ATP Ground- and Transition States of Bacterial Enhancer Binding AAA+ ATPases Support Complex Formation with Their Target Protein, σ54

Chen, Baoyu; Doucleff, Michaeleen; Wemmer, David E.; Carlo, Sacha De; Huang, Hongtai; Nogales, Eva; Hoover, Timothy R.; Kondrashkina, Elena; Guo, Liang; Nixon, B. Tracy

doi:10.1016/j.str.2007.02.007

Cited by 67 publications

(133 citation statements)

References 32 publications

(52 reference statements)

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“…As established earlier (Chen et al 2007), adding 1-5 mM ATP and ATP analogs to the assembled ring form of apo NtrC1 ATPase causes it to undergo large-scale conformational changes, but adding ADP does not. It was also shown that beginning near 1 mM concentration, ATP inhibits ATPase activity of the s54-dependent activators.…”

Section: Complexity Of Atp Binding To Ntrc1mentioning

confidence: 53%

“…Our prior biochemical and structural analyses suggested two things: (1) that apo and ADP-saturated rings form similar heptamer rings (SAXS data in Chen et al 2007) and (2) that strong clashes predicted for the interface between neighboring subunits that are alternately bound to ATP or ADP can be avoided by highly cooperative nucleotide binding and hydrolysis . In this study, we see that the symmetry in those ring structures is broken as binding of ATP analogs gradually drives the heptamers to form split-ring hexamers.…”

Section: Discussionmentioning

confidence: 99%

“…Several bEBPs have been crystallized as hexamers and heptamers, but no mechanism for hydrolysis has yet emerged from those structures (Lee et al 2003;Rappas et al 2005Rappas et al , 2006Sallai and Tucker 2005;Batchelor et al 2008;Chen et al 2010). We showed previously that binding of ATP but not ADP causes large structural changes in the bEBP NtrC1 from the extreme hyperthermophile Aquifex aeolicus (Chen et al 2007. Presumed symmetry required for modeling those small-angle solution X-ray scattering (SAXS) data and sevenfold symmetry in the ADP-and ATP-bound crystal structures suggested cooperative upward and downward motion of the crucial GAFTGA-containing loops that tracks the status of nucleotides in the hydrolysis cycle .…”

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confidence: 99%

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Nucleotide-induced asymmetry within ATPase activator ring drives σ54–RNAP interaction and ATP hydrolysis

et al. 2013

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It is largely unknown how the typical homomeric ring geometry of ATPases associated with various cellular activities enables them to perform mechanical work. Small-angle solution X-ray scattering, crystallography, and electron microscopy (EM) reconstructions revealed that partial ATP occupancy caused the heptameric closed ring of the bacterial enhancer-binding protein (bEBP) NtrC1 to rearrange into a hexameric split ring of striking asymmetry. The highly conserved and functionally crucial GAFTGA loops responsible for interacting with s54-RNA polymerase formed a spiral staircase. We propose that splitting of the ensemble directs ATP hydrolysis within the oligomer, and the ring's asymmetry guides interaction between ATPase and the complex of s54 and promoter DNA. Similarity between the structure of the transcriptional activator NtrC1 and those of distantly related helicases Rho and E1 reveals a general mechanism in homomeric ATPases whereby complex allostery within the ring geometry forms asymmetric functional states that allow these biological motors to exert directional forces on their target macromolecules.

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Section: Complexity Of Atp Binding To Ntrc1mentioning

confidence: 53%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Nucleotide-induced asymmetry within ATPase activator ring drives σ54–RNAP interaction and ATP hydrolysis

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“…Indeed, structural studies of several other hexameric ATPases have been interpreted as evidence that these enzymes cycle between states that are fully ATP-bound or ADP-bound. [23][24][25] Moreover, most HslU and HslUV crystal structures have six bound ATPs or ADPs (Fig. 1B), apparently supporting a symmetric or concerted mechanism of ATP hydrolysis.…”

Section: Introductionmentioning

confidence: 74%

Asymmetric Nucleotide Transactions of the HslUV Protease

Yakamavich

Baker

Sauer

2008

Journal of Molecular Biology

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SummaryATP binding and hydrolysis are critical for protein degradation by HslUV, a AAA+ machine containing one or two HslU 6 ATPases and the HslV 12 peptidase. Although each HslU homohexamer has six potential ATP-binding sites, we show that only three or four ATP molecules bind at saturation and present evidence for three functional subunit classes. These results imply that only a subset of HslU and HslUV crystal structures represent functional enzyme conformations. Our results support an asymmetric mechanism of ATP binding and hydrolysis and suggest that molecular contacts between HslU and HslV vary dynamically throughout the ATPase cycle. Nucleotide binding controls HslUV assembly and activity. Binding of a single ATP allows HslU to bind HslV, whereas additional ATPs must bind HslU to support substrate recognition and to activate ATP hydrolysis, which powers substrate unfolding and translocation. Thus, a simple thermodynamic hierarchy ensures that substrates bind to functional HslUV complexes, that ATP hydrolysis is efficiently coupled to protein degradation, and that working HslUV does not dissociate, allowing highly processive degradation.

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“…Thus, the hydrolysis transition state configuration will exist when the DNA-binding hairpins reach the highest position of the cycle. This situation resembles the that of NtrC where the GAFTGA loops are directed towards the top of complex when bound to an ATP analog and occupy a higher position when bound to an ATP-transition state analog [84 ]. The loops are not projected upward when bound to ADP [84 ,85].…”

Section: Perturbations Of the Atpase Active Site Tethermentioning

confidence: 90%

On helicases and other motor proteins

Enemark

Joshua‐Tor

2008

Current Opinion in Structural Biology

192

238

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Helicases are molecular machines that utilize energy derived from ATP hydrolysis to move along nucleic acids and to separate base-paired nucleotides. The movement of the helicase can also be described as a stationary helicase that pumps nucleic acid. Recent structural data for the hexameric E1 helicase of papillomavirus in complex with single-stranded DNA and MgADP has provided a detailed atomic and mechanistic picture of its ATP-driven DNA translocation. The structural and mechanistic features of this helicase are compared with the hexameric helicase prototypes T7gp4 and SV40 T-antigen. The ATP-binding site architectures of these proteins are structurally similar to the sites of other prototypical ATP-driven motors such as F1-ATPase, suggesting related roles for the individual site residues in the ATPase activity. IntroductionHelicases are essential enzymes that unwind duplex DNA, RNA, or DNA-RNA hybrids. This unwinding is driven by consumption of input energy that is harnessed to separate base-paired oligonucleotides and also to maintain a unidirectional advancement of the helicase upon the nucleic acid substrate. This translocation can alternatively be described as an immobile helicase pumping nucleic acid. The energy for these transformations is derived from the hydrolysis of nucleotide triphosphate (NTP). Helicases can be depicted as an internal combustion engine with each individual NTPase site serving as one cylinder. Each individual cylinder follows a defined series of events: injection (ATP binding), compression (optimally positioning the site for hydrolysis), combustion (ATP hydrolysis/work generation), and exhaust (ADP and phosphate release). In a helicase, the individual combustion cylinders coordinate these actions to carry out the repetitive mechanical operation of prying open base pairs and/or actively translocating with respect to the nucleic acid substrate. Many other molecular motors utilize similar engines to carry out multiple diverse functions such as translocation of peptides in the case of ClpX, movement along cellular structures in the case of dyenin, and rotation about an axle as in F 1 -ATPase.Based upon conserved sequence motifs, helicases have been classified into six superfamilies [1,2 ]. An extensive review of these superfamilies has been provided recently [3 ]. Superfamily 1 (SF1) and superfamily 2 (SF2) helicases are very prevalent, generally monomeric, and participate in several diverse DNA and RNA manipulations. The other helicase superfamilies form hexameric rings (reviewed in [4]), as demonstrated by biochemistry [5][6][7][8] and electron microscopy studies [9][10][11][12][13][14][15][16][17], and often participate at the replication fork. All of these helicases bind and hydrolyze NTP at the interface between two recA-like domains. The binding site consists of a Walker A (P-loop) and a Walker B motif from the first domain and other elements such as an arginine finger from the other domain. The SF1 and SF2 helicases contain two recAlike domains coupled by a short linker, and t...

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ATP Ground- and Transition States of Bacterial Enhancer Binding AAA+ ATPases Support Complex Formation with Their Target Protein, σ54

Cited by 67 publications

References 32 publications

Nucleotide-induced asymmetry within ATPase activator ring drives σ54–RNAP interaction and ATP hydrolysis

Nucleotide-induced asymmetry within ATPase activator ring drives σ54–RNAP interaction and ATP hydrolysis

Asymmetric Nucleotide Transactions of the HslUV Protease

On helicases and other motor proteins

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