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An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis.

Deery E, Schroeder S, Lawrence AD, Taylor SL, Seyedarabi A, Waterman J, Wilson KS, Brown D, Geeves MA, Howard MJ, Pickersgill RW, Warren MJ
Nat Chem Biol 8 933-40 (2012)
Related entries: 4au1, 4fdv

Cited: 36 times
EuropePMC logo PMID: 23042036

Abstract

The biosynthesis of many vitamins and coenzymes has often proven difficult to elucidate owing to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B(12)) pathway in Escherichia coli and by His tagging the terminal enzyme in the reaction sequence, we have observed that many unstable intermediates can be isolated as tightly bound enzyme-product complexes. Together, these approaches have been used to extract intermediates between precorrin-4 and hydrogenobyrinic acid in their free acid form and permitted the delineation of the overall reaction catalyzed by CobL, including the formal elucidation of precorrin-7 as a metabolite. Furthermore, a substrate-carrier protein, CobE, that can also be used to stabilize some of the transient metabolic intermediates and enhance their onward transformation, has been identified. The tight association of pathway intermediates with enzymes provides evidence for a form of metabolite channeling.

Articles - 3njr mentioned but not cited (2)

  1. An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis. Deery E, Schroeder S, Lawrence AD, Taylor SL, Seyedarabi A, Waterman J, Wilson KS, Brown D, Geeves MA, Howard MJ, Pickersgill RW, Warren MJ. Nat Chem Biol 8 933-940 (2012)
  2. Crystal structure of putative CbiT from Methanocaldococcus jannaschii: an intermediate enzyme activity in cobalamin (vitamin B12) biosynthesis. Padmanabhan B, Yokoyama S, Bessho Y. BMC Struct Biol 13 10 (2013)


Reviews citing this publication (7)

  1. Microbial production of vitamin B12: a review and future perspectives. Fang H, Kang J, Zhang D. Microb Cell Fact 16 15 (2017)
  2. Biosynthesis of the modified tetrapyrroles-the pigments of life. Bryant DA, Hunter CN, Warren MJ. J Biol Chem 295 6888-6925 (2020)
  3. Sharing vitamins: Cobamides unveil microbial interactions. Sokolovskaya OM, Shelton AN, Taga ME. Science 369 eaba0165 (2020)
  4. A New Facet of Vitamin B12: Gene Regulation by Cobalamin-Based Photoreceptors. Padmanabhan S, Jost M, Drennan CL, Elías-Arnanz M. Annu Rev Biochem 86 485-514 (2017)
  5. Vitamin B(12) metabolism in Mycobacterium tuberculosis. Gopinath K, Moosa A, Mizrahi V, Warner DF. Future Microbiol 8 1405-1418 (2013)
  6. Antivitamins for Medicinal Applications. Zelder F, Sonnay M, Prieto L. Chembiochem 16 1264-1278 (2015)
  7. The mitochondrial heme metabolon: Insights into the complex(ity) of heme synthesis and distribution. Piel RB, Dailey HA, Medlock AE. Mol Genet Metab 128 198-203 (2019)

Articles citing this publication (27)

  1. Identification of the Mitochondrial Heme Metabolism Complex. Medlock AE, Shiferaw MT, Marcero JR, Vashisht AA, Wohlschlegel JA, Phillips JD, Dailey HA. PLoS One 10 e0135896 (2015)
  2. The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Zheng K, Ngo PD, Owens VL, Yang XP, Mansoorabadi SO. Science 354 339-342 (2016)
  3. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12). Moore SJ, Lawrence AD, Biedendieck R, Deery E, Frank S, Howard MJ, Rigby SE, Warren MJ. Proc Natl Acad Sci U S A 110 14906-14911 (2013)
  4. Elucidation of the biosynthesis of the methane catalyst coenzyme F430. Moore SJ, Sowa ST, Schuchardt C, Deery E, Lawrence AD, Ramos JV, Billig S, Birkemeyer C, Chivers PT, Howard MJ, Rigby SE, Layer G, Warren MJ. Nature 543 78-82 (2017)
  5. Metabolic engineering of Escherichia coli for de novo biosynthesis of vitamin B12. Fang H, Li D, Kang J, Jiang P, Sun J, Zhang D. Nat Commun 9 4917 (2018)
  6. Recent advances in the biosynthesis of modified tetrapyrroles: the discovery of an alternative pathway for the formation of heme and heme d 1. Bali S, Palmer DJ, Schroeder S, Ferguson SJ, Warren MJ. Cell Mol Life Sci 71 2837-2863 (2014)
  7. Towards a cell factory for vitamin B12 production in Bacillus megaterium: bypassing of the cobalamin riboswitch control elements. Moore SJ, Mayer MJ, Biedendieck R, Deery E, Warren MJ. N Biotechnol 31 553-561 (2014)
  8. Calculating metalation in cells reveals CobW acquires CoII for vitamin B12 biosynthesis while related proteins prefer ZnII. Young TR, Martini MA, Foster AW, Glasfeld A, Osman D, Morton RJ, Deery E, Warren MJ, Robinson NJ. Nat Commun 12 1195 (2021)
  9. Biosynthesis of t-Butyl in Apratoxin A: Functional Analysis and Architecture of a PKS Loading Module. Skiba MA, Sikkema AP, Moss NA, Lowell AN, Su M, Sturgis RM, Gerwick L, Gerwick WH, Sherman DH, Smith JL. ACS Chem Biol 13 1640-1650 (2018)
  10. Total Synthesis, Structure, and Biological Activity of Adenosylrhodibalamin, the Non-Natural Rhodium Homologue of Coenzyme B12. Widner FJ, Lawrence AD, Deery E, Heldt D, Frank S, Gruber K, Wurst K, Warren MJ, Kräutler B. Angew Chem Int Ed Engl 55 11281-11286 (2016)
  11. Construction of Fluorescent Analogs to Follow the Uptake and Distribution of Cobalamin (Vitamin B12) in Bacteria, Worms, and Plants. Lawrence AD, Nemoto-Smith E, Deery E, Baker JA, Schroeder S, Brown DG, Tullet JMA, Howard MJ, Brown IR, Smith AG, Boshoff HI, Barry CE, Warren MJ. Cell Chem Biol 25 941-951.e6 (2018)
  12. Zinc Substitution of Cobalt in Vitamin B12 : Zincobyric acid and Zincobalamin as Luminescent Structural B12 -Mimics. Kieninger C, Baker JA, Podewitz M, Wurst K, Jockusch S, Lawrence AD, Deery E, Gruber K, Liedl KR, Warren MJ, Kräutler B. Angew Chem Int Ed Engl 58 14568-14572 (2019)
  13. Characterization of unstable products of flavin- and pterin-dependent enzymes by continuous-flow mass spectrometry. Roberts KM, Tormos JR, Fitzpatrick PF. Biochemistry 53 2672-2679 (2014)
  14. Co(ll)-detection does not follow Kco(ll) gradient: channelling in Co(ll)-sensing. Patterson CJ, Pernil R, Dainty SJ, Chakrabarti B, Henry CE, Money VA, Foster AW, Robinson NJ. Metallomics 5 352-362 (2013)
  15. The Hydrogenobyric Acid Structure Reveals the Corrin Ligand as an Entatic State Module Empowering B12 Cofactors for Catalysis. 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. Angew Chem Int Ed Engl 58 10756-10760 (2019)
  16. The Organocatalytic Approach to Enantiopure 2H- and 3H-Pyrroles: Inhibitors of the Hedgehog Signaling Pathway. Kötzner L, Leutzsch M, Sievers S, Patil S, Waldmann H, Zheng Y, Thiel W, List B. Angew Chem Int Ed Engl 55 7693-7697 (2016)
  17. Replacement of the Cobalt Center of Vitamin B12 by Nickel: Nibalamin and Nibyric Acid Prepared from Metal-Free B12  Ligands Hydrogenobalamin and Hydrogenobyric Acid. Kieninger C, Wurst K, Podewitz M, Stanley M, Deery E, Lawrence AD, Liedl KR, Warren MJ, Kräutler B. Angew Chem Int Ed Engl 59 20129-20136 (2020)
  18. The structure, function and properties of sirohaem decarboxylase--an enzyme with structural homology to a transcription factor family that is part of the alternative haem biosynthesis pathway. Palmer DJ, Schroeder S, Lawrence AD, Deery E, Lobo SA, Saraiva LM, McLean KJ, Munro AW, Ferguson SJ, Pickersgill RW, Brown DG, Warren MJ. Mol Microbiol 93 247-261 (2014)
  19. The Radical SAM enzyme NirJ catalyzes the removal of two propionate side chains during heme d1 biosynthesis. Boss L, Oehme R, Billig S, Birkemeyer C, Layer G. FEBS J 284 4314-4327 (2017)
  20. Exploring the onset of B12 -based mutualisms using a recently evolved Chlamydomonas auxotroph and B12 -producing bacteria. Bunbury F, Deery E, Sayer AP, Bhardwaj V, Harrison EL, Warren MJ, Smith AG. Environ Microbiol 24 3134-3147 (2022)
  21. A Light-Activated Acyl Carrier Protein "Trap" for Intermediate Capture in Type II Iterative Polyketide Biocatalysis. Kilgour SL, Kilgour DPA, Prasongpholchai P, O'Connor PB, Tosin M. Chemistry 25 16515-16518 (2019)
  22. Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap. Gu S, Sushko O, Deery E, Warren MJ, Pickersgill RW. Sci Rep 5 16943 (2015)
  23. Metabonomic Characteristics of Myocardial Diastolic Dysfunction in Type 2 Diabetic Cardiomyopathy Patients. Hao M, Deng J, Huang X, Li H, Ou H, Cai X, She J, Liu X, Chen L, Chen S, Liu W, Yan D. Front Physiol 13 863347 (2022)
  24. A synthetic cell-free 36-enzyme reaction system for vitamin B12 production. Kang Q, Fang H, Xiang M, Xiao K, Jiang P, You C, Lee SY, Zhang D. Nat Commun 14 5177 (2023)
  25. Biosynthesis of Tetrapyrrole Cofactors by Bacterial Community Inhabiting Porphyrine-Containing Shale Rock (Fore-Sudetic Monocline). Stasiuk R, Krucoń T, Matlakowska R. Molecules 26 6746 (2021)
  26. Optimization of hydrogenobyrinic acid biosynthesis in Escherichia coli using multi-level metabolic engineering strategies. Jiang P, Fang H, Zhao J, Dong H, Jin Z, Zhang D. Microb Cell Fact 19 118 (2020)
  27. Structure of full-length cobalamin-dependent methionine synthase and cofactor loading captured in crystallo. Mendoza J, Purchal M, Yamada K, Koutmos M. Nat Commun 14 6365 (2023)


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