Crystal Structure of the Cyanobacterial Signal Transduction Protein PII in Complex with PipX

Zhao, Mingyang; Jiang, Yong-Liang; Xu, Bo-Ying; Chen, Yuxing; Zhang, Cheng‐Cai; Zhou, Cong‐Zhao

doi:10.1016/j.jmb.2010.08.006

Cited by 40 publications

(65 citation statements)

References 42 publications

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“…1). Crystal structures for the PII-PipX [15,16] Abbreviations: NtcA, nitrogen control factor of cyanobacteria; CRP, cAMP receptor protein, also called CAP, catabolite gene activator protein; PipX, PIIinteracting protein X; SYCRP1, Synechocystis CRP; 2OG, 2-oxoglutarate; RU, relative unit; SPR, surface plasmon resonance; FC1 and FC2, flow cells 1 and 2, respectively of the Biacore chip; IPTG, isopropyl-b-D-thiogalactoside only binds to PII if MgATP also binds), three PipX molecules are sequestered by one PII trimer in such a way that they become unavailable for activating NtcA. 2OG activates NtcA-dependent gene expression regulation [10,11] and also triggers (when ATP is also bound) the release of PipX from PII [13], making PipX available for coactivation of NtcA.…”

Section: Introductionmentioning

confidence: 99%

SPR analysis of promoter binding of Synechocystis PCC6803 transcription factors NtcA and CRP suggests cross‐talk and sheds light on regulation by effector molecules

2014

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Edited by Miguel De la RosaKeywords: Protein-protein interaction PipX protein 2-Oxoglutarate Cyanobacteria Catabolite gene activator protein Nitrogen metabolism a b s t r a c t Surface plasmon resonance monitoring of the binding of transcription factors cAMP receptor protein (CRP) and nitrogen control factor of cyanobacteria (NtcA) from Synechocystis sp. PCC6803 to promoter fragments of glnA, glnN (NtcA regulon) and cccS (CRP regulon), revealed exclusive CRP binding to cccS, whereas NtcA was bound to all three promoters with different affinities, which were strongly increased by the NtcA activator 2-oxoglutarate. Effective NtcA affinity for 2-oxoglutarate varied with the promoter. High-affinity promoters and the NtcA-coactivating protein PII-interacting protein X (PipX) increased NtcA affinity towards 2-oxoglutarate, suggesting PipX-stabilization of the 2-oxoglutarate-bound NtcA conformation. PipX binding to NtcA required 2-oxoglutarate and was much tighter (K d % 85 nM) than to the PipX-sequestering PII protein. NtcA appears to require more strongly PipX and 2-oxoglutarate (2OG) for estimulating gene expression at promoters having ''imperfect'' NtcA binding sites.

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Section: Introductionmentioning

confidence: 99%

SPR analysis of promoter binding of Synechocystis PCC6803 transcription factors NtcA and CRP suggests cross‐talk and sheds light on regulation by effector molecules

2014

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“…In this way ADP-GlnZ/DraG is predisposed for efficient interaction with AmtB. Superposition of ADP-GlnK from the E. coli AmtB-GlnK complex [2NUU, (9)], or ADP-P II from the S. elongatus PipX-P II complex [3N5B, (13)], on the ADP-GlnZ structure in the A. brasilense GlnZ-DraG complex confirms that the ADP binding mode is essentially the same in all three complexes. In particular, the ADP bound state is characterized by interactions of the main chain N-H groups of T-loop residues R38 and Q39 with the α-phosphate of ADP and also by the side chain interaction between residues Q39 and K58 (13).…”

Section: Resultsmentioning

confidence: 84%

“…The third P II complex structure is that of S. elongatus P II with another of its targets, the PipX protein (12,13). PipX is a coactivator of the cyanobacterial transcription factor NtcA (14), and P II interaction with PipX prevents activating NtcA.…”

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confidence: 99%

Crystal structure of the GlnZ-DraG complex reveals a different form of P_II-target interaction

Rajendran

Gerhardt

Bjelić

et al. 2011

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

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Nitrogen metabolism in bacteria and archaea is regulated by a ubiquitous class of proteins belonging to the P II family. P II proteins act as sensors of cellular nitrogen, carbon, and energy levels, and they control the activities of a wide range of target proteins by protein-protein interaction. The sensing mechanism relies on conformational changes induced by the binding of small molecules to P II and also by P II posttranslational modifications. In the diazotrophic bacterium Azospirillum brasilense, high levels of extracellular ammonium inactivate the nitrogenase regulatory enzyme DraG by relocalizing it from the cytoplasm to the cell membrane. Membrane localization of DraG occurs through the formation of a ternary complex in which the P II protein GlnZ interacts simultaneously with DraG and the ammonia channel AmtB. Here we describe the crystal structure of the GlnZ-DraG complex at 2.1 Å resolution, and confirm the physiological relevance of the structural data by site-directed mutagenesis. In contrast to other known P II complexes, the majority of contacts with the target protein do not involve the T-loop region of P II . Hence this structure identifies a different mode of P II interaction with a target protein and demonstrates the potential for P II proteins to interact simultaneously with two different targets. A structural model of the AmtB-GlnZDraG ternary complex is presented. The results explain how the intracellular levels of ATP, ADP, and 2-oxoglutarate regulate the interaction between these three proteins and how DraG discriminates GlnZ from its close paralogue GlnB.N itrogen is an indispensable element for life. In bacteria and plants, many aspects of the regulation of nitrogen metabolism are controlled by a class of ubiquitous proteins called P II signal transduction proteins (1-4). P II proteins are present in all domains of life and are one of the most widely distributed signal transduction proteins in nature: some prokaryotes encode multiple P II homologues (2, 3). P II proteins act as a central processing unit receiving signals of carbon, energy, and nitrogen levels, integrating and transforming them into different P II conformational states. The multitude of P II conformations control their ability to interact with, and thus regulate the activity of, a variety of target proteins including transporters, enzymes, and transcriptional regulators (4). P II proteins form compact barrel-shaped homotrimeric structures, in which each monomer is 12-14 kDa containing three functionally important loops: the T-, B-, and C-loops (4). The 20-residue long T-loop is structurally very flexible and participates in protein interactions in all the structures of P II -target complexes solved to date. The T-loop also contains the site of posttranslational modification if it is needed. In Proteobacteria, Y51 in the T-loop is subjected to reversible uridylylation in response to the cellular glutamine levels (5). The effector molecules ATP, ADP, and 2-oxoglutarate (2-OG) influence the conformational states of P II pr...

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“…Binding of PipX to NtcA is favored by high 2-OG levels in vitro, whereas 2-OG in concert with Mg-ATP prevents binding of PipX to PII. The structures of PipX-NtcA and PipX-PII complexes have been solved (Llacer et al 2010;Zhao et al 2010). It is thought that PII binding of PipX tunes down NtcA-dependent gene expression (Espinosa et al 2007).…”

Section: Further Functions Of Pii Signaling In Oxygenic Phototrophsmentioning

confidence: 99%

From cyanobacteria to plants: conservation of PII functions during plastid evolution

Chellamuthu

Alva

Forchhammer

2012

Planta

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This article reviews the current state-of-the-art concerning the functions of the signal processing protein PII in cyanobacteria and plants, with a special focus on evolutionary aspects. We start out with a general introduction to PII proteins, their distribution, and their evolution. We also discuss PII-like proteins and domains, in particular, the similarity between ATP-phosphoribosyltransferase (ATP-PRT) and its PII-like domain and the complex between N-acetyl-L-glutamate kinase (NAGK) and its PII activator protein from oxygenic phototrophs. The structural basis of the function of PII as an ATP/ADP/ 2-oxoglutarate signal processor is described for Synechococcus elongatus PII. In both cyanobacteria and plants, a major target of PII regulation is NAGK, which catalyzes the committed step of arginine biosynthesis. The common principles of NAGK regulation by PII are outlined. Based on the observation that PII proteins from cyanobacteria and plants can functionally replace each other, the hypothesis that PII-dependent NAGK control was under selective pressure during the evolution of plastids of Chloroplastida and Rhodophyta is tested by bioinformatics approaches. It is noteworthy that two lineages of heterokont algae, diatoms and brown algae, also possess NAGK, albeit lacking PII; their NAGK however appears to have descended from an alphaproteobacterium and not from a cyanobacterium as in plants. We end this article by coming to the conclusion that during the evolution of plastids, PII lost its function in coordinating gene expression through the PipX-NtcA network but preserved its role in nitrogen (arginine) storage metabolism, and subsequently took over the fine-tuned regulation of carbon (fatty acid) storage metabolism, which is important in certain developmental stages of plants.

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Crystal Structure of the Cyanobacterial Signal Transduction Protein PII in Complex with PipX

Cited by 40 publications

References 42 publications

SPR analysis of promoter binding of Synechocystis PCC6803 transcription factors NtcA and CRP suggests cross‐talk and sheds light on regulation by effector molecules

SPR analysis of promoter binding of Synechocystis PCC6803 transcription factors NtcA and CRP suggests cross‐talk and sheds light on regulation by effector molecules

Crystal structure of the GlnZ-DraG complex reveals a different form of P_II-target interaction

From cyanobacteria to plants: conservation of PII functions during plastid evolution

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Crystal Structure of the Cyanobacterial Signal Transduction Protein PII in Complex with PipX

Cited by 40 publications

References 42 publications

SPR analysis of promoter binding of Synechocystis PCC6803 transcription factors NtcA and CRP suggests cross‐talk and sheds light on regulation by effector molecules

SPR analysis of promoter binding of Synechocystis PCC6803 transcription factors NtcA and CRP suggests cross‐talk and sheds light on regulation by effector molecules

Crystal structure of the GlnZ-DraG complex reveals a different form of PII-target interaction

From cyanobacteria to plants: conservation of PII functions during plastid evolution

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Crystal structure of the GlnZ-DraG complex reveals a different form of P_II-target interaction