The X‐ray crystal structure of <i>Shewanella oneidensis</i> OmcA reveals new insight at the microbe–mineral interface

Edwards, Marcus J.; Baiden, Nanakow; Johs, Alexander; Tomanicek, S.J.; Liang, Liyuan; Shi, Liang; Fredrickson, Jim K.; Zachara, John M.; Gates, Andrew J.; Butt, Julea N.; Richardson, David J.; Clarke, Thomas A.

doi:10.1016/j.febslet.2014.04.013

Cited by 75 publications

(93 citation statements)

References 36 publications

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“…These clades of extracellular cytochromes are distinguished by their size and amino acid composition; these properties will in turn define the specificity of their interactions with protein partners, solid surfaces and flavins ( §4.2). Structures have been resolved for MtrF, OmcA and UndA that reveal these proteins are folded as four distinct domains [70][71][72]. Domains 1 and 3 form Greek-key split b-barrel structures (figure 7a).…”

Section: Structuresmentioning

confidence: 99%

Multi-haem cytochromes inShewanella oneidensisMR-1: structures, functions and opportunities

Breuer

Rosso

Blumberger

et al. 2015

J. R. Soc. Interface.

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207

186

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Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multihaem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.

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Section: Structuresmentioning

confidence: 99%

Multi-haem cytochromes inShewanella oneidensisMR-1: structures, functions and opportunities

Breuer

Rosso

Blumberger

et al. 2015

J. R. Soc. Interface.

Self Cite

207

186

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“…From Equation (7) it can be seen that the same effects can be obtained by varying A act,cell or c s act with the same factor instead of k 0 . An increase of A act,cell could be justified by assuming a different larger size of the redox cofactor (for example, Edwards et al, 2014), a decrease by considering the cell surface not facing the other cell is unlikely to be used. Similarly, an increase in c s act is possible if redox cofactors are preferentially located where electron transfer to nanowires occurs, instead of homogeneously distributed over the cell surface.…”

Section: Mediated Vs Direct Interspecies Electron Transfer T Storck Ementioning

confidence: 99%

Modelling extracellular limitations for mediated versus direct interspecies electron transfer

2015

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Interspecies electron transfer (IET) is important for many anaerobic processes, but is critically dependent on mode of transfer. In particular, direct IET (DIET) has been recently proposed as a metabolically advantageous mode compared with mediated IET (MIET) via hydrogen or formate. We analyse relative feasibility of these IET modes by modelling external limitations using a reaction-diffusion-electrochemical approach in a three-dimensional domain. For otherwise identical conditions, external electron transfer rates per cell pair (cp) are considerably higher for formate-MIET (317 × 10 3 e − cp − 1 s − 1 ) compared with DIET (44.9 × 10 3 e − cp − 1 s − 1 ) or hydrogen-MIET (5.24 × 10 3 e − cp − 1 s − 1 ). MIET is limited by the mediator concentration gradient at which reactions are still thermodynamically feasible, whereas DIET is limited through redox cofactor (for example, cytochromes) activation losses. Model outcomes are sensitive to key parameters for external electron transfer including cofactor electron transfer rate constant and redox cofactor area, concentration or count per cell, but formate-MIET is generally more favourable for reasonable parameter ranges. Extending the analysis to multiple cells shows that the size of the network does not strongly influence relative or absolute favourability of IET modes. Similar electron transfer rates for formate-MIET and DIET can be achieved in our case with a slight (0.7 kJ mol − 1 ) thermodynamic advantage for DIET. This indicates that close to thermodynamic feasibility, external limitations can be compensated for by improved metabolic efficiency when using direct electron transfer.

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“…These domains with the extended Greek key split-barrel structures are possible binding sites of flavin mononucleotide (FMN). The crystal structure of the extracellular decaheme cytochrome OmcA shows similar structural features (4).…”

mentioning

confidence: 92%

Electron transfer pathways in a multiheme cytochrome MtrF

Watanabe

Yamashita

Ishikita

2017

Proc. Natl. Acad. Sci. U.S.A.

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In MtrF, an outer-membrane multiheme cytochrome, the 10 heme groups are arranged in heme binding domains II and IV along the pseudo-C 2 axis, forming the electron transfer (ET) pathways. Previous reports based on molecular dynamics simulations showed that the redox potential (E m ) values for the heme pairs located in symmetrical positions in domains II and IV were similar, forming bidirectional ET pathways [Breuer M, Zarzycki P, Blumberger J, Rosso KM (2012) J Am Chem Soc 134(24):9868-9871]. Here, we present the E m values of the 10 hemes in MtrF, solving the linear Poisson-Boltzmann equation and considering the protonation states of all titratable residues and heme propionic groups. In contrast to previous studies, the E m values indicated that the ET is more likely to be downhill from domain IV to II because of localization of acidic residues in domain IV. Reduction of hemes in MtrF lowered the E m values, resulting in switching to alternative downhill ET pathways that extended to the flavin binding sites. These findings present an explanation of how MtrF serves as an electron donor to extracellular substrates.decaheme | dissimilatory metal-reducing bacteria | flavin | Shewanella species | Mtr conduit

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The X‐ray crystal structure of Shewanella oneidensis OmcA reveals new insight at the microbe–mineral interface

Cited by 75 publications

References 36 publications

Multi-haem cytochromes inShewanella oneidensisMR-1: structures, functions and opportunities

Multi-haem cytochromes inShewanella oneidensisMR-1: structures, functions and opportunities

Modelling extracellular limitations for mediated versus direct interspecies electron transfer

Electron transfer pathways in a multiheme cytochrome MtrF

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