992] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Lofgren M, Banerjee R. Loss of allostery and coenzyme B12 delivery by a pathogenic mutation in adenosyltransferase. Biochemistry 2011; 50:5790-8. [PMID: 21604717 DOI: 10.1021/bi2006306] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ATP-dependent cob(I)alamin adenosyltransferase (ATR) is a bifunctional protein: an enzyme that catalyzes the adenosylation of cob(I)alamin and an escort that delivers the product, adenosylcobalamin (AdoCbl or coenzyme B(12)), to methylmalonyl-CoA mutase (MCM), resulting in holoenzyme formation. Failure to assemble holo-MCM leads to methylmalonic aciduria. We have previously demonstrated that only 2 equiv of AdoCbl bind per homotrimer of ATR and that binding of ATP to the vacant active site triggers ejection of 1 equiv of AdoCbl from an adjacent site. In this study, we have mimicked in the Methylobacterium extorquens ATR, a C-terminal truncation mutation, D180X, described in a patient with methylmalonic aciduria, and characterized the associated biochemical penalties. We demonstrate that while k(cat) and K(M)(Cob(I)) for D180X ATR are only modestly decreased (by 3- and 2-fold, respectively), affinity for the product, AdoCbl, is significantly diminished (400-fold), and the negative cooperativity associated with its binding is lost. We also demonstrate that the D180X mutation corrupts ATP-dependent cofactor ejection, which leads to transfer of AdoCbl from wild-type ATR to MCM. These results suggest that the pathogenicity of the corresponding human truncation mutant results from its inability to sequester AdoCbl for direct transfer to MCM. Instead, cofactor release into solution is predicted to reduce the capacity for holo-MCM formation, leading to disease.
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Affiliation(s)
- Michael Lofgren
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600, USA
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Crystal structure of PduO-Type ATP:Cob(I)alamin adenosyltransferase from Bacillus cereus in a complex with ATP. Biochem Biophys Res Commun 2011; 408:417-21. [PMID: 21514283 DOI: 10.1016/j.bbrc.2011.04.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 04/07/2011] [Indexed: 11/22/2022]
Abstract
ATP:Cobalamin adenosyltransferases catalyze the transfer a 5'-deoxyadenosyl moiety from ATP to cob(I)alamin in the synthesis of the Co-C bond of coenzyme B(12). There are three types of adenosyltransferases, CobA, PduO and EutT. Among these adenosyltransferases, the PduO-type adenosyltransferases is the most widely distributed enzyme. Structural comparisons between apo BcPduO and BcPduO in complex with MgATP revealed that the N-terminal strands of both structures were ordered, which is in contrast with the most previously available PduO-type adenosyltransferase structures. Furthermore, unlike other reported structures, apo BcPduO was bound to additional dioxane molecules causing a side chain conformational change at the Tyr30 residue, which is an important residue that mediates hydrogen bonding with ATP molecules upon binding of cobalamin to the active site. This study provides more structural information into the role of active site residues on substrate binding.
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Parsons JB, Lawrence AD, McLean KJ, Munro AW, Rigby SEJ, Warren MJ. Characterisation of PduS, the pdu metabolosome corrin reductase, and evidence of substructural organisation within the bacterial microcompartment. PLoS One 2010; 5:e14009. [PMID: 21103360 PMCID: PMC2982820 DOI: 10.1371/journal.pone.0014009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 10/16/2010] [Indexed: 11/19/2022] Open
Abstract
PduS is a corrin reductase and is required for the reactivation of the cobalamin-dependent diol dehydratase. It is one component encoded within the large propanediol utilisation (pdu) operon, which is responsible for the catabolism of 1,2-propanediol within a self-assembled proteinaceous bacterial microcompartment. The enzyme is responsible for the reactivation of the cobalamin coenzyme required by the diol dehydratase. The gene for the cobalamin reductase from Citrobacter freundii (pduS) has been cloned to allow the protein to be overproduced recombinantly in E. coli with an N-terminal His-tag. Purified recombinant PduS is shown to be a flavoprotein with a non-covalently bound FMN that also contains two coupled [4Fe-4S] centres. It is an NADH-dependent flavin reductase that is able to mediate the one-electron reductions of cob(III)alamin to cob(II)alamin and cob(II)alamin to cob(I)alamin. The [4Fe-4S] centres are labile to oxygen and their presence affects the midpoint redox potential of flavin. Evidence is presented that PduS is able to bind cobalamin, which is inconsistent with the view that PduS is merely a flavin reductase. PduS is also shown to interact with one of the shell proteins of the metabolosome, PduT, which is also thought to contain an [Fe-S] cluster. PduS is shown to act as a corrin reductase and its interaction with a shell protein could allow for electron passage out of the bacterial microcompartment.
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Affiliation(s)
- Joshua B. Parsons
- Centre for Molecular Processing, School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Andrew D. Lawrence
- Centre for Molecular Processing, School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Kirsty J. McLean
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Andrew W. Munro
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Stephen E. J. Rigby
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Martin J. Warren
- Centre for Molecular Processing, School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
- * E-mail:
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Mera PE, Escalante-Semerena JC. Multiple roles of ATP:cob(I)alamin adenosyltransferases in the conversion of B12 to coenzyme B12. Appl Microbiol Biotechnol 2010; 88:41-8. [PMID: 20677021 DOI: 10.1007/s00253-010-2773-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 07/06/2010] [Accepted: 07/08/2010] [Indexed: 10/19/2022]
Abstract
Our mechanistic understanding of the conversion of vitamin B(12) into coenzyme B(12) (a.k.a. adenosylcobalamin, AdoCbl) has been substantially advanced in recent years. Insights into the multiple roles played by ATP:cob(I)alamin adenosyltransferase (ACA) enzymes have emerged through the crystallographic, spectroscopic, biochemical, and mutational analyses of wild-type and variant proteins. ACA enzymes circumvent the thermodynamic barrier posed by the very low redox potential associated with the reduction of cob(II)alamin to cob(I)alamin by generating a unique four-coordinate cob(II)alamin intermediate that is readily converted to cob(I)alamin by physiological reductants. ACA enzymes not only synthesize AdoCbl but also they deliver it to the enzymes that use it, and in some cases, enzymes in which its function is needed to maintain the fidelity of the AdoCbl delivery process have been identified. Advances in our understanding of ACA enzyme function have provided valuable insights into the role of specific residues, and into why substitutions of these residues have profound negative effects on human health. From an applied science standpoint, a better understanding of the adenosylation reaction may lead to more efficient ways of synthesizing AdoCbl.
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Affiliation(s)
- Paola E Mera
- Department of Developmental Biology, Stanford University, 279 Campus Drive, Stanford, CA 94305, USA
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Characterization of the PduS cobalamin reductase of Salmonella enterica and its role in the Pdu microcompartment. J Bacteriol 2010; 192:5071-80. [PMID: 20656910 DOI: 10.1128/jb.00575-10] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Salmonella enterica degrades 1,2-propanediol (1,2-PD) in a coenzyme B12 (adenosylcobalamin, AdoCbl)-dependent fashion. Salmonella obtains AdoCbl by assimilation of complex precursors, such as vitamin B12 and hydroxocobalamin. Assimilation of these compounds requires reduction of their central cobalt atom from Co3+ to Co2+ to Co+, followed by adenosylation to AdoCbl. In this work, the His6-tagged PduS cobalamin reductase from S. enterica was produced at high levels in Escherichia coli, purified, and characterized. The anaerobically purified enzyme reduced cob(III)alamin to cob(II)alamin at a rate of 42.3±3.2 μmol min(-1) mg(-1), and it reduced cob(II)alamin to cob(I)alamin at a rate of 54.5±4.2 nmol min(-1) mg(-1) protein. The apparent Km values of PduS-His6 were 10.1±0.7 μM for NADH and 67.5±8.2 μM for hydroxocobalamin in cob(III)alamin reduction. The apparent Km values for cob(II)alamin reduction were 27.5±2.4 μM with NADH as the substrate and 72.4±9.5 μM with cob(II)alamin as the substrate. High-performance liquid chromatography (HPLC) and mass spectrometry (MS) indicated that each monomer of PduS contained one molecule of noncovalently bound flavin mononucleotide (FMN). Genetic studies showed that a pduS deletion decreased the growth rate of Salmonella on 1,2-PD, supporting a role in cobalamin reduction in vivo. Further studies demonstrated that the PduS protein is a component of the Pdu microcompartments (MCPs) used for 1,2-PD degradation and that it interacts with the PduO adenosyltransferase, which catalyzes the terminal step of AdoCbl synthesis. These studies further characterize PduS, an unusual MCP-associated cobalamin reductase, and, in conjunction with prior results, indicate that the Pdu MCP encapsulates a complete cobalamin assimilation system.
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Randaccio L, Geremia S, Demitri N, Wuerges J. Vitamin B12: unique metalorganic compounds and the most complex vitamins. Molecules 2010; 15:3228-59. [PMID: 20657474 PMCID: PMC6257451 DOI: 10.3390/molecules15053228] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 04/27/2010] [Accepted: 04/28/2010] [Indexed: 11/16/2022] Open
Abstract
The chemistry and biochemistry of the vitamin B(12) compounds (cobalamins, XCbl) are described, with particular emphasis on their structural aspects and their relationships with properties and function. A brief history of B(12), reveals how much the effort of chemists, biochemists and crystallographers have contributed in the past to understand the basic properties of this very complex vitamin. The properties of the two cobalamins, the two important B(12) cofactors Ado- and MeCbl are described, with particular emphasis on how the Co-C bond cleavage is involved in the enzymatic mechanisms. The main structural features of cobalamins are described, with particular reference to the axial fragment. The structure/property relationships in cobalamins are summarized. The recent studies on base-off/base-on equilibrium are emphasized for their relevance to the mode of binding of the cofactor to the protein scaffold. The absorption, transport and cellular uptake of cobalamins and the structure of the B(12) transport proteins, IF and TC, in mammals are reviewed. The B(12) transport in bacteria and the structure of the so far determined proteins are briefly described. The currently accepted mechanisms for the catalytic cycles of the AdoCbl and MeCbl enzymes are reported. The structure and function of B(12) enzymes, particularly the important mammalian enzymes methyltransferase (MetH) and methyl-malonyl-coenzyme A mutase (MMCM), are described and briefly discussed. Since fast proliferating cells require higher amount of vitamin B(12) than that required by normal cells, the study of B(12 )conjugates as targeting agents has recently gained importance. Bioconjugates have been studied as potential agents for delivering radioisotopes and NMR probes or as various cytotoxic agents towards cancer cells in humans and the most recent studies are described. Specifically, functionalized bioconjugates are used as "Trojan horses" to carry into the cell the appropriate antitumour or diagnostic label. Possible future developments of B(12) work are summarized.
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Affiliation(s)
- Lucio Randaccio
- Centre of Excellence in Biocrystallography, Department of Chemical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy.
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Mera PE, Escalante-Semerena JC. Dihydroflavin-driven adenosylation of 4-coordinate Co(II) corrinoids: are cobalamin reductases enzymes or electron transfer proteins? J Biol Chem 2009; 285:2911-7. [PMID: 19933577 DOI: 10.1074/jbc.m109.059485] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The identity of the source of the biological reductant needed to convert cobalamin to its biologically active form adenosylcobalamin has remained elusive. Here we show that free or protein-bound dihydroflavins can serve as the reductant of Co(2+)Cbl bound in the active site of PduO-type ATP-dependent corrinoid adenosyltransferase enzymes. Free dihydroflavins (dihydroriboflavin, FMNH(2), and FADH(2)) effectively drove the adenosylation of Co(2+)Cbl by the human and bacterial PduO-type enzymes at very low concentrations (1 microm). These data show that adenosyltransferase enzymes lower the thermodynamic barrier of the Co(2+) --> Co(+) reduction needed for the formation of the unique organometalic Co-C bond of adenosylcobalamin. Collectively, our in vivo and in vitro data suggest that cobalamin reductases identified thus far are most likely electron transfer proteins, not enzymes.
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Affiliation(s)
- Paola E Mera
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53726-1521, USA
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Padovani D, Banerjee R. A rotary mechanism for coenzyme B(12) synthesis by adenosyltransferase. Biochemistry 2009; 48:5350-7. [PMID: 19413290 DOI: 10.1021/bi900454s] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenosyltransferases (ATRs) catalyze the synthesis of the reactive cobalt-carbon bond found in coenzyme B(12) or 5'-deoxyadenosylcobalamin (AdoCbl), which serves as a cofactor for a number of isomerases. The reaction involves a reductive adenosylation of cob(II)alamin in which an electron delivered by a reductase reduces cob(II)alamin to cob(I)alamin, which attacks the 5'-carbon of ATP to form AdoCbl and inorganic triphosphate. Of the three classes of ATRs found in nature, the PduO type, which is also the only one found in mammals, is the most extensively studied. The crystal structures of a number of PduO-type ATRs are available and reveal a trimeric organization with the active sites located at the subunit interfaces. We have previously demonstrated that the ATR from Methylobacterium extorquens, which supports methylmalonyl-CoA mutase activity, serves dual functions; i.e., it tailors the active AdoCbl form of the cofactor and then transfers it directly to the dependent mutase (Padovani et al. (2008) Nat. Chem. Biol. 4, 194). Only two of the three active sites in ATR are simultaneously occupied by AdoCbl. In this study, we demonstrate that binding of the substrate ATP to ATR that is fully loaded with AdoCbl leads to the ejection of 1 equivalent of the cofactor into solution. In the presence of methylmalonyl-CoA mutase and ATP, AdoCbl is transferred from ATR to the acceptor protein in a process that exhibits an approximately 3.5-fold lower K(act) for ATP compared to the one in which cofactor is released into solution. Furthermore, ATP favorably influences cofactor transfer in the forward direction by reducing the ratio of apo-methylmalonyl-CoA mutase/holo-ATR required for delivery of 1 equivalent of AdoCbl, from 4 to 1. These results lead us to propose a rotary mechanism for ATR function in which, at any given time, only two of its active sites are used for AdoCbl synthesis and where binding of ATP to the vacant site leads to the transfer of the high value AdoCbl product to the acceptor mutase.
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Affiliation(s)
- Dominique Padovani
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-5606, USA
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Liptak MD, Fleischhacker AS, Matthews RG, Telser J, Brunold TC. Spectroscopic and computational characterization of the base-off forms of cob(II)alamin. J Phys Chem B 2009; 113:5245-54. [PMID: 19298066 DOI: 10.1021/jp810136d] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The one-electron-reduced form of vitamin B(12), cob(II)alamin (Co(2+)Cbl), is found in several essential human enzymes, including the cobalamin-dependent methionine synthase (MetH). In this work, experimentally validated electronic structure descriptions for two "base-off" Co(2+)Cbl species have been generated using a combined spectroscopic and computational approach, so as to obtain definitive clues as to how these and related enzymes catalyze the thermodynamically challenging reduction of Co(2+)Cbl to cob(I)alamin (Co(1+)Cbl). Specifically, electron paramagnetic resonance (EPR), electronic absorption (Abs), and magnetic circular dichroism (MCD) spectroscopic techniques have been employed as complementary tools to characterize the two distinct forms of base-off Co(2+)Cbl that can be trapped in the H759G variant of MetH, one containing a five-coordinate and the other containing a four-coordinate, square-planar Co(2+) center. Accurate spin Hamiltonian parameters for these low-spin Co(2+) centers have been determined by collecting EPR data using both X- and Q-band microwave frequencies, and Abs and MCD spectroscopic techniques have been employed to probe the corrin-centered pi --> pi* and Co-based d --> d excitations, respectively. By using these spectroscopic data to evaluate electronic structure calculations, we found that density functional theory provides a reasonable electronic structure description for the five-coordinate form of base-off Co(2+)Cbl. However, it was necessary to resort to a multireference ab initio treatment to generate a more realistic description of the electronic structure of the four-coordinate form. Consistent with this finding, our computational data indicate that, in the five-coordinate Co(2+)Cbl species, the unpaired spin density is primarily localized in the Co 3d(z(2))-based molecular orbital, as expected, whereas in the four-coordinate form, extensive Co 3d orbital mixing, configuration interaction, and spin-orbit coupling cause the unpaired electron to delocalize over several Co 3d orbitals. These results provide important clues to the mechanism of enzymatic Co(2+)Cbl --> Co(1+)Cbl reduction.
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Affiliation(s)
- Matthew D Liptak
- Department of Chemistry, University of Wisconsin-Madison, Madison Wisconsin 53706, USA
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Mera PE, St Maurice M, Rayment I, Escalante-Semerena JC. Residue Phe112 of the human-type corrinoid adenosyltransferase (PduO) enzyme of Lactobacillus reuteri is critical to the formation of the four-coordinate Co(II) corrinoid substrate and to the activity of the enzyme. Biochemistry 2009; 48:3138-45. [PMID: 19236001 DOI: 10.1021/bi9000134] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ATP:Corrinoid adenosyltransferases (ACAs) catalyze the transfer of the adenosyl moiety from ATP to cob(I)alamin via a four-coordinate cob(II)alamin intermediate. At present, it is unknown how ACAs promote the formation of the four-coordinate corrinoid species needed for activity. The published high-resolution crystal structure of the ACA from Lactobacillus reuteri (LrPduO) in complex with ATP and cob(II)alamin shows that the environment around the alpha face of the corrin ring consists of bulky hydrophobic residues. To understand how these residues promote the generation of the four-coordinate cob(II)alamin, variants of the human-type ACA enzyme from L. reuteri (LrPduO) were kinetically and structurally characterized. These studies revealed that residue Phe112 is critical in the displacement of 5,6-dimethylbenzimidazole (DMB) from its coordination bond with the Co ion of the ring, resulting in the formation of the four-coordinate species. An F112A substitution resulted in a 80% drop in the catalytic efficiency of the enzyme. The explanation for this loss of activity was obtained from the crystal structure of the mutant protein, which showed cob(II)alamin bound in the active site with DMB coordinated to the cobalt ion. The crystal structure of an LrPduO(F112H) variant showed a DMB-off/His-on interaction between the corrinoid and the enzyme, whose catalytic efficiency was 4 orders of magnitude lower than that of the wild-type protein. The analysis of the kinetic parameters of LrPduO(F112H) suggests that the F112H substitution negatively impacts product release. Substitutions of other hydrophobic residues in the Cbl binding pocket did not result in significant defects in catalytic efficiency in vitro; however, none of the variant enzymes analyzed in this work supported AdoCbl biosynthesis in vivo.
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Affiliation(s)
- Paola E Mera
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
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Moutevelis E, Woolfson DN. A Periodic Table of Coiled-Coil Protein Structures. J Mol Biol 2009; 385:726-32. [PMID: 19059267 DOI: 10.1016/j.jmb.2008.11.028] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 11/15/2008] [Accepted: 11/18/2008] [Indexed: 10/21/2022]
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Park K, Mera PE, Escalante-Semerena JC, Brunold TC. Kinetic and spectroscopic studies of the ATP:corrinoid adenosyltransferase PduO from Lactobacillus reuteri: substrate specificity and insights into the mechanism of Co(II)corrinoid reduction. Biochemistry 2008; 47:9007-15. [PMID: 18672897 DOI: 10.1021/bi800419e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri ( LrPduO) catalyzes the formation of the essential Co-C bond of adenosylcobalamin (coenzyme B 12) by transferring the adenosyl group from cosubstrate ATP to a transient Co (1+)corrinoid species generated in the enzyme active site. While PduO-type enzymes have previously been believed to be capable of adenosylating only Co (1+)cobalamin (Co (1+)Cbl (-)), our kinetic data obtained in this study provide in vitro evidence that LrPduO can in fact also utilize the incomplete corrinoid Co (1+)cobinamide (Co (1+)Cbi) as an alternative substrate. To explore the mechanism by which LrPduO overcomes the thermodynamically challenging reduction of its Co (2+)corrinoid substrates, we have examined how the enzyme active site alters the geometric and electronic properties of Co (2+)Cbl and Co (2+)Cbi (+) by using electronic absorption, magnetic circular dichroism, and electron paramagnetic resonance spectroscopic techniques. Our data reveal that upon binding to LrPduO that was preincubated with ATP, both Co (2+)corrinoids undergo a partial ( approximately 40-50%) conversion to distinct paramagnetic Co (2+) species. The spectroscopic signatures of these species are consistent with essentially four-coordinate, square-planar Co (2+) complexes, based on a comparison with the results obtained in our previous studies of related enzymes. Consequently, it appears that the general strategy employed by adenosyltransferases for effecting Co (2+) --> Co (1+) reduction involves the formation of an "activated" Co (2+)corrinoid intermediate that lacks any significant axial bonding interactions, to stabilize the redox-active, Co 3d z (2) -based molecular orbital.
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Affiliation(s)
- Kiyoung Park
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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