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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.

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Phylogenetic trees based on (A) AprBA, (B) QmoA, (C) QmoB, and (D) QmoC sequences.The trees were inferred using PhyML (maximum likelihood method). The SOB Apr lineage-I sequence group (A) and the Archaeglobus fulgidus QmoABC sequences (B–D) were used as outgroup, respectively. The scale bar corresponds to 10% estimated sequence divergence. Branching orders that were only supported by bootstrap resampling values below 50% are shown as multifurcations; percentages greater than 50% of bootstrap resampling supporting a topological element are indicated near the nodes.
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pone-0001514-g002: Phylogenetic trees based on (A) AprBA, (B) QmoA, (C) QmoB, and (D) QmoC sequences.The trees were inferred using PhyML (maximum likelihood method). The SOB Apr lineage-I sequence group (A) and the Archaeglobus fulgidus QmoABC sequences (B–D) were used as outgroup, respectively. The scale bar corresponds to 10% estimated sequence divergence. Branching orders that were only supported by bootstrap resampling values below 50% are shown as multifurcations; percentages greater than 50% of bootstrap resampling supporting a topological element are indicated near the nodes.

Mentions: In this study, full-length Apr sequences from 20 phylogenetically distinct SRP and SOB species were used for homology modeling that ranged in their sequence identity values to the A. fulgidus templates between 38.6 to 62.6% (beta-subunit) and 47.6 to 60.7% (alpha-subunit) (see supplementary data material Table S1 and S3). The lowest identity values were found for the sequences of SOB Apr lineage-I members, e.g. Pelagibacter ubique, (AprB: 38.6 to 45.8%; AprA: 47.7 to 51.5%) and the sequences of crenarchaeal Pyrobaculum spp. (38.7 to 42.4%; AprA: 47.6%) which is in accordance to the AprBA phylogeny (see Fig. 2A). The APS reductases of SRB species possessed sequence identities to the A. fulgidus templates that ranged between 53.1 to 62.6% (AprB) and 49.5 to 60.7% (AprA) with the highest values received for the Gram-positive SRB and the LGT-affected deltaproteobacterial members [16]; the APS reductases of SOB Apr lineage II had 49.0 to 61.4% (AprB) and 50.2 to 54.0% (AprA) sequence identity to the templates. The overall accuracy of all AprA and most AprB comparative models could be assumed to be sufficiently good to allow their structural and functional comparison (in the models, 78.8 to 99.3% (AprB) and 89.5 to 96.8% (AprA) of the main chain atoms had RMS deviations below 1 Å, see supplementary data material Table S1 and S3).


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

Meyer B, Kuever J - PLoS ONE (2008)

Phylogenetic trees based on (A) AprBA, (B) QmoA, (C) QmoB, and (D) QmoC sequences.The trees were inferred using PhyML (maximum likelihood method). The SOB Apr lineage-I sequence group (A) and the Archaeglobus fulgidus QmoABC sequences (B–D) were used as outgroup, respectively. The scale bar corresponds to 10% estimated sequence divergence. Branching orders that were only supported by bootstrap resampling values below 50% are shown as multifurcations; percentages greater than 50% of bootstrap resampling supporting a topological element are indicated near the nodes.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2211403&req=5

pone-0001514-g002: Phylogenetic trees based on (A) AprBA, (B) QmoA, (C) QmoB, and (D) QmoC sequences.The trees were inferred using PhyML (maximum likelihood method). The SOB Apr lineage-I sequence group (A) and the Archaeglobus fulgidus QmoABC sequences (B–D) were used as outgroup, respectively. The scale bar corresponds to 10% estimated sequence divergence. Branching orders that were only supported by bootstrap resampling values below 50% are shown as multifurcations; percentages greater than 50% of bootstrap resampling supporting a topological element are indicated near the nodes.
Mentions: In this study, full-length Apr sequences from 20 phylogenetically distinct SRP and SOB species were used for homology modeling that ranged in their sequence identity values to the A. fulgidus templates between 38.6 to 62.6% (beta-subunit) and 47.6 to 60.7% (alpha-subunit) (see supplementary data material Table S1 and S3). The lowest identity values were found for the sequences of SOB Apr lineage-I members, e.g. Pelagibacter ubique, (AprB: 38.6 to 45.8%; AprA: 47.7 to 51.5%) and the sequences of crenarchaeal Pyrobaculum spp. (38.7 to 42.4%; AprA: 47.6%) which is in accordance to the AprBA phylogeny (see Fig. 2A). The APS reductases of SRB species possessed sequence identities to the A. fulgidus templates that ranged between 53.1 to 62.6% (AprB) and 49.5 to 60.7% (AprA) with the highest values received for the Gram-positive SRB and the LGT-affected deltaproteobacterial members [16]; the APS reductases of SOB Apr lineage II had 49.0 to 61.4% (AprB) and 50.2 to 54.0% (AprA) sequence identity to the templates. The overall accuracy of all AprA and most AprB comparative models could be assumed to be sufficiently good to allow their structural and functional comparison (in the models, 78.8 to 99.3% (AprB) and 89.5 to 96.8% (AprA) of the main chain atoms had RMS deviations below 1 Å, see supplementary data material Table S1 and S3).

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