6HTQ

Stringent response control by a bifunctional RelA enzyme in the presence and absence of the ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Regulation of the Opposing (p)ppGpp Synthetase and Hydrolase within the Stringent Response Orchestrator Rel.

Pausch, P.Abdelshahid, M.Steinchen, W.Schafer, H.Gratani, F.L.Freibert, S.A.Wolz, C.Turgay, K.Wilson, D.N.Bange, G.

(2020) Cell Rep 32: 108157-108157

  • DOI: 10.1016/j.celrep.2020.108157
  • Primary Citation of Related Structures:  
    6HTQ, 6YXA

  • PubMed Abstract: 
  • The stringent response enables metabolic adaptation of bacteria under stress conditions and is governed by RelA/SpoT Homolog (RSH)-type enzymes. Long RSH-type enzymes encompass an N-terminal domain (NTD) harboring the second messenger nucleotide (p)ppGpp hydrolase and synthetase activity and a stress-perceiving and regulatory C-terminal domain (CTD) ...

    The stringent response enables metabolic adaptation of bacteria under stress conditions and is governed by RelA/SpoT Homolog (RSH)-type enzymes. Long RSH-type enzymes encompass an N-terminal domain (NTD) harboring the second messenger nucleotide (p)ppGpp hydrolase and synthetase activity and a stress-perceiving and regulatory C-terminal domain (CTD). CTD-mediated binding of Rel to stalled ribosomes boosts (p)ppGpp synthesis. However, how the opposing activities of the NTD are controlled in the absence of stress was poorly understood. Here, we demonstrate on the RSH-type protein Rel that the critical regulative elements reside within the TGS (ThrRS, GTPase, and SpoT) subdomain of the CTD, which associates to and represses the synthetase to concomitantly allow for activation of the hydrolase. Furthermore, we show that Rel forms homodimers, which appear to control the interaction with deacylated-tRNA, but not the enzymatic activity of Rel. Collectively, our study provides a detailed molecular view into the mechanism of stringent response repression in the absence of stress.


    Organizational Affiliation

    Center for Synthetic Microbiology & Department of Chemistry, Hans-Meerwein-Strasse, C07, Philipps-University Marburg, 35043 Marburg, Germany. Electronic address: gert.bange@synmikro.uni-marburg.de.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C272Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplBBSU01190
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Entity ID: 4
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50S ribosomal protein L3D206Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplCBSU01160
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Entity ID: 5
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50S ribosomal protein L4E205Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplDBSU01170
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Entity ID: 6
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50S ribosomal protein L5F176Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplEBSU01280
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Entity ID: 7
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50S ribosomal protein L6G175Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplFBSU01310
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50S ribosomal protein L13H [auth J]142Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplMBSU01490
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50S ribosomal protein L14I [auth K]122Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplNBSU01260
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50S ribosomal protein L15J [auth L]146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplOBSU01350
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50S ribosomal protein L16K [auth M]135Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplPBSU01230
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50S ribosomal protein L17L [auth N]119Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplQBSU01440
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50S ribosomal protein L18M [auth O]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplRBSU01320
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50S ribosomal protein L19N [auth P]115Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplSBSU16040
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50S ribosomal protein L20O [auth Q]117Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplTBSU28850
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50S ribosomal protein L21P [auth R]101Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplUBSU27960
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50S ribosomal protein L22Q [auth S]109Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplVBSU01210
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50S ribosomal protein L23R [auth T]90Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplWBSU01180
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Entity ID: 19
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50S ribosomal protein L24S [auth U]101Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplXBSU01270
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50S ribosomal protein L27T [auth V]82Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmABSU27940
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50S ribosomal protein L28U [auth W]58Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmByloTBSU15820
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50S ribosomal protein L29V [auth X]65Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmCBSU01240
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50S ribosomal protein L30W [auth Y]58Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmDBSU01340
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50S ribosomal protein L32X [auth 1]54Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmFBSU15080
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50S ribosomal protein L33 1Y [auth 2]48Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmGArpmG1BSU24900
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50S ribosomal protein L34Z [auth 3]44Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmHBSU41060
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50S ribosomal protein L35AA [auth 4]64Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmIBSU28860
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50S ribosomal protein L36BA [auth 5]37Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmJBSU01400
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50S ribosomal protein L31CA [auth Z]63Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmEBSU37070
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30S ribosomal protein S2EA [auth b]218Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsBBSU16490
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30S ribosomal protein S3FA [auth c]206Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsCBSU01220
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30S ribosomal protein S4GA [auth d]195Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsDBSU29660
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30S ribosomal protein S5HA [auth e]164Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsEspcABSU01330
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30S ribosomal protein S6IA [auth f]92Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsFBSU40910
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30S ribosomal protein S7JA [auth g]149Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsGBSU01110
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30S ribosomal protein S8KA [auth h]131Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsHBSU01300
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30S ribosomal protein S9LA [auth i]125Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsIBSU01500
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30S ribosomal protein S10MA [auth j]95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsJtetABSU01150
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30S ribosomal protein S11NA [auth k]114Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsKBSU01420
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30S ribosomal protein S12OA [auth l]136Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsLfunstrABSU01100
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30S ribosomal protein S13PA [auth m]108Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsMBSU01410
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30S ribosomal protein S14QA [auth n]60Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsN1rpsNrpsNArpsZBSU01290
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30S ribosomal protein S15RA [auth o]85Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsOBSU16680
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Entity ID: 45
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30S ribosomal protein S16SA [auth p]88Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsPBSU15990
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Find proteins for P21474 (Bacillus subtilis (strain 168))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17TA [auth q]84Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsQBSU01250
UniProt
Find proteins for P12874 (Bacillus subtilis (strain 168))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18UA [auth r]64Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsRBSU40890
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19VA [auth s]78Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsSBSU01200
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20WA [auth t]83Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsTyqeOBSU25550
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
GTP pyrophosphokinaseYA [auth x]341Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: relABSU27600
EC: 2.7.6.5
UniProt
Find proteins for O54408 (Bacillus subtilis (strain 168))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA 2925Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB 112Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 30
MoleculeChainsLengthOrganismImage
16S rRNADA [auth a]1533Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 50
MoleculeChainsLengthOrganismImage
P-tRNAXA [auth v]87Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 52
MoleculeChainsLengthOrganismImage
A/R-tRNAZA [auth u]76Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 53
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E-tRNAAB [auth w]75Bacillus subtilis subsp. subtilis str. 168
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2020-09-30
    Changes: Database references