Phosphorylated aspartate in the structure of a response regulator protein 1 1Edited by A. R. Fersht

Lewis, Richard J.; Brannigan, J.A.; Muchová, Katarı́na; Barák, Imrich; Wilkinson, Anthony J.

doi:10.1006/jmbi.1999.3261

Cited by 153 publications

(174 citation statements)

References 33 publications

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“…1) forming a hydrogen bond with the main chain carbonyl oxygen of Arg83 situated at the middle of the β4-α4 loop. Similar interactions have been reported for many structures of the activated regulatory domains, such as of Spo0A, 45 FixJ 46 and CheY. 47,48 The area that differs most between the two structures is the β4-α4 loop, specifically residues Thr81, Gly82 and Arg83 ( Fig.…”

Section: Coordination At the Active Site And Differences In The Two Ssupporting

confidence: 80%

Structural Analysis and Solution Studies of the Activated Regulatory Domain of the Response Regulator ArcA: A Symmetric Dimer Mediated by the α4-β5-α5 Face

Toro-Roman

Mack²,

Stock

2005

Journal of Molecular Biology

116

137

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SUMMARYEscherichia coli react to changes from aerobic to anaerobic conditions of growth using the ArcAArcB two-component signal transduction system. This system, in conjunction with other proteins, regulates the respiratory metabolic pathways in the organism. ArcA is a member of the OmpR/ PhoB subfamily of response regulator transcription factors that are known to regulate transcription by binding in tandem to target DNA direct repeats. It is still unclear in this subfamily how activation by phosphorylation of the regulatory domain of response regulators stimulates DNA binding by the effector domain and how dimerization and domain orientation, as well as intra-and intermolecular interactions, affect this process. In order to address these questions we have solved the crystal structure of the regulatory domain of ArcA in the presence and absence of the phosphoryl analog, BeF 3 − . In the crystal structures, the regulatory domain of ArcA forms a symmetric dimer mediated by the α4-β5-α5 face of the protein and involving a number of residues that are highly conserved in the OmpR/PhoB subfamily. It is hypothesized that members of this subfamily use a common mechanism of regulation by dimerization. Additional biophysical studies were employed to probe the oligomerization state of ArcA, as well as its individual domains, in solution. The solution studies show the propensity of the individual domains to associate into oligomers larger than the dimer observed for the intact protein, and suggest that the C-terminal DNA-binding domain also plays a role in oligomerization.

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Section: Coordination At the Active Site And Differences In The Two Ssupporting

confidence: 80%

Structural Analysis and Solution Studies of the Activated Regulatory Domain of the Response Regulator ArcA: A Symmetric Dimer Mediated by the α4-β5-α5 Face

Toro-Roman

Mack²,

Stock

2005

Journal of Molecular Biology

116

137

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“…To illustrate key discrepancies between canonical RDs, NblR RD and other atypical RDs, we produced a 3D structure model of the NblR RD and used it to generate a structural alignment with selected canonical and non-canonical RDs. In order to emphasize the catalytic residue disposition in the alignment, we chose the CheY and PhoB beryllium fluoride-activated structures as prototypical RDs, as well as the phosphorylated Spo0A structure (Lewis et al, 1999), the first canonical RD crystallized in the phosphorylated form. The structures of Myxococcus xanthus FrzS (Fraser et al, 2007) and Helicobacter pylori HP1043 (Schar et al, 2005) were used as a model of atypical RDs.…”

Section: Resultsmentioning

confidence: 99%

“…The quality of the final model was assessed using the PROCHECK suite of programs (Morris et al, 1992). The receiver domain structures of phosphorylated Spo0A from Bacillus stearothermophilus (RCSB code 1QMP) (Lewis et al, 1999), beryllium fluoride-activated PhoB from E. coli (RCSB code 1ZES) (Bachhawat et al, 2005), FrzS from Myxococcus xanthus (RCSB code 2GKG) (Fraser et al, 2007), beryllium fluoride-activated CheY from E. coli (RCSB code 1FQW) , HP1043 from Helicobacter pylori (RCSB code 2PLN) as well as the NblR model were structurally aligned using the LSQKAB program as implemented in the CCP4 suite (Collaborative Computational Project, Number 4, 1994).…”

Section: Methodsmentioning

confidence: 99%

Phosphorylation-independent activation of the atypical response regulator NblR

et al. 2008

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“…The short lifetime of the phospho-enzyme (k hydrolysis ¼ 0.05 s −1 (14); 0.026 AE 0.001 s −1 (15)) is unsurprising because acyl phosphates are highly reactive phosphorylating species (ΔG ∘ hydrolysis ¼ −10 kcal mol −1 ). Only in exceptional circumstances are the half-lives extended above 24 h (16).…”

mentioning

confidence: 99%

Atomic details of near-transition state conformers for enzyme phosphoryl transfer revealed by MgF3- rather than by phosphoranes

Baxter

Bowler

Alizadeh

et al. 2010

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

137

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Prior evidence supporting the direct observation of phosphorane intermediates in enzymatic phosphoryl transfer reactions was based on the interpretation of electron density corresponding to trigonal species bridging the donor and acceptor atoms. Close examination of the crystalline state of β-phosphoglucomutase, the archetypal phosphorane intermediate-containing enzyme, reveals that the trigonal species is not PO − 3 , but is MgF − 3 (trifluoromagnesate). Although MgF − 3 complexes are transition state analogues rather than phosphoryl group transfer reaction intermediates, the presence of fluorine nuclei in near-transition state conformations offers new opportunities to explore the nature of the interactions, in particular the independent measures of local electrostatic and hydrogen-bonding distributions using 19 F NMR. Measurements on three β-PGM-MgF − 3 -sugar phosphate complexes show a remarkable relationship between NMR chemical shifts, primary isotope shifts, NOEs, cross hydrogen bond F⋯H-N scalar couplings, and the atomic positions determined from the highresolution crystal structure of the β-PGM-MgF − 3 -G6P complex. The measurements provide independent validation of the structural and isoelectronic MgF − 3 model of near-transition state conformations.19F NMR | phosphoryl transfer enzyme | transition state analogue | trifluoromagnesate T he mono-and diesters of phosphoric acid have commanding and ubiquitous roles in all species of life. As structural components they show remarkable stability to spontaneous hydrolysis under near physiological conditions (25°C), with half-lives for P-O bond cleavage in phosphate diesters estimated at ca. 10 7 years and for monoesters ca. 10 12 years (1, 2). Yet, they are susceptible to enzyme-catalyzed hydrolysis and phosphoryl group transfer reactions either between two oxygens, or between oxygen and nitrogen or sulfur, with turnover numbers adequate to support a vast array of biological processes, e.g. Serratia nuclease k cat ca. 2; 500 s −1 (3), E. coli alkaline phosphatase k cat ≥ 45 s −1 (4), and human protein tyrosine phosphatase β k cat ca.

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Phosphorylated aspartate in the structure of a response regulator protein 1 1Edited by A. R. Fersht

Cited by 153 publications

References 33 publications

Structural Analysis and Solution Studies of the Activated Regulatory Domain of the Response Regulator ArcA: A Symmetric Dimer Mediated by the α4-β5-α5 Face

Structural Analysis and Solution Studies of the Activated Regulatory Domain of the Response Regulator ArcA: A Symmetric Dimer Mediated by the α4-β5-α5 Face

Phosphorylation-independent activation of the atypical response regulator NblR

Atomic details of near-transition state conformers for enzyme phosphoryl transfer revealed by MgF3- rather than by phosphoranes

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