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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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Three-dimensional ribbon structure of APS reductase from A. fulgidus.The beta-subunit segments are colored red (ferredoxin segment), blue (3 antiparallel beta-sheets segment), and green (tail segment); the alpha-subunit domains are colored light blue and orange (FAD-binding domain I and II), pink (capping domain), and grey (helical domain). The [4Fe-4S] clusters, FAD and substrate APS are shown as ball-and-stick representations; tryptophan Trp-B48 of AprB is highlighted by violet color. Ribbon structure is shown from (A) top view, (B) bottom view (substrate channel), (C) front view, and (D) back view.
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pone-0001514-g001: Three-dimensional ribbon structure of APS reductase from A. fulgidus.The beta-subunit segments are colored red (ferredoxin segment), blue (3 antiparallel beta-sheets segment), and green (tail segment); the alpha-subunit domains are colored light blue and orange (FAD-binding domain I and II), pink (capping domain), and grey (helical domain). The [4Fe-4S] clusters, FAD and substrate APS are shown as ball-and-stick representations; tryptophan Trp-B48 of AprB is highlighted by violet color. Ribbon structure is shown from (A) top view, (B) bottom view (substrate channel), (C) front view, and (D) back view.

Mentions: The X-ray structure of the dissimilatory APS reductase isolated from Archaeoglobus fulgidus has been elucidated at 1.6 Å resolution by Fritz and coworkers [18]: Its beta-subunit can be subdivided in three segments comprising a bacterial ferredoxin-like segment that envelopes both [4Fe-4S] clusters (amino acids B1-B68), followed by a three-stranded antiparallel beta-sheet (B69-B104) and a tail with a length of 50 Å (B105-B148) (see Fig. 1). The structure of the alpha-subunit can be grouped into the FAD cofactor-binding (amino acids A2-A261 and A394-A487), the capping (A262-A393) and the helical domains (A488-A643) (see Fig. 1); its overall structure classifies this subunit of the APS reductase as member of the fumarate reductase family [18]–[20]. The global part of the beta-subunit is embedded into a broad cleft of the alpha-subunit, while its long tail wraps around the latter increasing the contact surface between both subunits [18] (see Fig. 1). The reaction mechanism of APS reductase has been under debate [21], [22]; Schiffers and coworkers recently determined the X-ray structures of A. fulgidus APS reductases in different enzymatic states [23] that confirmed the proposed catalytic mechanism via a nucleophilic attack of the N5 atom of reduced FAD on the sulfur of APS. A covalent FAD-APS intermediate is formed that decomposes spontaneously to AMP and to the FAD-sulfite adduct which is subsequently cleaved, and sulfite is finally liberated [23], [24]. The two electrons required for the reduction of APS were postulated to be transferred one by one over 30 Å via [4Fe-4S] cluster II at the surface of the protein, cluster I and Trp-B48 to the isoalloxazine ring of the buried FAD [18], [23], [24] (see Fig. 1).


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

Meyer B, Kuever J - PLoS ONE (2008)

Three-dimensional ribbon structure of APS reductase from A. fulgidus.The beta-subunit segments are colored red (ferredoxin segment), blue (3 antiparallel beta-sheets segment), and green (tail segment); the alpha-subunit domains are colored light blue and orange (FAD-binding domain I and II), pink (capping domain), and grey (helical domain). The [4Fe-4S] clusters, FAD and substrate APS are shown as ball-and-stick representations; tryptophan Trp-B48 of AprB is highlighted by violet color. Ribbon structure is shown from (A) top view, (B) bottom view (substrate channel), (C) front view, and (D) back view.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0001514-g001: Three-dimensional ribbon structure of APS reductase from A. fulgidus.The beta-subunit segments are colored red (ferredoxin segment), blue (3 antiparallel beta-sheets segment), and green (tail segment); the alpha-subunit domains are colored light blue and orange (FAD-binding domain I and II), pink (capping domain), and grey (helical domain). The [4Fe-4S] clusters, FAD and substrate APS are shown as ball-and-stick representations; tryptophan Trp-B48 of AprB is highlighted by violet color. Ribbon structure is shown from (A) top view, (B) bottom view (substrate channel), (C) front view, and (D) back view.
Mentions: The X-ray structure of the dissimilatory APS reductase isolated from Archaeoglobus fulgidus has been elucidated at 1.6 Å resolution by Fritz and coworkers [18]: Its beta-subunit can be subdivided in three segments comprising a bacterial ferredoxin-like segment that envelopes both [4Fe-4S] clusters (amino acids B1-B68), followed by a three-stranded antiparallel beta-sheet (B69-B104) and a tail with a length of 50 Å (B105-B148) (see Fig. 1). The structure of the alpha-subunit can be grouped into the FAD cofactor-binding (amino acids A2-A261 and A394-A487), the capping (A262-A393) and the helical domains (A488-A643) (see Fig. 1); its overall structure classifies this subunit of the APS reductase as member of the fumarate reductase family [18]–[20]. The global part of the beta-subunit is embedded into a broad cleft of the alpha-subunit, while its long tail wraps around the latter increasing the contact surface between both subunits [18] (see Fig. 1). The reaction mechanism of APS reductase has been under debate [21], [22]; Schiffers and coworkers recently determined the X-ray structures of A. fulgidus APS reductases in different enzymatic states [23] that confirmed the proposed catalytic mechanism via a nucleophilic attack of the N5 atom of reduced FAD on the sulfur of APS. A covalent FAD-APS intermediate is formed that decomposes spontaneously to AMP and to the FAD-sulfite adduct which is subsequently cleaved, and sulfite is finally liberated [23], [24]. The two electrons required for the reduction of APS were postulated to be transferred one by one over 30 Å via [4Fe-4S] cluster II at the surface of the protein, cluster I and Trp-B48 to the isoalloxazine ring of the buried FAD [18], [23], [24] (see Fig. 1).

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