Intact Functional Fourteen-subunit Respiratory Membrane-bound [NiFe]-Hydrogenase Complex of the Hyperthermophilic Archaeon Pyrococcus furiosus

McTernan, Patrick M.; Chandrayan, Sanjeev K.; Wu, Chang Hao; Vaccaro, Brian J.; Lancaster, W. Andrew; Yang, Qingyuan; Fu, Dax; Hura, Greg L.; Tainer, John A.; Adams, Michael W. W.

doi:10.1074/jbc.m114.567255

Cited by 40 publications

(45 citation statements)

References 44 publications

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“…long-branch attraction). 91 Consistent with previous phylogenetic analyses 2,14,15 , this analysis showed the 19 , the 122 ferredoxin-coupled Mrp-linked complexes (Group 4d) 20 , the well-described 123 methanogenic Eha (Group 4h) and Ehb (Group 4i) supercomplexes 21 , and a more 124 loosely clustered class of unknown function (Group 4g). Three crenarchaeotal 125 hydrogenases were also classified as their own family (Group 2e); these enzymes 126 7…”

supporting

confidence: 78%

HydDB: A web tool for hydrogenase classification and analysis

Søndergaard

Pedersen

Greening

2016

Preprint

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supporting

confidence: 78%

HydDB: A web tool for hydrogenase classification and analysis

Søndergaard

Pedersen

Greening

2016

Preprint

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“…In Pyrococcus , the Na + gradient required for ATP synthesis is maintained by specific antiporters ( McTernan et al, 2014 ). We therefore assume that PaNhaP, like human NHE1, utilizes the Na + gradient across the membrane ( Cohen et al, 2003 ) for pH homeostasis.…”

Section: Discussionmentioning

confidence: 99%

Structure and substrate ion binding in the sodium/proton antiporter PaNhaP

Wöhlert

Kühlbrandt

Yıldız

2014

eLife

100

191

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Sodium/proton antiporters maintain intracellular pH and sodium levels. Detailed structures of antiporters with bound substrate ions are essential for understanding how they work. We have resolved the substrate ion in the dimeric, electroneutral sodium/proton antiporter PaNhaP from Pyrococcus abyssi at 3.2 Å, and have determined its structure in two different conformations at pH 8 and pH 4. The ion is coordinated by three acidic sidechains, a water molecule, a serine and a main-chain carbonyl in the unwound stretch of trans-membrane helix 5 at the deepest point of a negatively charged cytoplasmic funnel. A second narrow polar channel may facilitate proton uptake from the cytoplasm. Transport activity of PaNhaP is cooperative at pH 6 but not at pH 5. Cooperativity is due to pH-dependent allosteric coupling of protomers through two histidines at the dimer interface. Combined with comprehensive transport studies, the structures of PaNhaP offer unique new insights into the transport mechanism of sodium/proton antiporters.DOI: http://dx.doi.org/10.7554/eLife.03579.001

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“…Furthermore, biophysical methods such as SAXS, atomic force microscopy, fluorescent energy transfer, and electron microscopy are enabling the characterization of solution architectures, assemblies and conformations [233,234] that will help address the roles of Fe-S in conformational states and charge transfer in cells. SAXS can be powerfully combined with x-ray crystallography [235] and advanced SAXS methods, which define shape, flexibility, and agreement to atomic models [236-238] have, for example, allowed the characterization of multicomponent Fe-S proteins and membrane complexes [239], as well as conformation change for proteins acting in DNA complexes [224,240]. Collective X-ray scattering results suggest conformational variation is a general functional feature of macromolecules [241], but we know too little about the roles of Fe-S clusters in conformational changes of DNA bound complexes.…”

Section: Synopsis and Perspectivesmentioning

confidence: 99%

Emerging critical roles of Fe–S clusters in DNA replication and repair

Fuss

Tsai

Ishida

et al. 2015

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research

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211

191

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Fe-S clusters are partners in the origin of life that predate cells, acetyl-CoA metabolism, DNA, and the RNA world. The double helix solved the mystery of DNA replication by base pairing for accurate copying. Yet, for genome stability necessary to life, the double helix has equally important implications for damage repair. Here we examine striking advances that uncover Fe-S cluster roles both in copying the genetic sequence by DNA polymerases and in crucial repair processes for genome maintenance, as mutational defects cause cancer and degenerative disease. Moreover, we examine an exciting, controversial role for Fe-S clusters in a third element required for life – the long-range coordination and regulation of replication and repair events. By their ability to delocalize electrons over both Fe and S centers, Fe-S clusters have unbeatable features for protein conformational control and charge transfer via double-stranded DNA that may fundamentally transform our understanding of life, replication, and repair.

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Intact Functional Fourteen-subunit Respiratory Membrane-bound [NiFe]-Hydrogenase Complex of the Hyperthermophilic Archaeon Pyrococcus furiosus

Cited by 40 publications

References 44 publications

HydDB: A web tool for hydrogenase classification and analysis

HydDB: A web tool for hydrogenase classification and analysis

Structure and substrate ion binding in the sodium/proton antiporter PaNhaP

Emerging critical roles of Fe–S clusters in DNA replication and repair

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