Common Chelatase Design in the Branched Tetrapyrrole Pathways of Heme and Anaerobic Cobalamin Synthesis

Schubert, Heidi; Raux, Evelyne; Wilson, K.S.; Warren, Martin J.

doi:10.1021/bi9906773

Cited by 102 publications

(79 citation statements)

References 25 publications

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“…CbiK is an anaerobic cobalt chelatase that inserts cobalt into the tetrapyrrole ring of precorrin and has been proposed to be part of the cobalamin biosynthesis pathway in S. typhimurium (35,40). CbiK is a single-subunit, ATP-independent enzyme that, on the basis of biochemical characterization and sequence similarity, has been proposed to be a member of a class of enzymes including the PPIX ferrochelatase (HemZ), sirohydrochlorin ferrochelatases (CysG and Met8P), and the other known anaerobic cobalt chelatase (CbiX) (40). Although there is low overall sequence identity between the proteins within the PPIX ferrochelatase-anaerobic cobalt chelatase class, 14 residues are conserved within this class of enzyme.…”

Section: Discussionmentioning

confidence: 99%

Characterization of a Novel Outer Membrane Hemin-Binding Protein of Porphyromonas gingivalis

et al. 2000

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Porphyromonas gingivalis is a gram-negative, anaerobic coccobacillus that has been implicated as a major etiological agent in the development of chronic periodontitis. In this paper, we report the characterization of a protein, IhtB (iron heme transport; formerly designated Pga30), that is an outer membrane hemin-binding protein potentially involved in iron assimilation by P. gingivalis. IhtB was localized to the cell surface of P. gingivalis by Western blot analysis of a Sarkosyl-insoluble outer membrane preparation and by immunocytochemical staining of whole cells using IhtB peptide-specific antisera. The protein, released from the cell surface, was shown to bind to hemin using hemin-agarose. The growth of heme-limited, but not heme-replete, P. gingivalis cells was inhibited by preincubation with IhtB peptide-specific antisera. The ihtB gene was located between an open reading frame encoding a putative TonB-linked outer membrane receptor and three open reading frames that have sequence similarity to ATP binding cassette transport system operons in other bacteria. Analysis of the deduced amino acid sequence of IhtB showed significant similarity to the Salmonella typhimurium protein CbiK, a cobalt chelatase that is structurally related to the ATP-independent family of ferrochelatases. Molecular modeling indicated that the IhtB amino acid sequence could be threaded onto the CbiK fold with the IhtB structural model containing the active-site residues critical for chelatase activity. These results suggest that IhtB is a peripheral outer membrane chelatase that may remove iron from heme prior to uptake by P. gingivalis.

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Section: Discussionmentioning

confidence: 99%

Characterization of a Novel Outer Membrane Hemin-Binding Protein of Porphyromonas gingivalis

et al. 2000

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“…The cocrystallization of Dv-CbiK P with cobalt was achieved by mixing 1.0 μL Dv-CbiK P with 1.8 μL reservoir solution and 0.2 μL 1.0 M cobalt chloride. Both the Se-CbiK and Af-CbiX S were purified and crystallized as previously described (5,6). The SHC complexes of Se-CbiK and Af-CbiX S were produced by anaerobic cocrystallization of equimolar quantities of CbiK and SHC.…”

Section: Methodsmentioning

confidence: 99%

“…The active site of CbiK contains two conserved histidine residues, corresponding to the Glu and His found in protoporphyrin ferrochelatases (6). The site also contains the phenylalanine residue against which the macrocycle is likely to stack.…”

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confidence: 99%

Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization

Romão

Ladakis

Lobo

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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The class II chelatases associated with heme, siroheme, and cobalamin biosynthesis are structurally related enzymes that insert a specific metal ion (Fe 2þ or Co 2þ ) into the center of a modified tetrapyrrole (protoporphyrin or sirohydrochlorin). The structures of two related class II enzymes, CbiX S from Archaeoglobus fulgidus and CbiK from Salmonella enterica, that are responsible for the insertion of cobalt along the cobalamin biosynthesis pathway are presented in complex with their metallated product. A further structure of a CbiK from Desulfovibrio vulgaris Hildenborough reveals how cobalt is bound at the active site. The crystal structures show that the binding of sirohydrochlorin is distinctly different to porphyrin binding in the protoporphyrin ferrochelatases and provide a molecular overview of the mechanism of chelation. The structures also give insights into the evolution of chelatase form and function. Finally, the structure of a periplasmic form of Desulfovibrio vulgaris Hildenborough CbiK reveals a novel tetrameric arrangement of its subunits that are stabilized by the presence of a heme b cofactor. Whereas retaining colbaltochelatase activity, this protein has acquired a central cavity with the potential to chaperone or transport metals across the periplasmic space, thereby evolving a new use for an ancient protein subunit.enzyme mechanism | tetrapyrrole biosynthesis

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“…Nevertheless, genes similar to the Mg-chelatase subunits, namely chlID, were found in clusters with various CBL genes, most often with cobN. Notably, similar to CobNST, ATP-dependent Mg-chelatase involved in the bacteriochlorophyll biosynthesis consists of three subunits, ChlH, ChlI, and ChlD, and ChlH is a close homolog of CobN (34). The hypothesis that ChlI and ChlD are the missing components of the late cobalt chelatase was proved by phylogenetic analysis.…”

Section: Table 1 Cobalamin Biosynthesis and Transport Genes And B12-ementioning

confidence: 99%

Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes

Rodionov

Vitreschak

Mironov

et al. 2003

Journal of Biological Chemistry

409

426

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Using comparative analysis of genes, operons, and regulatory elements, we describe the cobalamin (vitamin B 12 ) biosynthetic pathway in available prokaryotic genomes. Here we found a highly conserved RNA secondary structure, the regulatory B12 element, which is widely distributed in the upstream regions of cobalamin biosynthetic/transport genes in eubacteria. In addition, the binding signal (CBL-box) for a hypothetical B 12 regulator was identified in some archaea. A search for B12 elements and CBL-boxes and positional analysis identified a large number of new candidate B 12 -regulated genes in various prokaryotes. Among newly assigned functions associated with the cobalamin biosynthesis, there are several new types of cobalt transporters, ChlI and ChlD subunits of the CobN-dependent cobaltochelatase complex, cobalt reductase BluB, adenosyltransferase PduO, several new proteins linked to the lower ligand assembly pathway, L-threonine kinase PduX, and a large number of other hypothetical proteins. Most missing genes detected within the cobalamin biosynthetic pathways of various bacteria were identified as nonorthologous substitutes. The variable parts of the cobalamin metabolism appear to be the cobalt transport and insertion, the CobG/CbiG-and CobF/CbiD-catalyzed reactions, and the lower ligand synthesis pathway. The most interesting result of analysis of B12 elements is that B 12 -independent isozymes of the methionine synthase and ribonucleotide reductase are regulated by B12 elements in bacteria that have both B 12 -dependent and B 12 -independent isozymes. Moreover, B 12 regulons of various bacteria are thought to include enzymes from known B 12 -dependent or alternative pathways. Cobalamin (CBL),1 along with chlorophyll, heme, siroheme, and coenzyme F 430 , constitute a class of the most structurally complex cofactors synthesized by bacteria. The distinctive feature of these cofactors is their tetrapyrrole-derived framework with a centrally chelated metal ion (cobalt, magnesium, iron, or nickel). Methylcobalamin and Ado-CBL, two derivatives of vitamin B 12 (cyanocobalamin) with different upper axial ligands, are essential cofactors for several important enzymes that catalyze a variety of transmethylation and rearrangement reactions. Among the most prominent vitamin B 12 -dependent enzymes in bacteria and archaea are the methionine synthase isozyme MetH from enteric bacteria; the ribonucleotide reductase isozyme NrdJ from deeply rooted eubacteria and archaea; diol dehydratases and ethanolamine ammonia lyase from enteric bacteria involved in anaerobic glycerol, 1,2-propanediol, and ethanolamine fermentation; glutamate and methylmalonyl-CoA mutases from clostridia and streptomycetes; and various CBL-dependent methyltransferases from methane-producing archaea (1-5).Most prokaryotic organisms as well as animals (including humans) and protists have enzymes that require CBL as cofactor, whereas plants and fungi are thought not to use it. Among the CBL-utilizing organisms, only some bacterial and archaeal species ...

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Common Chelatase Design in the Branched Tetrapyrrole Pathways of Heme and Anaerobic Cobalamin Synthesis

Cited by 102 publications

References 25 publications

Characterization of a Novel Outer Membrane Hemin-Binding Protein of Porphyromonas gingivalis

Characterization of a Novel Outer Membrane Hemin-Binding Protein of Porphyromonas gingivalis

Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization

Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes

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