Molecular insights into the binding of coenzyme <scp>F420</scp> to the conserved protein <scp>R</scp>v1155 from <scp>M</scp>ycobacterium tuberculosis

Mashalidis, Ellene H.; Gittis, Apostolos G.; Tomczak, Aurelie; Abell, Chris; Barry, Clifton E.; Garboczi, David N.

doi:10.1002/pro.2645

Cited by 17 publications

(18 citation statements)

References 56 publications

(105 reference statements)

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“…In many respects, the binding of F 420 to Rv2074 is similar to that observed in Rv1155 [Fig. (B)], particularly at the phosphate group, which is coordinated by a highly conserved lysine residue (Lys‐61) that is present in all members of the FDOR‐B superfamily . However, whereas the deazaflavin moiety in Rv1155 was observed to be present in a bent “butterfly” conformation, it is planar in Rv2074.…”

Section: Resultsmentioning

confidence: 69%

“…Omit electron density corresponding to one molecule of F 420 with an oligoglutamate tail consisting of three residues is observed in the cofactor binding site of each of the four protein chains in the asymmetric unit. Each monomer adopts the conserved split β‐barrel protein fold characteristic of the FDORs, as previously described, and the proteins are arranged as homodimers, which is supported by analysis from the Proteins, Interfaces, Structures and Assemblies (PISA) server [Fig. (A)] .…”

Section: Resultsmentioning

confidence: 99%

“…B. Structure shown in A overlaid with the homodimeric Rv1155:F 420 complex in cyan (PDB ID: 4QVB) . C. Residues involved in interacting with F 420 in Rv2074.…”

Section: Resultsmentioning

confidence: 99%

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Rv2074 is a novel F₄₂₀H₂‐dependent biliverdin reductase in Mycobacterium tuberculosis

et al. 2016

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Bilirubin is a potent antioxidant that is produced from the reduction of the heme degradation product biliverdin. In mammalian cells and Cyanobacteria, NADH/NADPH-dependent biliverdin reductases (BVRs) of the Rossmann-fold have been shown to catalyze this reaction. Here, we describe the characterization of Rv2074 from Mycobacterium tuberculosis, which belongs to a structurally and mechanistically distinct family of F 420 H 2 -dependent BVRs (F-BVRs) that are exclusively found in Actinobacteria. We have solved the crystal structure of Rv2074 bound to its cofactor, F 420 , and used this alongside molecular dynamics simulations, site-directed mutagenesis and NMR spectroscopy to elucidate its catalytic mechanism. The production of bilirubin by Rv2074 could exploit the anti-oxidative properties of bilirubin and contribute to the range of immunoevasive mechanisms that have evolved in M. tuberculosis to allow persistent infection.

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Section: Resultsmentioning

confidence: 69%

Section: Resultsmentioning

confidence: 99%

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Rv2074 is a novel F₄₂₀H₂‐dependent biliverdin reductase in Mycobacterium tuberculosis

et al. 2016

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“…All three FbiB constructs were cloned with an N-terminal His 6 tag to facilitate the subsequent purification steps. The His 6 tag on both pDEST vectors is cleavable using tobacco etch virus (TEV) protease.…”

Section: Pcr Amplification and Cloning-mentioning

confidence: 99%

“…F 420 has been emerging as a new player in the biology of mycobacteria (1), with increasing numbers of F 420 -utilizing proteins characterized from different mycobacterial species (2)(3)(4)(5)(6)(7)(8). This cofactor has been suggested to protect Mycobacterium tuberculosis, the causative agent of tuberculosis, against oxidative and nitrosative stress during pathogenesis (9 -11).…”

mentioning

confidence: 99%

Elongation of the Poly-γ-glutamate Tail of F420 Requires Both Domains of the F420:γ-Glutamyl Ligase (FbiB) of Mycobacterium tuberculosis

Bashiri

Rehan

Sreebhavan

et al. 2016

Journal of Biological Chemistry

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Cofactor F 420 is an electron carrier with a major role in the oxidoreductive reactions of Mycobacterium tuberculosis, the causative agent of tuberculosis. A ␥-glutamyl ligase catalyzes the final steps of the F 420 biosynthesis pathway by successive additions of L-glutamate residues to F 420 -0, producing a poly-␥-glutamate tail. The enzyme responsible for this reaction in archaea (CofE) comprises a single domain and produces F 420 -2 as the major species. The homologous M. tuberculosis enzyme, FbiB, is a two-domain protein and produces F 420 with predominantly 5-7 L-glutamate residues in the poly-␥-glutamate tail. The N-terminal domain of FbiB is homologous to CofE with an annotated ␥-glutamyl ligase activity, whereas the C-terminal domain has sequence similarity to an FMN-dependent family of nitroreductase enzymes. Here we demonstrate that full-length FbiB adds multiple L-glutamate residues to F 420 -0 in vitro to produce F 420 -5 after 24 h; communication between the two domains is critical for full ␥-glutamyl ligase activity. We also present crystal structures of the C-terminal domain of FbiB in apo-, F 420 -0-, and FMN-bound states, displaying distinct sites for F 420 -0 and FMN ligands that partially overlap. Finally, we discuss the features of a full-length structural model produced by small angle x-ray scattering and its implications for the role of N-and C-terminal domains in catalysis.The cofactor F 420 is a flavin derivative that is sporadically distributed among microorganisms, mainly archaea and actinobacteria (including mycobacteria). F 420 has been emerging as a new player in the biology of mycobacteria (1), with increasing numbers of F 420 -utilizing proteins characterized from different mycobacterial species (2-8). This cofactor has been suggested to protect Mycobacterium tuberculosis, the causative agent of tuberculosis, against oxidative and nitrosative stress during pathogenesis (9 -11). At the biochemical level, cofactor F 420 functions as a hydride transfer agent in oxidoreductive reactions with a lower redox potential than that of NAD(P) ϩ (12). The biosynthesis pathway of cofactor F 420 has been investigated in both archaeal and mycobacterial species. In the current view of the proposed pathway, the first intermediate with the complete chromophore (7, ) is produced by FO synthase (FbiC in mycobacteria (13) and CofGH in archaea (14)). A transferase enzyme (FbiA in mycobacteria (15) and CofD in archaea (16)) subsequently catalyzes the addition of a 2-phospho-L-lactate moiety to FO to produce F 420 -0 (F 420 with no poly-␥-glutamate tail). The final step of the pathway is performed by a ␥-glutamyl ligase (FbiB in mycobacteria (15) and CofE in archaea (17)) that catalyzes successive additions of L-glutamate residues to F 420 -0 (Fig. 1A).The length of the poly-␥-glutamate tail varies between archaeal and mycobacterial species; in archaea, two L-glutamate residues are seen (18), whereas in mycobacteria, up to nine residues are present (3, 19). There exists an intriguing difference between the ...

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On the diversity of F₄₂₀‐dependent oxidoreductases: A sequence‐ and structure‐based classification

2021

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The F420 deazaflavin cofactor is an intriguing molecule as it structurally resembles the canonical flavin cofactor, although behaves as a nicotinamide cofactor due to its obligate hydride‐transfer reactivity and similar low redox potential. Since its discovery, numerous enzymes relying on it have been described. The known deazaflavoproteins are taxonomically restricted to Archaea and Bacteria. The biochemistry of the deazaflavoenzymes is diverse and they exhibit great structural variability. In this study a thorough sequence and structural homology evolutionary analysis was performed in order to generate an overarching classification of the F420‐dependent oxidoreductases. Five different deazaflavoenzyme Classes (I–V) are described according to their structural folds as follows: Class I encompassing the TIM‐barrel F420‐dependent enzymes; Class II including the Rossmann fold F420‐dependent enzymes; Class III comprising the β‐roll F420‐dependent enzymes; Class IV which exclusively gathers the SH3 barrel F420‐dependent enzymes and Class V including the three layer ββα sandwich F420‐dependent enzymes. This classification provides a framework for the identification and biochemical characterization of novel deazaflavoenzymes.

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Molecular insights into the binding of coenzyme F₄₂₀ to the conserved protein Rv1155 from Mycobacterium tuberculosis

Cited by 17 publications

References 56 publications

Rv2074 is a novel F₄₂₀H₂‐dependent biliverdin reductase in Mycobacterium tuberculosis

Rv2074 is a novel F₄₂₀H₂‐dependent biliverdin reductase in Mycobacterium tuberculosis

Elongation of the Poly-γ-glutamate Tail of F420 Requires Both Domains of the F420:γ-Glutamyl Ligase (FbiB) of Mycobacterium tuberculosis

On the diversity of F₄₂₀‐dependent oxidoreductases: A sequence‐ and structure‐based classification

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Molecular insights into the binding of coenzyme F420 to the conserved protein Rv1155 from Mycobacterium tuberculosis

Cited by 17 publications

References 56 publications

Rv2074 is a novel F420H2‐dependent biliverdin reductase in Mycobacterium tuberculosis

Rv2074 is a novel F420H2‐dependent biliverdin reductase in Mycobacterium tuberculosis

Elongation of the Poly-γ-glutamate Tail of F420 Requires Both Domains of the F420:γ-Glutamyl Ligase (FbiB) of Mycobacterium tuberculosis

On the diversity of F420‐dependent oxidoreductases: A sequence‐ and structure‐based classification

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Molecular insights into the binding of coenzyme F₄₂₀ to the conserved protein Rv1155 from Mycobacterium tuberculosis

Rv2074 is a novel F₄₂₀H₂‐dependent biliverdin reductase in Mycobacterium tuberculosis

Rv2074 is a novel F₄₂₀H₂‐dependent biliverdin reductase in Mycobacterium tuberculosis

On the diversity of F₄₂₀‐dependent oxidoreductases: A sequence‐ and structure‐based classification