Limits...
Homology modeling of dissimilatory APS reductases (AprBA) of sulfur-oxidizing and sulfate-reducing prokaryotes.

Meyer B, Kuever J - PLoS ONE (2008)

Bottom Line: These structural alterations correlated with the protein phylogeny (three major phylogenetic lineages: (1) SRP including LGT-affected Archaeoglobi and SOB of Apr lineage II, (2) crenarchaeal SRP Caldivirga and Pyrobaculum, and (3) SOB of the distinct Apr lineage I) and the presence of potential APS reductase-interacting redox complexes.The almost identical protein matrices surrounding both [4Fe-4S] clusters, the FAD cofactor, the active site channel and center within the AprB/A models of SRP and SOB point to a highly similar catalytic process of APS reduction/sulfite oxidation independent of the metabolism type the APS reductase is involved in and the species it has been originated from.Based on the comparative models, there are no significant structural differences between dissimilatory APS reductases from SRP and SOB; this might be indicative for a similar catalytic process of APS reduction/sulfite oxidation.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Marine Microbiology, Bremen, Germany.

ABSTRACT

Background: The dissimilatory adenosine-5'-phosphosulfate (APS) reductase (cofactors flavin adenine dinucleotide, FAD, and two [4Fe-4S] centers) catalyzes the transformation of APS to sulfite and AMP in sulfate-reducing prokaryotes (SRP); in sulfur-oxidizing bacteria (SOB) it has been suggested to operate in the reverse direction. Recently, the three-dimensional structure of the Archaeoglobus fulgidus enzyme has been determined in different catalytically relevant states providing insights into its reaction cycle.

Methodology/principal findings: Full-length AprBA sequences from 20 phylogenetically distinct SRP and SOB species were used for homology modeling. In general, the average accuracy of the calculated models was sufficiently good to allow a structural and functional comparison between the beta- and alpha-subunit structures (78.8-99.3% and 89.5-96.8% of the AprB and AprA main chain atoms, respectively, had root mean square deviations below 1 A with respect to the template structures). Besides their overall conformity, the SRP- and SOB-derived models revealed the existence of individual adaptations at the electron-transferring AprB protein surface presumably resulting from docking to different electron donor/acceptor proteins. These structural alterations correlated with the protein phylogeny (three major phylogenetic lineages: (1) SRP including LGT-affected Archaeoglobi and SOB of Apr lineage II, (2) crenarchaeal SRP Caldivirga and Pyrobaculum, and (3) SOB of the distinct Apr lineage I) and the presence of potential APS reductase-interacting redox complexes. The almost identical protein matrices surrounding both [4Fe-4S] clusters, the FAD cofactor, the active site channel and center within the AprB/A models of SRP and SOB point to a highly similar catalytic process of APS reduction/sulfite oxidation independent of the metabolism type the APS reductase is involved in and the species it has been originated from.

Conclusions: Based on the comparative models, there are no significant structural differences between dissimilatory APS reductases from SRP and SOB; this might be indicative for a similar catalytic process of APS reduction/sulfite oxidation.

Show MeSH

Related in: MedlinePlus

Selected, homology modeling-based AprA models from Allochromatium vinosum (A) and Pelagibacter ubique (B) (as representatives of SOB from Apr lineage-I), Pyrobaculum calidifontis (C) (as representative of crenarchaeal SRP), Desulfotomaculum reducens (D) (as representative of Gram-positive SRB and LGT-affected deltaproteobacterial SRB), Thermodesulfobacterium commune (E) (as representative of thermophilic SRB), Desulfovibrio vulgaris (F) (as representative of non-LGT-affected deltaproteobacterial SRB), Chlorobaculum tepidum (G) and Thiobacillus denitrificans (H) (as representatives of LGT-affected SOB from Apr lineage-II).Ribbon structure shown from front view (position of FAD cofactor and substrate APS are indicated). Ribbon structure of AprA models colored by model confidence factor provided by SWISS-MODEL (green, respective region of model and reference structure superpose; red, respective region of model deviates from the reference structure).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2211403&req=5

pone-0001514-g007: Selected, homology modeling-based AprA models from Allochromatium vinosum (A) and Pelagibacter ubique (B) (as representatives of SOB from Apr lineage-I), Pyrobaculum calidifontis (C) (as representative of crenarchaeal SRP), Desulfotomaculum reducens (D) (as representative of Gram-positive SRB and LGT-affected deltaproteobacterial SRB), Thermodesulfobacterium commune (E) (as representative of thermophilic SRB), Desulfovibrio vulgaris (F) (as representative of non-LGT-affected deltaproteobacterial SRB), Chlorobaculum tepidum (G) and Thiobacillus denitrificans (H) (as representatives of LGT-affected SOB from Apr lineage-II).Ribbon structure shown from front view (position of FAD cofactor and substrate APS are indicated). Ribbon structure of AprA models colored by model confidence factor provided by SWISS-MODEL (green, respective region of model and reference structure superpose; red, respective region of model deviates from the reference structure).

Mentions: The A. fulgidus alpha-subunit has been described to be subdivided into three domains, the FAD-binding (A2-261, A394-487), capping (A262-393), and the helical domain (A488-643) (see Fig. 1 and 6). The FAD-binding domain constitutes the center, while the capping and helical domains form the periphery of the alpha-subunit (the helical domain is firmly attached to the first whereas the capping domain is partly exposed from the core region). The FAD-binding domain is composed of a central six-stranded parallel beta-sheet (sec. str. elm. 1, 3, 11, 12, 13, 14) that is flanked by four alpha-helices on one side (sec. str. elm. 2, 6, 10, 36) and by a four-stranded mixed beta-sheet on the other (sec. str. elm. 15, 17, 19, 32) (see Fig. 6 panel B). The capping domain is inserted into the polypeptide chain of the aforementioned domain and consists of a four-stranded antiparallel beta-sheet (sec. str. elm. 20. 22, 27, 31) surrounded by eight (mostly short) alpha-helices (see Fig. 6 panel C), whereas the helical domain is primarily composed of three long alpha-helices (sec. str. elm. 39, 41, 42) (see Fig. 6 panel D) [18], [23]. This general fold scheme was present in all comparative AprA models of APS reductases from SOB and SRP (irrespective of species metabolism type and protein phylogenetic affiliation) (see Fig. 7, for details see supplementary data material Table S3 and Figure S3). The conserved nature of the AprA structure was reflected in the low main chain atom RMS deviations from the template structure that ranged between 0.66 Å (uncultured SRB fosws7f8) and 1.20 Å (O. algarvensis Delta 1 symbiont) in the SRB and SOB Apr lineage II models (except the model of Desulfovibrio vulgaris with 1.54 Å RMSD), between 0.79 Å (Thiobacillus denitrificans) and 1.46 Å (environmental sequence EBAC2C11) in the SOB Apr lineage I, and in the crenarchaeal SRP group between 0.88 Å (Caldivirga maquilingensis) and 1.16 Å (Pyrobaculum calidifontis) (see Table 1). The helical domain which has been suggested to mainly build up the interface region between two αβ-heterodimers [18], [23] constituted the most highly conserved protein region in the AprA models with regard to the presence and orientation of the secondary structure elements (RMSD from 0.06 to 0.99 Å; see supplementary data material Table S3 and Figure S3). In contrast, the FAD-binding and the capping domains of the comparative AprA models showed more structural differences; nevertheless, these alterations were predominantly restricted to certain loop amino acid stretches (e.g. between sec. str. elm. 10 and 11 or 36 and 37) and short secondary structure elements (e.g. alpha-helices, sec. str. elm. 23, 24 or 33) located at the protein surface (see supplementary data material Table S3 and Figure S3). As mentioned in a previous section, the higher structural variability among the latter might reflect the individual adaptations at the contact areas between both APS reductase subunits of each species because these domains comprise the AprA interface areas to the second and third segment of AprB. Overall, the alpha-subunit core region was conserved and structurally uniform among the enzymes of sulfur-oxidizers and sulfate-reducers. Notably, the comparative models of Thermodesulfovibrio yellowstonii, Thermodesulfobacterium commune, the non-LGT-affected deltaproteobacterial SRB and the SOB of Apr lineage II contained 17 to 21 amino acids long insertions between the secondary structure elements 7 and 8; the inserted amino acid stretches were predicted by SWISS-MODEL to primarily form two extended, antiparallel beta-sheets that are exposed from the core region (see Fig. 7 panel E to H, see also supplementary data material Table S3 and Figure S3). The accuracy of the proposed structures in this AprA model area is highly speculative because of the current computational limitations in calculating the correct fold of loop regions encompassing more than eight residues. Its solvent-exposed location at the AprB-interacting site of the alpha-subunit might be an indication for an involvement in stabilizing the contact between the native electron donor/acceptor protein and the electron-transferring smaller subunit of APS reductase.


Homology modeling of dissimilatory APS reductases (AprBA) of sulfur-oxidizing and sulfate-reducing prokaryotes.

Meyer B, Kuever J - PLoS ONE (2008)

Selected, homology modeling-based AprA models from Allochromatium vinosum (A) and Pelagibacter ubique (B) (as representatives of SOB from Apr lineage-I), Pyrobaculum calidifontis (C) (as representative of crenarchaeal SRP), Desulfotomaculum reducens (D) (as representative of Gram-positive SRB and LGT-affected deltaproteobacterial SRB), Thermodesulfobacterium commune (E) (as representative of thermophilic SRB), Desulfovibrio vulgaris (F) (as representative of non-LGT-affected deltaproteobacterial SRB), Chlorobaculum tepidum (G) and Thiobacillus denitrificans (H) (as representatives of LGT-affected SOB from Apr lineage-II).Ribbon structure shown from front view (position of FAD cofactor and substrate APS are indicated). Ribbon structure of AprA models colored by model confidence factor provided by SWISS-MODEL (green, respective region of model and reference structure superpose; red, respective region of model deviates from the reference structure).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2211403&req=5

pone-0001514-g007: Selected, homology modeling-based AprA models from Allochromatium vinosum (A) and Pelagibacter ubique (B) (as representatives of SOB from Apr lineage-I), Pyrobaculum calidifontis (C) (as representative of crenarchaeal SRP), Desulfotomaculum reducens (D) (as representative of Gram-positive SRB and LGT-affected deltaproteobacterial SRB), Thermodesulfobacterium commune (E) (as representative of thermophilic SRB), Desulfovibrio vulgaris (F) (as representative of non-LGT-affected deltaproteobacterial SRB), Chlorobaculum tepidum (G) and Thiobacillus denitrificans (H) (as representatives of LGT-affected SOB from Apr lineage-II).Ribbon structure shown from front view (position of FAD cofactor and substrate APS are indicated). Ribbon structure of AprA models colored by model confidence factor provided by SWISS-MODEL (green, respective region of model and reference structure superpose; red, respective region of model deviates from the reference structure).
Mentions: The A. fulgidus alpha-subunit has been described to be subdivided into three domains, the FAD-binding (A2-261, A394-487), capping (A262-393), and the helical domain (A488-643) (see Fig. 1 and 6). The FAD-binding domain constitutes the center, while the capping and helical domains form the periphery of the alpha-subunit (the helical domain is firmly attached to the first whereas the capping domain is partly exposed from the core region). The FAD-binding domain is composed of a central six-stranded parallel beta-sheet (sec. str. elm. 1, 3, 11, 12, 13, 14) that is flanked by four alpha-helices on one side (sec. str. elm. 2, 6, 10, 36) and by a four-stranded mixed beta-sheet on the other (sec. str. elm. 15, 17, 19, 32) (see Fig. 6 panel B). The capping domain is inserted into the polypeptide chain of the aforementioned domain and consists of a four-stranded antiparallel beta-sheet (sec. str. elm. 20. 22, 27, 31) surrounded by eight (mostly short) alpha-helices (see Fig. 6 panel C), whereas the helical domain is primarily composed of three long alpha-helices (sec. str. elm. 39, 41, 42) (see Fig. 6 panel D) [18], [23]. This general fold scheme was present in all comparative AprA models of APS reductases from SOB and SRP (irrespective of species metabolism type and protein phylogenetic affiliation) (see Fig. 7, for details see supplementary data material Table S3 and Figure S3). The conserved nature of the AprA structure was reflected in the low main chain atom RMS deviations from the template structure that ranged between 0.66 Å (uncultured SRB fosws7f8) and 1.20 Å (O. algarvensis Delta 1 symbiont) in the SRB and SOB Apr lineage II models (except the model of Desulfovibrio vulgaris with 1.54 Å RMSD), between 0.79 Å (Thiobacillus denitrificans) and 1.46 Å (environmental sequence EBAC2C11) in the SOB Apr lineage I, and in the crenarchaeal SRP group between 0.88 Å (Caldivirga maquilingensis) and 1.16 Å (Pyrobaculum calidifontis) (see Table 1). The helical domain which has been suggested to mainly build up the interface region between two αβ-heterodimers [18], [23] constituted the most highly conserved protein region in the AprA models with regard to the presence and orientation of the secondary structure elements (RMSD from 0.06 to 0.99 Å; see supplementary data material Table S3 and Figure S3). In contrast, the FAD-binding and the capping domains of the comparative AprA models showed more structural differences; nevertheless, these alterations were predominantly restricted to certain loop amino acid stretches (e.g. between sec. str. elm. 10 and 11 or 36 and 37) and short secondary structure elements (e.g. alpha-helices, sec. str. elm. 23, 24 or 33) located at the protein surface (see supplementary data material Table S3 and Figure S3). As mentioned in a previous section, the higher structural variability among the latter might reflect the individual adaptations at the contact areas between both APS reductase subunits of each species because these domains comprise the AprA interface areas to the second and third segment of AprB. Overall, the alpha-subunit core region was conserved and structurally uniform among the enzymes of sulfur-oxidizers and sulfate-reducers. Notably, the comparative models of Thermodesulfovibrio yellowstonii, Thermodesulfobacterium commune, the non-LGT-affected deltaproteobacterial SRB and the SOB of Apr lineage II contained 17 to 21 amino acids long insertions between the secondary structure elements 7 and 8; the inserted amino acid stretches were predicted by SWISS-MODEL to primarily form two extended, antiparallel beta-sheets that are exposed from the core region (see Fig. 7 panel E to H, see also supplementary data material Table S3 and Figure S3). The accuracy of the proposed structures in this AprA model area is highly speculative because of the current computational limitations in calculating the correct fold of loop regions encompassing more than eight residues. Its solvent-exposed location at the AprB-interacting site of the alpha-subunit might be an indication for an involvement in stabilizing the contact between the native electron donor/acceptor protein and the electron-transferring smaller subunit of APS reductase.

Bottom Line: These structural alterations correlated with the protein phylogeny (three major phylogenetic lineages: (1) SRP including LGT-affected Archaeoglobi and SOB of Apr lineage II, (2) crenarchaeal SRP Caldivirga and Pyrobaculum, and (3) SOB of the distinct Apr lineage I) and the presence of potential APS reductase-interacting redox complexes.The almost identical protein matrices surrounding both [4Fe-4S] clusters, the FAD cofactor, the active site channel and center within the AprB/A models of SRP and SOB point to a highly similar catalytic process of APS reduction/sulfite oxidation independent of the metabolism type the APS reductase is involved in and the species it has been originated from.Based on the comparative models, there are no significant structural differences between dissimilatory APS reductases from SRP and SOB; this might be indicative for a similar catalytic process of APS reduction/sulfite oxidation.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Marine Microbiology, Bremen, Germany.

ABSTRACT

Background: The dissimilatory adenosine-5'-phosphosulfate (APS) reductase (cofactors flavin adenine dinucleotide, FAD, and two [4Fe-4S] centers) catalyzes the transformation of APS to sulfite and AMP in sulfate-reducing prokaryotes (SRP); in sulfur-oxidizing bacteria (SOB) it has been suggested to operate in the reverse direction. Recently, the three-dimensional structure of the Archaeoglobus fulgidus enzyme has been determined in different catalytically relevant states providing insights into its reaction cycle.

Methodology/principal findings: Full-length AprBA sequences from 20 phylogenetically distinct SRP and SOB species were used for homology modeling. In general, the average accuracy of the calculated models was sufficiently good to allow a structural and functional comparison between the beta- and alpha-subunit structures (78.8-99.3% and 89.5-96.8% of the AprB and AprA main chain atoms, respectively, had root mean square deviations below 1 A with respect to the template structures). Besides their overall conformity, the SRP- and SOB-derived models revealed the existence of individual adaptations at the electron-transferring AprB protein surface presumably resulting from docking to different electron donor/acceptor proteins. These structural alterations correlated with the protein phylogeny (three major phylogenetic lineages: (1) SRP including LGT-affected Archaeoglobi and SOB of Apr lineage II, (2) crenarchaeal SRP Caldivirga and Pyrobaculum, and (3) SOB of the distinct Apr lineage I) and the presence of potential APS reductase-interacting redox complexes. The almost identical protein matrices surrounding both [4Fe-4S] clusters, the FAD cofactor, the active site channel and center within the AprB/A models of SRP and SOB point to a highly similar catalytic process of APS reduction/sulfite oxidation independent of the metabolism type the APS reductase is involved in and the species it has been originated from.

Conclusions: Based on the comparative models, there are no significant structural differences between dissimilatory APS reductases from SRP and SOB; this might be indicative for a similar catalytic process of APS reduction/sulfite oxidation.

Show MeSH
Related in: MedlinePlus