X-ray Structure Analysis of the Iron-dependent Superoxide Dismutase fromMycobacterium tuberculosisat 2.0 Ångstroms Resolution Reveals Novel Dimer–Dimer Interactions

Cooper, J.B.; McIntyre, Kim W.; Badasso, M.; Wood, Stephen P.; Zhang, Ying; Garbe, Thomas R.; Young, Douglas B.

doi:10.1006/jmbi.1994.0105

Cited by 94 publications

(66 citation statements)

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“…Figure 4 shows that the structure can be divided into 2 domains, the N-terminal domain involving an extended region followed by 2 alpha-helices (Ala22-Tyr29, His32-Tyr44) and the C-terminal domain containing 3 alpha-helices (Ser66-Asn79, Gly97-Gly108, and Arg176-Asn185), and 3 beta-sheets (Ser127-Gly136, Gly137-Pro145, and Lys155-Asp162) inserted sequentially between the fourth and fifth helices (see Figure 3). This structure is comparable to that in a report of an X-ray analysis of Fe-SOD from Mycobacterium tuberculosis, implying that the prediction is considerably reliable (Cooper et al, 1995). The tertiary structure of Fe-SOD from Nostoc commune stain CHEN by RasMol 2.6.…”

Section: Structure and Function Analysissupporting

confidence: 83%

Evolutive and structural characterization of Nostoc commune iron-superoxide dismutase that is fit for modification

Lü²,

Li³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Superoxide dismutase (SOD) has extensive clinical applications for protecting organisms from toxic oxidation. In this study, the integrated iron-superoxide dismutase gene (fe-sod) coding sequence of Nostoc commune stain CHEN was cloned from genomic DNA and compared to sods from other reported algae. These analyses of immunology and phylogenetics indicated that this Fe-SOD is considerably homologous with SODs from lower prokaryotes (Fe-SOD or Mn-SOD) but not those from higher animals (Cu/Zn-SOD). In addition, the N. commune Fe-SOD shows 67 to 93% protein sequence identity to 10 other algal Fe-SODs (or Mn-SODs) and 69 to 93% gene sequence identity. Rare nonsynonymous substitutions imply that algal SODs are being subjected to strong natural selection. Interestingly, the N. commune Fe-SOD enzyme molecule has a compact active center that is highly conserved (38.1% of residues are absolutely conserved), and 2 loose ends localized outside the molecule and inclined to mutate (only 11.5% of residues are absolutely conserved). Based on associative analyses of evolution, structure, and function, this special phenomenon is attributed to function- dependent evolution through negative natural selection. Under strong natural selection, although the mutation is random on the gene level, the exterior region is inclined to mutate on the protein level owing to more nonsynonymous substitutions in the exterior region, which demonstrates the theoretical feasibility of modifying Fe-SOD on its ends to overcome its disadvantages in clinical applications.

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Section: Structure and Function Analysissupporting

confidence: 83%

Evolutive and structural characterization of Nostoc commune iron-superoxide dismutase that is fit for modification

Lü²,

Li³

et al. 2012

Genet. Mol. Res.

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“…For visualization of Ag expression, blots were probed with polyclonal sera at a dilution of 1/3000. Antisera to the M. tuberculosis 19-kDa Ag and SOD were obtained by immunizing rabbits with recombinant proteins purified from E. coli (39) and M. vaccae (40), respectively; the Abs recognized single bands during Western blot analysis of M. tuberculosis. Blots were then incubated with HRP-conjugated goat antirabbit Abs (Dako, Cambridge, U.K.) and stained for peroxidase activity using chemiluminescence detection as described by the supplier (Pierce, Chester, U.K.).…”

Section: Gel Electrophoresis and Western Blottingmentioning

confidence: 99%

Lipoprotein Access to MHC Class I Presentation During Infection of Murine Macrophages with Live Mycobacteria

Neyrolles¹,

Gould²,

Gares³

et al. 2001

The Journal of Immunology

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Following uptake by macrophages, live mycobacteria initially reside within an immature phagosome that resists acidification and retains access to recycling endosomes. Glycolipids are exported from the mycobacterial phagosome and become available for immune recognition by CD1-restricted T cells. The aim of this study was to explore the possibility that lipoproteins might similarly escape from the phagosome and act as immune targets in cells infected with live mycobacteria. We have focused on a 19-kDa lipoprotein from Mycobacterium tuberculosis that was previously shown to be recognized by CD8+ T cells. The 19-kDa Ag was found to traffic separately from live mycobacteria within infected macrophages by a pathway that was dependent on acylation of the protein. When expressed as a recombinant protein in rapid-growing mycobacteria, the 19-kDa Ag was able to deliver peptides for recognition by MHC class I-restricted T cells by a TAP-independent mechanism. Entry into the class I pathway was rapid, dependent on acylation, and could be blocked by killing the mycobacteria by heating before infection. Although the pattern of 19-kDa trafficking was similar with different mycobacterial species, preliminary experiments suggest that class I presentation is more efficient during infection with rapid-growing mycobacteria than with the slow-growing bacillus Calmette-Guérin vaccine strain.

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“…6 In the resting states of both proteins, the metal ions are in five-coordinate, distorted trigonal bipyramidal ligand environments with a histidine (His) and a solvent molecule in the axial positions and two His residues and an aspartate (Asp) in the equatorial plane (Figure 1, left). [6][7][8][9][10][11] The substrate is proposed to bind trans to the Asp ligand (i.e., between the two equatorial His residues) to yield a six-coordinate, roughly octahedral complex. The rate constants for the reaction of Mn-and FeSODs with superoxide approach the diffusion-controlled limit, thus largely preventing direct studies of catalytic intermediates.…”

Section: Introductionmentioning

confidence: 99%

Synthesis, X-Ray Crystallographic Characterization, and Electronic Structure Studies of a Di-Azide Iron(III) Complex: Implications for the Azide Adducts of Iron(III) Superoxide Dismutase

et al. 2008

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We have synthesized and characterized, using X-ray crystallographic, spectroscopic, and computational techniques, a six-coordinate diazide Fe 3+ complex, LFe(N 3 ) 2 (where L is the tetradentate ligand 7-diisopropyl-1,4,7-triazacyclononane-1-acetic acid), that serves as a model of the azide adducts of Fe 3+ superoxide dismutase (Fe 3+ SOD). While previous spectroscopic studies revealed that two distinct azide-bound Fe 3+ SOD species can be obtained at cryogenic temperatures depending on protein and azide concentrations, the number of azide ligands coordinated to the Fe 3+ ion in each species has been the subject of some controversy. In the case of LFe(N 3 ) 2 , the electronic absorption and magnetic circular dichroism spectra are dominated by two broad features centered at 21 500 cm −1 (ε ≈ 4000 M −1 cm −1 ) and ~30 300 cm −1 (ε ≈ 7400 M −1 cm −1 ) attributed to N 3 − → Fe 3+ charge transfer (CT) transitions. A normal coordinate analysis of resonance Raman (RR) data obtained for LFe(N 3 ) 2 indicates that the vibrational features at 363 and 403 cm −1 correspond to the Fe-N 3 stretching modes (ν Fe-N3 ) associated with the two different azide ligands and yields Fe-N 3 force constants of 1.170 and 1.275 mdyne/Å, respectively. RR excitation profile data obtained with laser excitation between 16 000 and 22 000 cm −1 reveal that the ν Fe-N3 modes at 363 and 403 cm −1 are preferentially enhanced upon excitation in resonance with the N 3 − → Fe 3+ CT transitions at lower and higher energies, respectively. Consistent with this result, density functional theory electronic structure calculations predict a larger stabilization of the molecular orbitals of the more strongly bound azide due to increased σ-symmetry orbital overlap with the Fe 3d orbitals, thus yielding higher N 3 − → Fe 3+ CT transition energies. Comparison of our data obtained for LFe(N 3 ) 2 with those reported previously for the two azide adducts of Fe 3+ SOD provides compelling evidence that a single azide is coordinated to the Fe 3+ center in each protein species.© 2008 American Chemical Society * Author to whom correspondence should be addressed. brunold@chem.wisc.edu. Supporting Information Available: Cartesian coordinates of crystal-structure and DFT geometry-optimized LFe(N 3 ) 2 models, INDO/S-CI calculated ZFS parameters for all models of LFe(N 3 ) 2 , DFT predicted MO energies and compositions for LFe(N 3 ) 2 models, TD-DFT calculated electronic excitation energies, Abs and MCD data of LFe(N 3 ) 2 collected at 4.5 K, and analysis of VTVH MCD data collected at 20 661 cm −1 . This material is available free of charge via the Internet at

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X-ray Structure Analysis of the Iron-dependent Superoxide Dismutase fromMycobacterium tuberculosisat 2.0 Ångstroms Resolution Reveals Novel Dimer–Dimer Interactions

Cited by 94 publications

References 0 publications

Evolutive and structural characterization of Nostoc commune iron-superoxide dismutase that is fit for modification

Evolutive and structural characterization of Nostoc commune iron-superoxide dismutase that is fit for modification

Lipoprotein Access to MHC Class I Presentation During Infection of Murine Macrophages with Live Mycobacteria

Synthesis, X-Ray Crystallographic Characterization, and Electronic Structure Studies of a Di-Azide Iron(III) Complex: Implications for the Azide Adducts of Iron(III) Superoxide Dismutase

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