Atomic structure of and valine binding to the regulatory ACT domain of the <i>Mycobacterium tuberculosis</i> Rel protein

Shin, Joon; Singal, Bharti; Manimekalai, Malathy Sony Subramanian; Chen, Luyang; Ragunathan, Priya; Grüber, Gerhard

doi:10.1111/febs.15600

Cited by 6 publications

(9 citation statements)

References 61 publications

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“…The MODELER-generated and AMBER-minimized structures were used for docking. Ambiguous interaction restraints were selected based on reported ACT domain dimer structures ( 52 , 53 ). The pairwise “ligand interface Rmsd matrix” over all structures was calculated, and the final structures were clustered using an Rmsd cutoff value of 3.5 Å for both SCRM and SPCH/MUTE/FAMA.…”

Section: Methodsmentioning

confidence: 99%

Intragenic suppressors unravel the role of the SCREAM ACT-like domain for bHLH partner selectivity in stomatal development

Seo

Sepuru

Putarjunan

et al. 2022

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

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Multicellular organisms develop specialized cell types to achieve complex functions of tissues and organs. The basic helix–loop–helix (bHLH) proteins act as master regulatory transcription factors of such specialized cell types. Plant stomata are cellular valves in the aerial epidermis for efficient gas exchange and water control. Stomatal differentiation is governed by sequential actions of three lineage-specific bHLH proteins, SPEECHLESS (SPCH), MUTE, and FAMA, specifying initiation and proliferation, commitment, and terminal differentiation, respectively. A broadly expressed bHLH, SCREAM (SCRM), heterodimerizes with SPCH/MUTE/FAMA and drives stomatal differentiation via switching its partners. Yet nothing is known about its heterodimerization properties or partner preference. Here, we report the role of the SCRM C-terminal ACT-like (ACTL) domain for heterodimerization selectivity. Our intragenic suppressor screen of a dominant scrm-D mutant identified the ACTL domain as a mutation hotspot. Removal of this domain or loss of its structural integrity abolishes heterodimerization with MUTE, but not with SPCH or FAMA, and selectively abrogates the MUTE direct target gene expression. Consequently, the scrm-D ACTL mutants confer massive clusters of arrested stomatal precursor cells that cannot commit to differentiation when redundancy is removed. Structural and biophysical studies further show that SPCH, MUTE, and FAMA also possess the C-terminal ACTL domain, and that ACTL•ACTL heterodimerization is sufficient for partner selectivity. Our work elucidates a role for the SCRM ACTL domain in the MUTE-governed proliferation–differentiation switch and suggests mechanistic insight into the biological function of the ACTL domain, a module uniquely associated with plant bHLH proteins, as a heterodimeric partner selectivity interface.

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Section: Methodsmentioning

confidence: 99%

Intragenic suppressors unravel the role of the SCREAM ACT-like domain for bHLH partner selectivity in stomatal development

Seo

Sepuru

Putarjunan

et al. 2022

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

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“…The CTD elements are predicted to play a role in regulating hydrolysis of Mt Rel, anchoring Mt Rel to the ribosome, and controlling amino acid metabolism by binding branched‐chain amino acids [12,13,25,26]. Specific binding of the amino acid valine occurs within the dimer interface of the Mt Rel ACT domain [26]. Its dimeric solution structure reveals a head‐to‐tail orientation of the two Mt Rel ACT domains, each consisting of four β‐strands and two α‐helices [26]…”

Section: Figmentioning

confidence: 99%

“…Specific binding of the amino acid valine occurs within the dimer interface of the Mt Rel ACT domain [26]. Its dimeric solution structure reveals a head‐to‐tail orientation of the two Mt Rel ACT domains, each consisting of four β‐strands and two α‐helices [26]…”

Section: Figmentioning

confidence: 99%

“…The CTD elements are predicted to play a role in regulating hydrolysis of MtRel, anchoring MtRel to the ribosome, and controlling amino acid metabolism by binding branched-chain amino acids [12,13,25,26]. Specific binding of the amino acid valine occurs within the dimer interface of the MtRel ACT domain [26]. Its dimeric solution structure reveals a head-to-tail orientation of the two MtRel ACT domains, each consisting of four b-strands and two a-helices [26] The structural and mechanistic insights into MtRel are incomplete in the absence of its key regulatory domain, the TGS domain, which is required for the complete activation of the synthetase domain to produce (p)ppGpp [12].…”

mentioning

confidence: 99%

“…Specific binding of the amino acid valine occurs within the dimer interface of the MtRel ACT domain [26]. Its dimeric solution structure reveals a head-to-tail orientation of the two MtRel ACT domains, each consisting of four b-strands and two a-helices [26] The structural and mechanistic insights into MtRel are incomplete in the absence of its key regulatory domain, the TGS domain, which is required for the complete activation of the synthetase domain to produce (p)ppGpp [12]. Studies of the Escherichia coli TGS domain have shown that the domain interacts with deacylated tRNA and ribosomal RNA to stabilize the RelA-ribosomal complex for (p)ppGpp formation [27,28].…”

mentioning

confidence: 99%

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Atomic structure of the regulatory TGS domain of Rel protein from Mycobacterium tuberculosis and its interaction with deacylated tRNA

et al. 2021

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The stringent response is critical for the survival of Mycobacterium tuberculosis (Mtb) under nutrient starvation. The mechanism is mediated by a GTP pyrophosphokinase known as Rel, containing N-terminal synthetase and hydrolase domains and C-terminal regulatory domains, which include the TGS domain (ThrRS, GTPase, and SpoT proteins) that has been proposed to activate the synthetase domain via interaction with deacylated tRNA. Here, we present the NMR solution structure of the Mtb Rel TGS domain (MtRel TGS), consisting of five antiparallel b-strands and one helix-loop-helix motif. The interaction of MtRel TGS with deacylated tRNA is shown, indicating the critical amino acids of MtRel TGS in tRNA binding, and presenting the first structural evidence of MtRel TGS binding to deacylated tRNA in solution in the absence of the translational machinery.

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Mycobacterial Regulatory Systems Involved in the Regulation of Gene Expression Under Respiration-Inhibitory Conditions

Lee

et al. 2023

J Microbiol.

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Atomic structure of and valine binding to the regulatory ACT domain of the Mycobacterium tuberculosis Rel protein

Cited by 6 publications

References 61 publications

Intragenic suppressors unravel the role of the SCREAM ACT-like domain for bHLH partner selectivity in stomatal development

Intragenic suppressors unravel the role of the SCREAM ACT-like domain for bHLH partner selectivity in stomatal development

Atomic structure of the regulatory TGS domain of Rel protein from Mycobacterium tuberculosis and its interaction with deacylated tRNA

Mycobacterial Regulatory Systems Involved in the Regulation of Gene Expression Under Respiration-Inhibitory Conditions

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