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:  
    6YXA, 6HTQ

  • 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 L2 C272Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplBBSU01190
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Entity ID: 4
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50S ribosomal protein L3 D206Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplCBSU01160
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Entity ID: 5
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50S ribosomal protein L4 E205Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplDBSU01170
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Entity ID: 6
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50S ribosomal protein L5 F176Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplEBSU01280
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Entity ID: 7
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50S ribosomal protein L6 G175Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplFBSU01310
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Entity ID: 8
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50S ribosomal protein L13 J142Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplMBSU01490
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Entity ID: 9
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50S ribosomal protein L14 K122Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplNBSU01260
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Entity ID: 10
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50S ribosomal protein L15 L146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplOBSU01350
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Entity ID: 11
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50S ribosomal protein L16 M135Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplPBSU01230
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Entity ID: 12
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50S ribosomal protein L17 N119Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplQBSU01440
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Entity ID: 13
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50S ribosomal protein L18 O120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplRBSU01320
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Entity ID: 14
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50S ribosomal protein L19 P115Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplSBSU16040
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Entity ID: 15
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50S ribosomal protein L20 Q117Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplTBSU28850
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Entity ID: 16
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50S ribosomal protein L21 R101Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplUBSU27960
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Entity ID: 17
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50S ribosomal protein L22 S109Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplVBSU01210
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Entity ID: 18
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50S ribosomal protein L23 T90Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplWBSU01180
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Entity ID: 19
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50S ribosomal protein L24 U101Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplXBSU01270
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Entity ID: 20
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50S ribosomal protein L27 V82Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmABSU27940
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Entity ID: 21
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50S ribosomal protein L28 W58Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmByloTBSU15820
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Entity ID: 22
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50S ribosomal protein L29 X65Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmCBSU01240
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Entity ID: 23
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50S ribosomal protein L30 Y58Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmDBSU01340
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Entity ID: 24
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50S ribosomal protein L32 154Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmFBSU15080
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Entity ID: 25
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50S ribosomal protein L33 1 248Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmGArpmG1BSU24900
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Entity ID: 26
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50S ribosomal protein L34 344Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmHBSU41060
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Entity ID: 27
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50S ribosomal protein L35 464Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmIBSU28860
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50S ribosomal protein L36 537Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmJBSU01400
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Entity ID: 29
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50S ribosomal protein L31 Z63Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmEBSU37070
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Entity ID: 31
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30S ribosomal protein S2 b218Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsBBSU16490
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Entity ID: 32
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30S ribosomal protein S3 c206Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsCBSU01220
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Entity ID: 33
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30S ribosomal protein S4 d195Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsDBSU29660
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Entity ID: 34
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30S ribosomal protein S5 e164Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsEspcABSU01330
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Entity ID: 35
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30S ribosomal protein S6 f92Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsFBSU40910
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Entity ID: 36
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30S ribosomal protein S7 g149Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsGBSU01110
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Entity ID: 37
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30S ribosomal protein S8 h131Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsHBSU01300
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Entity ID: 38
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30S ribosomal protein S9 i125Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsIBSU01500
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Entity ID: 39
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30S ribosomal protein S10 j95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsJtetABSU01150
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Entity ID: 40
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30S ribosomal protein S11 k114Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsKBSU01420
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Entity ID: 41
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30S ribosomal protein S12 l136Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsLfunstrABSU01100
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Entity ID: 42
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30S ribosomal protein S13 m108Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsMBSU01410
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Entity ID: 43
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30S ribosomal protein S14 n60Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsN1rpsNrpsNArpsZBSU01290
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Entity ID: 44
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30S ribosomal protein S15 o85Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsOBSU16680
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Entity ID: 45
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30S ribosomal protein S16 p88Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsPBSU15990
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Entity ID: 46
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30S ribosomal protein S17 q84Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsQBSU01250
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Entity ID: 47
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30S ribosomal protein S18 r64Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsRBSU40890
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Entity ID: 48
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30S ribosomal protein S19 s78Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsSBSU01200
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Entity ID: 49
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30S ribosomal protein S20 t83Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsTyqeOBSU25550
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Entity ID: 51
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GTP pyrophosphokinase x341Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: relABSU27600
EC: 2.7.6.5
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Entity ID: 1
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23S ribosomal RNAA2925Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 2
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5S ribosomal RNAB112Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 30
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16S rRNAa1533Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 50
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P-tRNAv87Bacillus subtilis subsp. subtilis str. 168
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A/R-tRNAu76Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 53
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E-tRNAw75Bacillus subtilis subsp. subtilis str. 168
Experimental Data & Validation

Experimental Data

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

Structure Validation

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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