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Usai R, Kaluka D, Cai S, Sem DS, Kincaid JR. Solution phase refinement of active site structure using 2D NMR and judiciously 13C-labeled cytochrome P450. J Inorg Biochem 2023; 241:112126. [PMID: 36682280 PMCID: PMC10725731 DOI: 10.1016/j.jinorgbio.2023.112126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
The Cytochrome P450 (CYP450) superfamily has been the subject of intense research for over six decades. Here the HU227 strain of E. coli, lacking the δ-aminolevulinic acid (δ-ALA) synthase gene, was employed, along with [5-13C] δ-ALA, in the heterologous expression of P450cam harboring a prosthetic group labeled with 13C at the four methine carbons (Cm) and pyrrole Cα positions. The product was utilized as a proof of principle strategy for defining and refining solution phase active site structure in cytochrome P450cam, providing proton-to-proton distances from 13CmH to protons on bound substrate or nearby amino acid residues, using short mixing time 2D or 3D NOESY-HMQC methods. The results reveal the interesting finding that 2D 13C-filtered NOESY-HMQC can be used to obtain distances between protons on labeled 13C to positions of protons nearby in the active site, confirming the utility of this NMR-based approach to probing active site structure under physiological conditions. Such 13C-heme-filtered NOE data complement X-ray crystallographic and T1-based NMR measurements; and, may also be of potentially significant utility in furnishing experimental distance constraints in validations of docking routines commonly employed for determining the relative affinities and binding orientations of drug candidates with CYP450s.
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Affiliation(s)
- Remigio Usai
- Department of Chemistry, Marquette University, Wisconsin 53233, United States
| | - Daniel Kaluka
- Department of Chemistry and Biochemistry, Taylor University, Upland, IN 46989, United States
| | - Sheng Cai
- School of Pharmacy, University of Wisconsin Madison, Madison, Wisconsin 53705, United States
| | - Daniel S. Sem
- Department of Pharmaceutical Sciences, Concordia University of Wisconsin, Mequon, WI, 53097, United States
| | - James R. Kincaid
- Department of Chemistry, Marquette University, Wisconsin 53233, United States
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Iida K, Nakamura M, Hanamitsu H, Kajiwara M. Identification of tetrapyrrole compounds excreted by Rhodobacter sphaeroides and sources of the methyl hydrogens of bacteriochlorophyll a biosynthesized by R. sphaeroides, based on 13C-NMR spectral analysis of coproporphyrin III tetramethyl ester. Chem Pharm Bull (Tokyo) 2007; 55:1067-9. [PMID: 17603203 DOI: 10.1248/cpb.55.1067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Red-fluorescent tetrapyrrole compounds excreted by Rhodobacter sphaeroides into the culture broth were concluded to be coproporphyrinogen (Copro'gen) III and uroporphyrinogen (Uro'gen) I, based on the (13)C-NMR spectral identification of coproporphyrin (Copro) III tetramethyl ester and uroproporphyrin (Uro) I octamethyl ester. The sources of the methyl hydrogens of bacteriochlorophyll a were established by analysis of the (13)C-NMR spectra of (2)H,(13)C-Copro III tetramethyl ester chemically derived from (2)H,(13)C-Copro'gen III biosynthesized through the feeding of delta-amino[2-(13)C]levulinic acid (ALA) to R. sphaeroides in medium containing 50% (2)H(2)O. We confirmed the previous finding that one of the methyl hydrogens was derived from water in the medium during decarboxylation of four acetyl side chains of Uro'gen III to generate Copro'gen III. It was further shown that the other hydrogen atoms, previously reported to be derived from methylene hydrogens at C-2 of ALA, had been exchanged with hydrogen of water in the medium in the biosynthetic pathways leading from ALA to Copro'gen III.
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Affiliation(s)
- Katsumi Iida
- Department of Medicinal Chemistry, Meiji Pharmaceutical University, Noshio, Kiyose, Tokyo, Japan.
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3
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Thamyongkit P, Muresan AZ, Diers JR, Holten D, Bocian DF, Lindsey JS. Meso-13C-Labeled Porphyrins for Studies of Ground-State Hole Transfer in Multiporphyrin Arrays. J Org Chem 2007; 72:5207-17. [PMID: 17579453 DOI: 10.1021/jo070593x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding electronic communication among interacting chromophores provides the foundation for a variety of applications. The ground-state electronic communication in diphenylethyne-linked zinc-porphyrin dyads has been investigated by a novel molecular design strategy that entails introduction of a 13C-atom (*) at specific sites of the porphyrins where there is substantial electron density in the relevant frontier (highest occupied) molecular orbital. The site of 13C substitution is at a meso-position, either the site of attachment of the linker (proximal, "P") or the site trans to the linker (distal, "D"). The substituents (R) at the non-linking meso-positions are mesityl, tridec-7-yl ("swallowtail"), or p-tolyl groups. Altogether five isotopically labeled porphyrin dyads have been prepared. The hole/electron-transfer properties of one-electron oxidized dyads have been examined by electron paramagnetic resonance (EPR) spectroscopy. The introduction of the meso-13C label provides a "clock" (via the hyperfine interactions) that allows investigation of a time scale for hole transfer that is 3-4 times shorter than that provided by the natural abundance 14N nuclei of the pyrrole nitrogen atoms. The EPR studies indicate that the hole transfer, which has been previously shown to be fast on the time scale of the 14N hyperfine clock ( approximately 220 ns), remains fast on the time scale of the 13C hyperfine clock ( approximately 50 ns).
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Affiliation(s)
- Patchanita Thamyongkit
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
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Iida K, Ohtaka K, Kajiwara M. Mechanism of the ring contraction process in vitamin B12 biosynthesis by the anaerobe Propionibacterium shermanii under aerobic conditions. FEBS J 2007; 274:3475-81. [PMID: 17561959 DOI: 10.1111/j.1742-4658.2007.05880.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of the ring contraction process during vitamin B(12) biosynthesis by the anaerobe Propionibacterium shermanii was investigated under both aerobic and anaerobic conditions by means of feeding experiments with delta-amino[1-(13)C]levulinic acid (a biosynthetic intermediate of tetrapyrrole) and delta-amino[1-(13)C,1,1,4-(18)O(3)]levulinic acid in combination with (13)C-NMR spectroscopy. We showed that the characteristic mechanism of the ring contraction process (the generation of precorrin-3x from formation of the gamma-lactone from the ring A acetate group at C1 and hydroxylation at C20 by molecular oxygen catalyzed by CobG, and the migration of ring D by cleavage of the carbon-oxygen bond at C1 of precorrin-3x) in the aerobe Pseudomonas denitrificans was not seen in P. shermanii under aerobic conditions, and the mechanism of the ring contraction process in P. shermanii was the same irrespective of the presence or absence of oxygen.
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Affiliation(s)
- Katsumi Iida
- Department of Medicinal Chemistry, Meiji Pharmaceutical University, Kiyose-shi, Tokyo, Japan.
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Iida K, Ohtaka K, Kajiwara M. Synthesis of 1-[15N]amino-2-propanol hydrochloride. J Labelled Comp Radiopharm 2007. [DOI: 10.1002/jlcr.1291] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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6
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Iida K, Kajiwara M. Synthesis of optically pure 13C-labelled propionate from alanine by asymmetric hydrolysis using porcine kidney acylase. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580290210] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Cambell JB, Johnston JS. A short synthesis of 5-amino[4-14]laevulinic acid hydrochloride. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580271202] [Citation(s) in RCA: 5] [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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Iida K, Uegaki R, Kajiwara M. Simple synthesis of multiply labelled sodium propionate. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580340712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Takatori K, Sakamoto T, Kajiwara M. Asymmetric synthesis ofL-[4-13C]glutamic acid and glutamine. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.1055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Abstract
3-Amino-1-hydroxypropan-2-one (3-amino-1-hydroxyacetone) was prepared in an overall yield of 52% in 6 steps starting with N-phthaloylglycine. This synthesis is readily adaptable for the preparation of bond-labeled samples, i.e., samples that are labeled intramolecularly at contiguous sites.Key words: 3-amino-1-hydroxyacetone, 3-amino-1-hydroxypropan-2-one.
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Iida K, Tokiwa S, Ishii T, Kajiwara M. Synthesis of 5-[4,5-13C2]- and 5-[1,5-13C2]aminolevulinic acid. J Labelled Comp Radiopharm 2002. [DOI: 10.1002/jlcr.583] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Iida K, Chiyoda T, Kajiwara M. Concomitant oxygen‐18 enrichment in commercial carbon‐13 labelled urea. J Labelled Comp Radiopharm 1998. [DOI: 10.1002/(sici)1099-1344(199612)38:12<1133::aid-jlcr935>3.0.co;2-#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Katsumi Iida
- Department of Medicinal Chemistry, Meiji College of Pharmacy, 1‐22‐1 Yato‐cho, Tanashi‐shi, Tokyo 188, Japan
| | - Takeshi Chiyoda
- Department of Medicinal Chemistry, Meiji College of Pharmacy, 1‐22‐1 Yato‐cho, Tanashi‐shi, Tokyo 188, Japan
| | - Masahiro Kajiwara
- Department of Medicinal Chemistry, Meiji College of Pharmacy, 1‐22‐1 Yato‐cho, Tanashi‐shi, Tokyo 188, Japan
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Iida K, Kajiwara M. Synthesis of p-Di[1-13C]ethoxybenzene from [1-13C]iodoethane with high labeling efficiency. J Labelled Comp Radiopharm 1998. [DOI: 10.1002/(sici)1099-1344(199803)41:3<235::aid-jlcr72>3.0.co;2-f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Iida K, Chiyoda T, Hirasawa R, Iwata A, Kajiwara M. Synthesis of
13
C‐labelled compounds having a urea unit, and observation of
13
C‐isotope effect in their infrared spectra. J Labelled Comp Radiopharm 1997. [DOI: 10.1002/(sici)1099-1344(199701)39:1<69::aid-jlcr941>3.0.co;2-#] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Katsumi Iida
- Department of Medicinal Chemistry, Meiji College of Pharmacy, 1‐22‐1 Yato‐cho, Tanashi‐shi, Tokyo 188, Japan
| | - Takeshi Chiyoda
- Department of Medicinal Chemistry, Meiji College of Pharmacy, 1‐22‐1 Yato‐cho, Tanashi‐shi, Tokyo 188, Japan
| | - Ryo Hirasawa
- Department of Medicinal Chemistry, Meiji College of Pharmacy, 1‐22‐1 Yato‐cho, Tanashi‐shi, Tokyo 188, Japan
| | - Akiko Iwata
- Department of Medicinal Chemistry, Meiji College of Pharmacy, 1‐22‐1 Yato‐cho, Tanashi‐shi, Tokyo 188, Japan
| | - Masahiro Kajiwara
- Department of Medicinal Chemistry, Meiji College of Pharmacy, 1‐22‐1 Yato‐cho, Tanashi‐shi, Tokyo 188, Japan
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Stolowich NJ, Wang J, Spencer JB, Santander PJ, Roessner CA, Scott AI. Absolute Stereochemistry of Precorrin-3x and Its Relevance to the Dichotomy of Ring Contraction Mechanism in Vitamin B12 Biosynthesis. J Am Chem Soc 1996. [DOI: 10.1021/ja952739s] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Neal J. Stolowich
- Contribution from the Center for Biological NMR, Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| | - Jianji Wang
- Contribution from the Center for Biological NMR, Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| | - Jonathan B. Spencer
- Contribution from the Center for Biological NMR, Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| | - Patricio J. Santander
- Contribution from the Center for Biological NMR, Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| | - Charles A. Roessner
- Contribution from the Center for Biological NMR, Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| | - A. Ian Scott
- Contribution from the Center for Biological NMR, Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
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Ragnarsson U. Proteinogenic amino acids labelled with 15N and/or 13C for application in peptide synthesis: a short review with a comprehensive list of published derivatives. J Pept Sci 1995; 1:149-56. [PMID: 9222992 DOI: 10.1002/psc.310010302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A review is given of the literature dealing with the most common protected derivatives of 15N- and/or 13C-labelled amino acids of interest in peptide synthesis. The list contains all such Boc-, Z- and Fmoc-amino acids as well as published methyl, ethyl, t-butyl and benzyl esters.
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Affiliation(s)
- U Ragnarsson
- Department of Biochemistry, University of Uppsala, Biomedical Center, Sweden
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22
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Sattler I, Roessner CA, Stolowich NJ, Hardin SH, Harris-Haller LW, Yokubaitis NT, Murooka Y, Hashimoto Y, Scott AI. Cloning, sequencing, and expression of the uroporphyrinogen III methyltransferase cobA gene of Propionibacterium freudenreichii (shermanii). J Bacteriol 1995; 177:1564-9. [PMID: 7883713 PMCID: PMC176773 DOI: 10.1128/jb.177.6.1564-1569.1995] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We cloned, sequenced, and overexpressed cobA, the gene encoding uroporphyrinogen III methyltransferase in Propionibacterium freudenreichii, and examined the catalytic properties of the enzyme. The methyltransferase is similar in mass (27 kDa) and homologous to the one isolated from Pseudomonas denitrificans. In contrast to the much larger isoenzyme encoded by the cysG gene of Escherichia coli (52 kDa), the P. freudenreichii enzyme does not contain the additional 22-kDa peptide moiety at its N-terminal end bearing the oxidase-ferrochelatase activity responsible for the conversion of dihydrosirohydrochlorin (precorrin-2) to siroheme. Since it does not contain this moiety, it is not a likely candidate for synthesis of a cobalt-containing early intermediate that has been proposed for the vitamin B12 biosynthetic pathway in P. freudenreichii. Uroporphyrinogen III methyltransferase of P. freudenreichii not only catalyzes the addition of two methyl groups to uroporphyrinogen III to afford the early vitamin B12 intermediate, precorrin-2, but also has an overmethylation property that catalyzes the synthesis of several tri- and tetra-methylated compounds that are not part of the vitamin B12 pathway. The enzyme catalyzes the addition of three methyl groups to uroporphyrinogen I to form trimethylpyrrocorphin, the intermediate necessary for biosynthesis of the natural products, factors S1 and S3, previously isolated from this organism. A second gene found upstream from the cobA gene encodes a protein homologous to CbiO of Salmonella typhimurium, a membrane-bound, ATP-dependent transport protein thought to be part of the cobalt transport system involved in vitamin B12 synthesis. These two genes do not appear to constitute part of an extensive cobalamin operon.
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Affiliation(s)
- I Sattler
- Center for Biological NMR, Chemistry Department, Texas A&M University, College Station 77843
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23
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Kajiwara M, Mizutani M, Matsuda R, Hara KI, Kojima I. A new biosynthetic pathway of porphyrins from isopropanol. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/0922-338x(94)90144-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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24
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Roessner CA, Warren MJ, Santander PJ, Atshaves BP, Ozaki S, Stolowich NJ, Iida K, Scott AI. Expression of 9 Salmonella typhimurium enzymes for cobinamide synthesis. Identification of the 11-methyl and 20-methyl transferases of corrin biosynthesis. FEBS Lett 1992; 301:73-8. [PMID: 1451790 DOI: 10.1016/0014-5793(92)80213-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nine of the cbi genes from the 17.5 kb cob operon of Salmonella typhimurium previously shown by genetic studies to be involved in the biosynthesis of cobinamide from precorrin-2, have been subcloned and expressed in Escherichia coli. Seven of the gene products were found in the soluble fraction of cell lysates and have been purified. The gene products corresponding to cbi E, F, H and L were shown by SAM binding and by homology with other SAM-binding proteins to be candidates for the methyltransferases of vitamin B12 biosynthesis. The enzymatic functions of the gene products of cbiL and cbiF are associated with C-methylation at C-20 of precorrin-2 and C-11 of precorrin-3.
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Affiliation(s)
- C A Roessner
- Department of Chemistry, Texas A&M University, College Station 77843-3255
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25
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Warren MJ, Roessner CA, Ozaki S, Stolowich NJ, Santander PJ, Scott AI. Enzymatic synthesis and structure of precorrin-3, a trimethyldipyrrocorphin intermediate in vitamin B12 biosynthesis. Biochemistry 1992; 31:603-9. [PMID: 1731915 DOI: 10.1021/bi00117a043] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The trimethylated intermediate of vitamin B12 (corrin) biosynthesis, precorrin-3, was produced from various 13C-enriched isotopomers of 5-aminolevulinic acid (ALA), using a multiple-enzyme system containing ALA dehydratase, porphobilinogen deaminase, uro'gen III synthetase, and the S-adenosyl-L-methionine-(SAM)-dependent uro'gen III methyltransferase (M-1) and precorrin-2 methyltransferase (M-2) in the presence of [13C]SAM. Structural analysis of the resulting product, precorrin-3, reveals a close similarity to precorrin-2 but with several subtle differences in the conjugated array of C = C and C = N bonds which reflect the presence of the new C-methyl group at C20 and its influence on the electronic distribution in the dipyrrocorphin chromophore. The implications of this structure for corrin biosynthesis are discussed.
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Affiliation(s)
- M J Warren
- Department of Chemistry, Texas A&M University, College Station 77843-3255
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26
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Leeper FJ, Rock M. The synthesis of a fluorinated analogue of 5-aminolaevulinic acid, a potential inhibitor of porphyrin biosynthesis. J Fluor Chem 1991. [DOI: 10.1016/s0022-1139(00)80192-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Iida K, Kajiwara M. Isolation of the insect metabolite trehalose by high-performance liquid chromatography. J Chromatogr A 1990. [DOI: 10.1016/s0021-9673(01)89356-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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