{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T10:11:22Z","timestamp":1777543882232,"version":"3.51.4"},"reference-count":46,"publisher":"Portland Press Ltd.","issue":"2","content-domain":{"domain":["portlandpress.com"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2009,6,1]]},"abstract":"<jats:p>The biosynthesis of the tetrapyrrole framework has been investigated in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough by characterization of the enzymes required for the transformation of aminolaevulinic acid into sirohydrochlorin. PBG (porphobilinogen) synthase (HemB) was found to be a zinc-dependent enzyme that exists in its native state as a homohexamer. PBG deaminase (HemC) was shown to contain the dipyrromethane cofactor. Uroporphyrinogen III synthase is found fused with a uroporphyrinogen III methyltransferase (HemD-CobA). Both activities could be demonstrated in this amalgamated protein and the individual enzyme activities were separated by dissecting the relevant gene to allow the production of two distinct proteins. A gene annotated in the genome as a bifunctional precorrin-2 dehydrogenase\/sirohydrochlorin ferrochelatase was in fact shown to act only as a dehydrogenase and is simply capable of synthesizing sirohydrochlorin rather than sirohaem. Genome analysis also reveals a lack of any uroporphyrinogen III decarboxylase, an enzyme necessary for the classical route to haem synthesis. However, the genome does encode some predicted haem d1 biosynthetic enzymes even though the bacterium does not contain the cd1 nitrite reductase. We suggest that sirohydrochlorin acts as a substrate for haem synthesis using a novel pathway that involves homologues of the d1 biogenesis system. This explains why the uroporphyrinogen III synthase is found fused with the methyltransferase, bypassing the need for uroporphyrinogen III decarboxylase activity.<\/jats:p>","DOI":"10.1042\/bj20090151","type":"journal-article","created":{"date-parts":[[2009,3,10]],"date-time":"2009-03-10T12:43:34Z","timestamp":1236689014000},"page":"317-326","update-policy":"https:\/\/doi.org\/10.1042\/crossmark_policy","source":"Crossref","is-referenced-by-count":35,"title":["Functional characterization of the early steps of tetrapyrrole biosynthesis and modification in <i>Desulfovibrio vulgaris<\/i> Hildenborough"],"prefix":"10.1042","volume":"420","author":[{"given":"Susana\u00a0A.\u00a0L.","family":"Lobo","sequence":"first","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Universidade Nova de Lisboa, Avenida da Rep\u00fablica (EAN), 2780-157 Oeiras, Portugal"}]},{"given":"Amanda","family":"Brindley","sequence":"additional","affiliation":[{"name":"Protein Science Group, Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K."}]},{"given":"Martin\u00a0J.","family":"Warren","sequence":"additional","affiliation":[{"name":"Protein Science Group, Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K."}]},{"given":"L\u00edgia\u00a0M.","family":"Saraiva","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Universidade Nova de Lisboa, Avenida da Rep\u00fablica (EAN), 2780-157 Oeiras, Portugal"}]}],"member":"288","published-online":{"date-parts":[[2009,5,13]]},"reference":[{"key":"2021112214195501900_B1","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1042\/bj0700071","article-title":"Initial stages in the biosynthesis of porphyrins. 2. The formation of delta-aminolevulinic acid from glycine and succinyl-coenzyme A by particles from chicken erythrocytes","volume":"70","author":"Gibson","year":"1958","journal-title":"Biochem. J."},{"key":"2021112214195501900_B2","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/0968-0004(92)90380-R","article-title":"Glutamyl-transfer RNA: a precursor of heme and chlorophyll biosynthesis","volume":"17","author":"Jahn","year":"1992","journal-title":"Trends Biochem. Sci."},{"key":"2021112214195501900_B3","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1016\/S0021-9258(19)56978-2","article-title":"Delta-aminolevulinic acid dehydratase of Rhodopseudomonas spheroides. 3. Mechanism of porphobilinogen synthesis","volume":"243","author":"Nandi","year":"1968","journal-title":"J. Biol. 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J."},{"key":"2021112214195501900_B7","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/0014-5793(87)81136-5","article-title":"Evidence for a dipyrromethane cofactor at the catalytic site of E. coli porphobilinogen deaminase","volume":"225","author":"Jordan","year":"1987","journal-title":"FEBS Lett."},{"key":"2021112214195501900_B8","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1042\/bj1950177","article-title":"Mechanism of action of porphobilinogen deaminase. The participation of stable enzyme substrate covalent intermediates between porphobilinogen and the porphobilinogen deaminase from Rhodopseudomonas spheroides","volume":"195","author":"Jordan","year":"1981","journal-title":"Biochem. J."},{"key":"2021112214195501900_B9","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1039\/c39790000202","article-title":"13C-NMR evidence for a new intermediate preuroporphyrinogen in the enzymic transformation of porphobilinogen into uroporphyrinogens","author":"Burton","year":"1979","journal-title":"J. Chem. Soc. Chem. Commun."},{"key":"2021112214195501900_B10","doi-asserted-by":"crossref","first-page":"4893","DOI":"10.1128\/jb.173.15.4893-4896.1991","article-title":"Primary structure, expression in Escherichia coli, and properties of S-adenosyl-L-methionine:uroporphyrinogen III methyltransferase from Bacillus megaterium","volume":"173","author":"Robin","year":"1991","journal-title":"J. Bacteriol."},{"key":"2021112214195501900_B11","doi-asserted-by":"crossref","first-page":"1564","DOI":"10.1128\/jb.177.6.1564-1569.1995","article-title":"Cloning, sequencing, and expression of the uroporphyrinogen III methyltransferase cobA gene of Propionibacterium freudenreichii (shermanii)","volume":"177","author":"Sattler","year":"1995","journal-title":"J. Bacteriol."},{"key":"2021112214195501900_B12","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1038\/nsb1007","article-title":"CysG structure reveals tetrapyrrole-binding features and novel regulation of siroheme biosynthesis","volume":"10","author":"Stroupe","year":"2003","journal-title":"Nat. Struct. Biol."},{"key":"2021112214195501900_B13","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1042\/bj3020837","article-title":"Gene dissection demonstrates that the Escherichia coli cysG gene encodes a multifunctional protein","volume":"302","author":"Warren","year":"1994","journal-title":"Biochem. J."},{"key":"2021112214195501900_B14","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/S0014-5793(96)01423-8","article-title":"Siroheme biosynthesis in Saccharomyces cerevisiae requires the products of both the MET1 and MET8 genes","volume":"401","author":"Hansen","year":"1997","journal-title":"FEBS Lett."},{"key":"2021112214195501900_B15","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1042\/bj20021443","article-title":"Identification and functional analysis of enzymes required for precorrin-2 dehydrogenation and metal ion insertion in the biosynthesis of sirohaem and cobalamin in Bacillus megaterium","volume":"370","author":"Raux","year":"2003","journal-title":"Biochem. J."},{"key":"2021112214195501900_B16","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/S0378-1119(01)00820-4","article-title":"A gene, cobA+hemD, from Selenomonas ruminantium encodes a bifunctional enzyme involved in the synthesis of vitamin B12","volume":"281","author":"Anderson","year":"2001","journal-title":"Gene"},{"key":"2021112214195501900_B17","doi-asserted-by":"crossref","first-page":"5643","DOI":"10.1128\/JB.185.18.5643-5647.2003","article-title":"Lactobacillus reuteri CRL1098 produces cobalamin","volume":"185","author":"Taranto","year":"2003","journal-title":"J. Bacteriol."},{"key":"2021112214195501900_B18","doi-asserted-by":"crossref","first-page":"5169","DOI":"10.1128\/jb.177.17.5169-5175.1995","article-title":"Cloning and sequencing of some genes responsible for porphyrin biosynthesis from the anaerobic bacterium Clostridium josui","volume":"177","author":"Fujino","year":"1995","journal-title":"J. Bacteriol."},{"key":"2021112214195501900_B19","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1006\/bioo.1994.1022","article-title":"Iron uroporphyrin I and a heme c-derivative are prosthetic groups in Desulfovibrio gigas rubredoxin oxidase","volume":"22","author":"Timkovich","year":"1994","journal-title":"Bioorg. Chem."},{"key":"2021112214195501900_B20","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/S0014-5793(00)01939-6","article-title":"Iron-coproporphyrin III is a natural cofactor in bacterioferritin from the anaerobic bacterium Desulfovibrio desulfuricans","volume":"480","author":"Romao","year":"2000","journal-title":"FEBS Lett."},{"key":"2021112214195501900_B21","doi-asserted-by":"crossref","first-page":"6911","DOI":"10.1016\/S0021-9258(19)43436-4","article-title":"Siroheme and sirohydrochlorin. The basis for a new type of porphyrin-related prosthetic group common to both assimilatory and dissimilatory sulfite reductases","volume":"248","author":"Murphy","year":"1973","journal-title":"J. Biol. Chem."},{"key":"2021112214195501900_B22","doi-asserted-by":"crossref","first-page":"12185","DOI":"10.1021\/ja00078a075","article-title":"L-methionine methyl is specifically incorporated into the C-2 and C-7 positions of the porphyrin of cytochrome c3 in a strictly anaerobic bacterium, Desulfovibrio vulgaris","volume":"115","author":"Akutsu","year":"1993","journal-title":"J. Am. Chem. Soc."},{"key":"2021112214195501900_B23","doi-asserted-by":"crossref","first-page":"4853","DOI":"10.1073\/pnas.95.9.4853","article-title":"A primitive pathway of porphyrin biosynthesis and enzymology in Desulfovibrio vulgaris","volume":"95","author":"Ishida","year":"1998","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2021112214195501900_B24","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1038\/nbt959","article-title":"The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough","volume":"22","author":"Heidelberg","year":"2004","journal-title":"Nat. Biotechnol."},{"key":"2021112214195501900_B25","doi-asserted-by":"crossref","first-page":"3202","DOI":"10.1128\/jb.179.10.3202-3212.1997","article-title":"A role for Salmonella typhimurium cbiK in cobalamin (vitamin B12) and siroheme biosynthesis","volume":"179","author":"Raux","year":"1997","journal-title":"J. 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Chem."},{"key":"2021112214195501900_B29","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1042\/bj2540427","article-title":"Purification, crystallization and properties of porphobilinogen deaminase from a recombinant strain of Escherichia coli K12","volume":"254","author":"Jordan","year":"1988","journal-title":"Biochem. J."},{"key":"2021112214195501900_B30","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/emboj\/21.9.2068","article-title":"The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase","volume":"21","author":"Schubert","year":"2002","journal-title":"EMBO J."},{"key":"2021112214195501900_B31","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1042\/bj3380701","article-title":"The role of Saccharomyces cerevisiae Met1p and Met8p in sirohaem and cobalamin biosynthesis","volume":"338","author":"Raux","year":"1999","journal-title":"Biochem. J."},{"key":"2021112214195501900_B32","doi-asserted-by":"crossref","first-page":"8227","DOI":"10.1021\/bi010656k","article-title":"Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity","volume":"40","author":"Kervinen","year":"2001","journal-title":"Biochemistry"},{"key":"2021112214195501900_B33","doi-asserted-by":"crossref","first-page":"4266","DOI":"10.1021\/bi982137w","article-title":"X-ray structure of 5-aminolevulinic acid dehydratase from Escherichia coli complexed with the inhibitor levulinic acid at 2.0 \u00c5 resolution","volume":"38","author":"Erskine","year":"1999","journal-title":"Biochemistry"},{"key":"2021112214195501900_B34","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1006\/jmbi.1999.2808","article-title":"High resolution crystal structure of a Mg2+-dependent sporphobilinogen synthase","volume":"289","author":"Frankenberg","year":"1999","journal-title":"J. Mol. Biol."},{"key":"2021112214195501900_B35","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1016\/S0021-9258(19)44365-2","article-title":"Purification and properties of uroporphyrinogen I synthetase from Rhodopseudomonas spheroides","volume":"248","author":"Jordan","year":"1973","journal-title":"J. Biol. Chem."},{"key":"2021112214195501900_B36","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1016\/0005-2744(80)90147-3","article-title":"Purification by affinity chromatography and properties of uroporphyrinogen I synthetase from Chlorella regularis","volume":"616","author":"Shioi","year":"1980","journal-title":"Biochim. Biophys. Acta"},{"key":"2021112214195501900_B37","doi-asserted-by":"crossref","first-page":"5851","DOI":"10.1021\/bi800342c","article-title":"Two distinct roles for two functional cobaltochelatases (CbiK) in Desulfovibrio vulgaris Hildenborough","volume":"47","author":"Lobo","year":"2008","journal-title":"Biochemistry"},{"key":"2021112214195501900_B38","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1099\/00221287-110-1-61","article-title":"Uroporphyrin- and coproporphyrin I-accumulating mutant of Escherichia coli K12","volume":"110","author":"Chartrand","year":"1979","journal-title":"J. Gen. Microbiol."},{"key":"2021112214195501900_B39","first-page":"760","article-title":"Fluorescence-based method for selection of recombinant plasmids","volume":"19","author":"Roessner","year":"1995","journal-title":"BioTechniques"},{"key":"2021112214195501900_B40","doi-asserted-by":"crossref","first-page":"4222","DOI":"10.1128\/jb.171.8.4222-4231.1989","article-title":"Purification and characterization of S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase from Pseudomonas denitrificans","volume":"171","author":"Blanche","year":"1989","journal-title":"J. Bacteriol."},{"key":"2021112214195501900_B41","doi-asserted-by":"crossref","first-page":"4637","DOI":"10.1128\/jb.173.15.4637-4645.1991","article-title":"Purification, characterization, and molecular cloning of S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase from Methanobacterium ivanovii","volume":"173","author":"Blanche","year":"1991","journal-title":"J. Bacteriol."},{"key":"2021112214195501900_B42","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1096\/fasebj.10.11.8836039","article-title":"The nicotinamide dinucleotide binding motif: a comparison of nucleotide binding proteins","volume":"10","author":"Bellamacina","year":"1996","journal-title":"FASEB J."},{"key":"2021112214195501900_B43","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1093\/nar\/29.5.1097","article-title":"Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods","volume":"29","author":"Sofia","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2021112214195501900_B44","doi-asserted-by":"crossref","first-page":"8666","DOI":"10.1128\/JB.01349-06","article-title":"Heme biosynthesis in Methanosarcina barkeri via a pathway involving two methylation reactions","volume":"188","author":"Buchenau","year":"2006","journal-title":"J. Bacteriol."},{"key":"2021112214195501900_B45","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and Clustal X version 2.0","volume":"23","author":"Larkin","year":"2007","journal-title":"Bioinformatics"},{"key":"2021112214195501900_B46","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1007\/PL00000670","article-title":"Biosynthesis of cobalamin (vitamin B12): a bacterial conundrum","volume":"57","author":"Raux","year":"2000","journal-title":"Cell. Mol. 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