Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8

Sakai, Hiroaki; Wang, Hongfei; Takemoto-Hori, Chie; Kaminishi, T.; Yamaguchi, Hiroto; Kamewari, Yuki; Terada, Takaho; Kuramitsu, Seiki; Shirouzu, Mikako; Yokoyama, Shigeyuki

doi:10.1016/j.jsb.2004.08.007

Cited by 35 publications

(50 citation statements)

References 46 publications

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“…The overall fold of GlnK is very similar to that of the uncomplexed protein (21). However, the T-loop exhibits a conformation that has not been seen previously in P II proteins (21,(31)(32)(33). It forms a short two-stranded antiparallel ␤-sheet (residues E44-Y46 and A49-Y51), the strands of which are separated by a ␤-turn.…”

Section: Resultsmentioning

confidence: 62%

“…Bound ADP has been reported on two previous occasions: in Thermus thermophilus GlnK where ADP was added during crystallization (33), and in Thermotoga maritima where ADP was found in the crystal structure of a P II protein purified from cells where the growth conditions were not defined (34), the latter case being the only one to date where nucleotide was found to copurify with P II . Consequently for E. coli GlnB and GlnK, the only comparisons that can be made are with bound ATP that was added during crystallization (21,26).…”

Section: Discussionmentioning

confidence: 84%

“…In each of the four previous P II structures in which the T-loop was ordered, the ability to resolve the loop is a direct consequence of stabilization of the structure by crystal-packing contacts (21,(31)(32)(33). Although two of the previous structures exhibit an extended conformation, in each of those cases this is a consequence of extension of ␤-strands 2 and 3 (32,33). Neither exhibits the short ␤-strands observed in our structure, which are composed of distinctly different residues.…”

Section: Discussionmentioning

confidence: 99%

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The crystal structure of the Escherichia coli AmtB–GlnK complex reveals how GlnK regulates the ammonia channel

Conroy

Durand

Lupo

et al. 2007

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

169

257

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Amt proteins are ubiquitous channels for the conduction of ammonia in archaea, eubacteria, fungi, and plants. In Escherichia coli, previous studies have indicated that binding of the P II signal transduction protein GlnK to the ammonia channel AmtB regulates the channel thereby controlling ammonium influx in response to the intracellular nitrogen status. Here, we describe the crystal structure of the complex between AmtB and GlnK at a resolution of 2.5 Å. This structure of P II in a complex with one of its targets reveals physiologically relevant conformations of both AmtB and GlnK. GlnK interacts with AmtB almost exclusively via a long surface loop containing Y51 (T-loop), the tip of which inserts deeply into the cytoplasmic pore exit, blocking ammonia conduction. Y51 of GlnK is also buried in the pore exit, explaining why uridylylation of this residue prevents complex formation.regulation ͉ x-ray structure ͉ PII protein

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Section: Resultsmentioning

confidence: 62%

Section: Discussionmentioning

confidence: 84%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

The crystal structure of the Escherichia coli AmtB–GlnK complex reveals how GlnK regulates the ammonia channel

Conroy

Durand

Lupo

et al. 2007

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

169

257

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show abstract

“…These T loops can adopt multiple conformations and mediate the versatile protein-protein interactions (3). Each subunit further comprises two small loops (B and C loop) in the intersubunit clefts, facing each other from opposing subunits and taking part in a unique mode of ATP-ADP binding (13)(14)(15). ADP and ATP compete here for the same site.…”

mentioning

confidence: 99%

Mechanism of 2-oxoglutarate signaling by the Synechococcus elongatus P _II signal transduction protein

Fokina

Chellamuthu²,

Forchhammer³

et al. 2010

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

110

160

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P II proteins control key processes of nitrogen metabolism in bacteria, archaea, and plants in response to the central metabolites ATP, ADP, and 2-oxoglutarate (2-OG), signaling cellular energy and carbon and nitrogen abundance. This metabolic information is integrated by P II and transmitted to regulatory targets (key enzymes, transporters, and transcription factors), modulating their activity. In oxygenic phototrophs, the controlling enzyme of arginine synthesis, N-acetyl-glutamate kinase (NAGK), is a major P II target, whose activity responds to 2-OG via P II . Here we show structures of the Synechococcus elongatus P II protein in complex with ATP, Mg 2þ , and 2-OG, which clarify how 2-OG affects P II -NAGK interaction. P II trimers with all three sites fully occupied were obtained as well as structures with one or two 2-OG molecules per P II trimer. These structures identify the site of 2-OG located in the vicinity between the subunit clefts and the base of the T loop. The 2-OG is bound to a Mg 2þ ion, which is coordinated by three phosphates of ATP, and by ionic interactions with the highly conserved residues K58 and Q39 together with B-and T-loop backbone interactions. These interactions impose a unique T-loop conformation that affects the interactions with the P II target. Structures of P II trimers with one or two bound 2-OG molecules reveal the basis for anticooperative 2-OG binding and shed light on the intersubunit signaling mechanism by which P II senses effectors in a wide range of concentrations.metabolic signaling | nitrogen regulation | cyanobacteria | chloroplasts T he P II proteins constitute one of the largest and most widely distributed family of signal transduction proteins present in archaea, bacteria, and plants. They control key processes of nitrogen metabolism in response to central metabolites ATP, ADP, and 2-oxoglutarate (2-OG), signaling cellular energy and carbon and nitrogen abundance (1-4). These effectors bind to P II in an interdependent manner (see below), thereby transmitting metabolic information into structural states of this sensor protein (3, 5). Furthermore, P II proteins may be posttranslationally modified (1, 6). Depending on the signal input states, P II proteins bind and thereby regulate the activity of key metabolic and regulatory enzymes, transcription factors, or transport proteins (1-3). In cyanobacteria and plants, the controlling enzyme of arginine biosynthesis, N-acetyl-L-glutamate kinase (NAGK), is a major P II target (7-9). Moreover, P II affects gene expression in cyanobacteria through binding to the transcriptional coactivator of NtcA, PipX (10). In plants, acetyl-CoA carboxylase was recently shown to be regulated by P II , providing an additional link between carbon and nitrogen regulation (11). Although these P II targets share no common structural element, interaction with P II is inhibited by 2-OG.P II proteins are homotrimers of 12-to 13-kDa subunits, built of a double ferredoxin-like fold-containing core (βαβ-βαβ), with a characteristic and highly cons...

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“…The C-terminal residues extend out from the b4 strand to form a C-loop (Asp97 to Leu112) and has a 3 10 helix embedded within it between Gly108 and Ala111, consistent with other PII like protein structures. 16,24,[30][31][32][33][34][35] Structure of the ATP bound Mtb PII protein…”

Section: Structure Of the Mtb Apo Pii Proteinmentioning

confidence: 99%

Crystal structures of the apo and ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein

et al. 2010

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PII constitutes a family of signal transduction proteins that act as nitrogen sensors in microorganisms and plants. Mycobacterium tuberculosis (Mtb) has a single homologue of PII whose precise role has as yet not been explored. We have solved the crystal structures of the Mtb PII protein in its apo and ATP bound forms to 1.4 and 2.4 Å resolutions, respectively. The protein forms a trimeric assembly in the crystal lattice and folds similarly to the other PII family proteins. The Mtb PII:ATP binary complex structure reveals three ATP molecules per trimer, each bound between the base of the T-loop of one subunit and the C-loop of the neighboring subunit. In contrast to the apo structure, at least one subunit of the binary complex structure contains a completely ordered T-loop indicating that ATP binding plays a role in orienting this loop region towards target proteins like the ammonium transporter, AmtB. Arg38 of the T-loop makes direct contact with the c-phosphate of the ATP molecule replacing the Mg 21 position seen in the Methanococcus jannaschii GlnK1 structure. The C-loop of a neighboring subunit encloses the other side of the ATP molecule, placing the GlnK specific C-terminal 3 10 helix in the vicinity. Homology modeling studies with the E. coli GlnK:AmtB complex reveal that Mtb PII could form a complex similar to the complex in E. coli. The structural conservation and operon organization suggests that the Mtb PII gene encodes for a GlnK protein and might play a key role in the nitrogen regulatory pathway.

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Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8

Cited by 35 publications

References 46 publications

The crystal structure of the Escherichia coli AmtB–GlnK complex reveals how GlnK regulates the ammonia channel

The crystal structure of the Escherichia coli AmtB–GlnK complex reveals how GlnK regulates the ammonia channel

Mechanism of 2-oxoglutarate signaling by the Synechococcus elongatus P _II signal transduction protein

Crystal structures of the apo and ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein

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Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8

Cited by 35 publications

References 46 publications

The crystal structure of the Escherichia coli AmtB–GlnK complex reveals how GlnK regulates the ammonia channel

The crystal structure of the Escherichia coli AmtB–GlnK complex reveals how GlnK regulates the ammonia channel

Mechanism of 2-oxoglutarate signaling by the Synechococcus elongatus P II signal transduction protein

Crystal structures of the apo and ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein

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Mechanism of 2-oxoglutarate signaling by the Synechococcus elongatus P _II signal transduction protein