Crystal Structure of the Archaeal A1AO ATP Synthase Subunit B from Methanosarcina mazei Gö1: Implications of Nucleotide-binding Differences in the Major A1AO Subunits A and B

The archaeal ATP synthase is a multisubunit complex that consists of a catalytic A 1 part and a transmembrane, ion translocation domain A 0 . The A 1 A 0 complex from the hyperthermophile Pyrococcus furiosus was isolated. Mass analysis of the complex by laser-induced liquid bead ion desorption (LILBID) indicated a size of 730 ؎ 10 kDa. A three-dimensional map was generated by electron microscopy from negatively stained images. The map at a resolution of 2.3 nm shows the A 1 and A 0 domain, connected by a central stalk and two peripheral stalks, one of which is connected to A 0 , and both connected to A 1 via prominent knobs. X-ray structures of subunits from related proteins were fitted to the map. On the basis of the fitting and the LILBID analysis, a structural model is presented with the stoichiometry A 3 B 3 CDE 2 FH 2 ac 10 .Archaea produce ATP by an ATP synthase that is distinct from the well known F 1 F 0 -type ATP synthase occurring in bacteria, mitochondria, and chloroplasts. The A-type ATP synthases are more closely related to vacuolar (V-type) ATPase, which, however, is functionally different and acts as an ATPdriven ion pump (1). Some bacteria also harbor A-type ATP synthases, probably acquired by horizontal gene transfer (2, 3).Like F 1 F 0 ATP synthases and V 1 V 0 ATPases, A 1 A 0 ATP synthases consist of a soluble enzymatic head in the cytoplasm and a transmembrane ion-translocating domain, forming a pair of coupled rotary motors. There is clear homology in the main catalytic subunits of all types, showing a common evolutionary origin, but many of the peripheral subunits are unique for the distinct groups. The A-and V-type enzymes are considerably larger than the F-type (1).The catalytic heads are made up of three A and three B subunits, where A is the catalytic subunit equivalent to F-type ␤. The A subunit contains a 90-amino acid insert near the N terminus, known as the non-homologous region, which makes this subunit with Ϸ66 kDa considerably larger than its homologues (4 -7). The central stalk consists of the C, D, and F subunits, and the D subunit is thought to be the equivalent of the ␥ subunit, responsible for conformational changes in the nucleotide-binding pockets upon rotation (8, 9). The transmembrane domain contains a rotor of a number of identical c-subunits and part of the a-subunit. The a-subunit is large, comprising a transmembrane domain with seven to eight predicted transmembrane helices and a soluble domain, which probably forms part of the stator. In addition, the A-type ATP synthases contain subunits H and E (10).Structural information on the A-type and V-type ATPases has been forthcoming in recent years. For several subunits, x-ray structures have been determined, including isolated archaeal A (11) and B (12) subunits, the E subunit (13), and a bacterial A-type C subunit (14, 15). The archaeal F subunit has been solved by NMR spectroscopy (16), and the shape of an H subunit dimer is known from small angle x-ray scattering (17). Information about the whole complex has been pro...

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“…It is clear that the peripheral stalks connect to the B subunits exclusively (Fig. 7a), as was observed for the T. thermophilus structure (12).…”

Section: Purification and Characterization Of The A 1 A 0 Atp Synthassupporting

confidence: 71%

Three-dimensional Structure of A1A0 ATP Synthase from the Hyperthermophilic Archaeon Pyrococcus furiosus by Electron Microscopy

Vonck

Pisa

Morgner

et al. 2009

Journal of Biological Chemistry

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“…A previous three-dimensional reconstruction of T. thermophilus A-ATPase to 23 Å showed that the two peripheral stalks are arranged 120°about the hexameric A 3 B 3 headgroup of A 1 (16). Docking of the nucleotide binding subunits A and B into this density suggested that the peripheral stalks are in contact with two of the three B subunits (40), and it is therefore likely that the same interactions are used to affix both peripheral stalks to the A 3 B 3 headgroup. A recent x-ray structure of subunit E from P. horikoshii (17) suggested a homodimeric arrangement of this subunit, but the authors speculate the homodimer to be located asymmetrically to the A-ATPase complex in only one peripheral stalk.…”

Section: Discussionmentioning

confidence: 91%

Stoichiometry and Localization of the Stator Subunits E and Gin Thermus thermophilus H+-ATPase/Synthase

Esteban

Bernal

Donohoe

et al. 2008

Journal of Biological Chemistry

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Proton-translocating ATPases are central to biological energy conversion. Although eukaryotes contain specialized F-ATPases for ATP synthesis and V-ATPases for proton pumping, eubacteria and archaea typically contain only one enzyme for both tasks. Although many eubacteria contain ATPases of the F-type, some eubacteria and all known archaea contain ATPases of the A-type. A-ATPases are closely related to V-ATPases but simpler in design. Although the nucleotidebinding and transmembrane rotor subunits share sequence homology between A-, V-, and F-ATPases, the peripheral stalk is strikingly different in sequence, composition, and stoichiometry. We have analyzed the peripheral stalk of Thermus thermophilus A-ATPase by using phage display-derived single-domain antibody fragments in combination with electron microscopy and tandem mass spectrometry. Our data provide the first direct evidence for the existence of two peripheral stalks in the A-ATPase, each one composed of heterodimers of subunits E and G arranged symmetrically around the soluble A 1 domain. To our knowledge, this is the first description of phage display-derived antibody selection against a multi-subunit membrane protein used for purification and single particle analysis by electron microscopy. It is also the first instance of the derivation of subunit stoichiometry by tandem mass spectrometry to an intact membrane protein complex. Both approaches could be applicable to the structural analysis of other membrane protein complexes.F-, V-, and A-ATPases 2 are evolutionary related protein complexes (1) that couple ATP synthesis/hydrolysis with proton (or Na ϩ ) translocation across membranes (2-4). A-and V-ATPases are evolutionarily closer to each other than they are to F-ATPases (5). However, A-ATPases are functionally more similar to F-ATPases because both synthesize ATP using energy derived from proton translocation (5). V-ATPases work in reverse by actively pumping protons through membranes using ATP hydrolysis as the driving force (6).Although eukaryotes contain both types of ATPases, each one highly specialized in its physiological function, archaea and eubacteria typically contain only one. Both eubacterial F-ATPases and eubacterial and archaeal V-ATPases are simpler than their eukaryotic counterparts but are functionally more versatile in that they can operate in both directions. Archaeal and eubacterial V-ATPases are closely related and are often referred to as A-ATPases (4).F-, V-, and A-ATPases share an overall conservation of structure that includes a water-soluble F 1 /V 1 /A 1 domain and a membrane-bound F o /V o /A o domain (7-10). The Thermus thermophilus ATPase-active A 1 domain is composed of a head group that contains a heterotrimer of the nucleotide-binding proteins A and B and a central stalk composed of proteins C, D, and F (11). The proton-translocating A o domain contains a ring of L proteolipids and a single copy of protein I that is located adjacent to the ring. The L ring, in association with the central stalk components (CDF), for...

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“…Suitable structural models for ATP6V1B2 (48) and CREBBP (49) were identified using the Protein Model Portal (50). Coordinate files of the models were downloaded from ModBase (51) and SWISS-MODEL (52), respectively.…”

Section: Methodsmentioning

confidence: 99%

Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation

Green

Kihira²,

Liu³

et al. 2015

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

325

372

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Follicular lymphoma (FL) is incurable with conventional therapies and has a clinical course typified by multiple relapses after therapy. These tumors are genetically characterized by B-cell leukemia/lymphoma 2 (BCL2) translocation and mutation of genes involved in chromatin modification. By analyzing purified tumor cells, we identified additional novel recurrently mutated genes and confirmed mutations of one or more chromatin modifier genes within 96% of FL tumors and two or more in 76% of tumors. We defined the hierarchy of somatic mutations arising during tumor evolution by analyzing the phylogenetic relationship of somatic mutations across the coding genomes of 59 sequentially acquired biopsies from 22 patients. Among all somatically mutated genes, CREBBP mutations were most significantly enriched within the earliest inferable progenitor. These mutations were associated with a signature of decreased antigen presentation characterized by reduced transcript and protein abundance of MHC class II on tumor B cells, in line with the role of CREBBP in promoting class II transactivator (CIITA)-dependent transcriptional activation of these genes. CREBBP mutant B cells stimulated less proliferation of T cells in vitro compared with wild-type B cells from the same tumor. Transcriptional signatures of tumor-infiltrating T cells were indicative of reduced proliferation, and this corresponded to decreased frequencies of tumor-infiltrating CD4 helper T cells and CD8 memory cytotoxic T cells. These observations therefore implicate CREBBP mutation as an early event in FL evolution that contributes to immune evasion via decreased antigen presentation. lymphoma | exome | hierarchy | antigen presentation | CREBBP

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Crystal Structure of the Archaeal A1AO ATP Synthase Subunit B from Methanosarcina mazei Gö1: Implications of Nucleotide-binding Differences in the Major A1AO Subunits A and B

Cited by 66 publications

References 64 publications

Three-dimensional Structure of A1A0 ATP Synthase from the Hyperthermophilic Archaeon Pyrococcus furiosus by Electron Microscopy

Three-dimensional Structure of A1A0 ATP Synthase from the Hyperthermophilic Archaeon Pyrococcus furiosus by Electron Microscopy

Stoichiometry and Localization of the Stator Subunits E and Gin Thermus thermophilus H+-ATPase/Synthase

Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation

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