Sulfate Respiration in Desulfovibrio vulgaris Hildenborough

Abstract

The crystal structure of the high molecular mass cytochrome c HmcA from Desulfovibrio vulgaris Hildenborough is described. HmcA contains the unprecedented number of sixteen hemes c attached to a single polypeptide chain, is associated with a membranebound redox complex, and is involved in electron transfer from the periplasmic oxidation of hydrogen to the cytoplasmic reduction of sulfate. The structure of HmcA is organized into four tetraheme cytochrome c 3 -like domains, of which the first is incomplete and contains only three hemes, and the final two show great similarity to the nine-heme cytochrome c from Desulfovibrio desulfuricans. An isoleucine residue fills the vacant coordination space above the iron atom in the five-coordinated high-spin Heme 15. The characteristics of each of the tetraheme domains of HmcA, as well as its surface charge distribution, indicate this cytochrome has several similarities with the nine-heme cytochrome c and the Type II cytochrome c 3 molecules, in agreement with their similar genetic organization and mode of reactivity and further support an analogous physiological function for the three cytochromes. Based on the present structure, the possible electron transfer sites between HmcA and its redox partners (namely Type I cytochrome c 3 and other proteins of the Hmc complex), as well as its physiological role, are discussed.

Redox-Bohr and Other Cooperativity Effects in the Nine-heme Cytochrome c from Desulfovibrio desulfuricans ATCC 27774

“…9HcA is encoded by the first gene of an operon, which also encodes for three other proteins (9HcB, 9HcC, and 9HcD) and is mainly involved in sulfate respiration (30). The four proteins that compose this putative redox complex (9Hc) are similar in sequence to four of the proteins identified in another related redox complex, the Hmc complex (HmcB, HmcC, HmcD, HmcE, and HmcF), isolated from D. vulgaris Hildenborough (DvH) (31,32). 9HcA has 39% sequence identity with the C-terminal region of the 16-heme high molecular mass cytochrome c (HmcA), 9HcB has 51% sequence identity with HmcB, 9HcC has 64% sequence identity with HmcC, and 9HcD has 30% sequence identity with HmcD (30).…”

Recent advances in theCRANKsoftware suite for experimental phasing

“…A total of 132 data sets were used and were composed of 78 data sets from the Joint Center for Structural Genomics (JCSG; http://www.jcsg.org/), 1vjn, 1vjr, 1vjz, 1vk4, 1vkm, 1vlm, 1vqr, 1z82, 1zy9, 1zyb, 2a2m, 2a2o, 2a3n, 2a6b, 2aml, 2avn, 2b8m, 2etd, 2etj, 2ets, 2etv, 2evr, 2f4p, 2fea, 2ffj, 2fg0, 2fg9, 2fna, 2fqp, 2fur, 2fzt, 2g0t, 2g42, 2gc9, 2nlv, 2nuj, 2nwv, 2o08, 2o1q, 2o2x, 2o2z, 2o3l, 2o62, 2o7t, 2o8q, 2obp, 2oc5, 2od5, 2od6, 2oh3, 2okc, 2okf, 2ooj, 2opk, 2osd, 2otm, 2ozg, 2ozj, 2p10, 2p4o, 2p7h, 2p7i, 2p97, 2pg3, 2pg4, 2pgc, 2pim, 2pn1, 2pnk, 2ppv, 2pr7, 2prr, 2prv, 2prx, 2pv4, 2pw4, 2b78 and 2b79; 23 data sets from Mueller-Dieckmann et al (2007), 2g4h, 2g4i, 2g4j, 2g4k, 2g4p, 2g4q, 2g4l, 2g4n, 2g4o, 2g4r, 2g4s, 2g4t, 2g4u, 2g4v, 2g4w, 2g4x, 2g4y, 2g4z, 2ill, 2g51, 2g52, 2g54 and 2g55; and 31 from various other individual data-set contributors, 1e42 (Owen, Vallis et al, 2000), 1e6i (Owen, Ornaghi et al, 2000), 1hf8 (Ford et al, 2001), 2ahy (Shi et al, 2006), 2hba (J.-H. Cho, S. Sato, E. Y. Kim, H Schindelin & D. P. Raleigh, unpublished work), 2o0h (Sun et al, 2007), 2rkk (Xiao et al, 2008), 3bpj (L. Nedyalkova, B. Hong, W. Tempel, F. MacKenzie, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, A. Bochkarev & H. Park, unpublished work), 2fdn (Dauter et al, 1997), 1of3 (Boraston et al, 2003), 1i4u (Gordon et al, 2001), 1dw9 (Walsh et al, 2000), 1v0o (Holton et al, 2003), 1fse (Ducros et al, 2001), 1xib (Carrell et al, 1989), 1fj2 (Devedjiev et al, 2000), 1h29 (Matias et al, 2002), 1c8u (Jia et al, 2000), 1lvy (Schiltz et al, 1997), 1lz8 (Dauter et al, 1999), 1e3m (Lamers et al, 2000), 1ga1 (Dauter et al, 2001), 1djl (White et al, 2000), 1dtx (Skarzynski, 1992), 1dpx (Weiss, 2001), 1mso (Smith et al, 2003), 1ocy …”

Biosynthesized Iron Sulfide Nanocluster Enhanced Anodic Current Generation by Sulfate Reducing Bacteria in Microbial Fuel Cells

“…To get insight into the electron transport pathway from the lactate oxidation metabolism of SRB to FeS, we examined the current production by using a mutant strain of D. vulgaris Hildenborough, C‐cytochrome mutants (Δ cycA ), lacking periplasmic cytochrome c3 (DVU3171) which is involved in electron transfer across the periplasm . The Δ cycA mutant showed the peak current production considerably less than wild type (Figure S3).…”

“…To get insight into the electron transport pathway from the lactate oxidation metabolism of SRB to FeS, we examined the current production by using a mutant strain of D. vulgaris Hildenborough, C-cytochrome mutants (ΔcycA), lacking periplasmic cytochrome c3 (DVU3171) which is involved in electron transfer across the periplasm. [38] The ΔcycA mutant showed the peak current production considerably less than wild type ( Figure S3). However, the current started to increase as early as wild type, which is distinct from sulfide-mediated current production, indicating that deletion of periplasmic cytochrome c3 did not totally inactivate the mechanism of FeS-mediated electron transport mechanism.…”