7O1C

Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome-RF2 complex stalled in response to L-tryptophan


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling.

van der Stel, A.X.Gordon, E.R.Sengupta, A.Martinez, A.K.Klepacki, D.Perry, T.N.Herrero Del Valle, A.Vazquez-Laslop, N.Sachs, M.S.Cruz-Vera, L.R.Innis, C.A.

(2021) Nat Commun 12: 5340-5340

  • DOI: https://doi.org/10.1038/s41467-021-25663-8
  • Primary Citation of Related Structures:  
    7O19, 7O1A, 7O1C

  • PubMed Abstract: 

    Free L-tryptophan (L-Trp) stalls ribosomes engaged in the synthesis of TnaC, a leader peptide controlling the expression of the Escherichia coli tryptophanase operon. Despite extensive characterization, the molecular mechanism underlying the recognition and response to L-Trp by the TnaC-ribosome complex remains unknown. Here, we use a combined biochemical and structural approach to characterize a TnaC variant (R23F) with greatly enhanced sensitivity for L-Trp. We show that the TnaC-ribosome complex captures a single L-Trp molecule to undergo termination arrest and that nascent TnaC prevents the catalytic GGQ loop of release factor 2 from adopting an active conformation at the peptidyl transferase center. Importantly, the L-Trp binding site is not altered by the R23F mutation, suggesting that the relative rates of L-Trp binding and peptidyl-tRNA cleavage determine the tryptophan sensitivity of each variant. Thus, our study reveals a strategy whereby a nascent peptide assists the ribosome in detecting a small metabolite.


  • Organizational Affiliation

    Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Pessac, France.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB]241Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC]233Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth AD]206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE]167Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth AF]135Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth AG]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth AH]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth AI]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
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30S ribosomal protein S10J [auth AJ]103Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S11K [auth AK]129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth AL]124Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth AM]118Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth AN]102Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth AO]89Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth AP]82Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth AQ]84Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth AR]75Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth AS]92Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth AT]87Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth AU]71Escherichia coli K-12Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2X [auth BC]273Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3Y [auth BD]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4Z [auth BE]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5AA [auth BF]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6BA [auth BG]177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9CA [auth BH]149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31DA [auth BI]70Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13EA [auth BJ]142Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L14FA [auth BK]123Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15GA [auth BL]144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16HA [auth BM]136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 35
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50S ribosomal protein L17IA [auth BN]127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 36
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50S ribosomal protein L18JA [auth BO]117Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L19KA [auth BP]115Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20LA [auth BQ]118Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21MA [auth BR]103Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22NA [auth BS]110Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L23OA [auth BT]100Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PA [auth BU]104Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L25QA [auth BV]94Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27RA [auth BW]85Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28SA [auth BX]78Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29TA [auth BY]63Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30UA [auth BZ]59Escherichia coli K-12Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32VA [auth B0]57Escherichia coli K-12Mutation(s): 0 
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UniProt GroupP0A7N4
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33WA [auth B1]55Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34XA [auth B2]46Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35YA [auth B3]65Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36ZA [auth B4]38Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
TnaC-(R23F) - Tryptophanase leader peptideAB [auth B5]17Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0AD89 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor RF2DB [auth B9]365Escherichia coli K-12Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
Ribosomal RNA 16SA [auth AA]1,534Escherichia coli K-12
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Entity ID: 22
MoleculeChains LengthOrganismImage
Ribosomal RNA 23SV [auth BA]2,897Escherichia coli K-12
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Entity ID: 23
MoleculeChains LengthOrganismImage
Ribosomal RNA 5SW [auth BB]120Escherichia coli K-12
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Entity ID: 54
MoleculeChains LengthOrganismImage
mRNABB [auth B7]10Escherichia coli K-12
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Entity ID: 55
MoleculeChains LengthOrganismImage
P-site tRNA-ProCB [auth B8]77Escherichia coli K-12
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

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BG [auth BA]TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
ZN
Query on ZN

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ST [auth BI],
XT [auth B4],
ZF [auth AB]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AF [auth AA]
AG [auth AM]
AQ [auth BA]
AR [auth BA]
AS [auth BA]
AF [auth AA],
AG [auth AM],
AQ [auth BA],
AR [auth BA],
AS [auth BA],
AT [auth BA],
BF [auth AA],
BQ [auth BA],
BR [auth BA],
BS [auth BA],
BT [auth BA],
CF [auth AA],
CQ [auth BA],
CR [auth BA],
CS [auth BA],
CT [auth BA],
DF [auth AA],
DQ [auth BA],
DR [auth BA],
DS [auth BA],
DT [auth BA],
EF [auth AA],
EQ [auth BA],
ER [auth BA],
ES [auth BA],
ET [auth BA],
FF [auth AA],
FQ [auth BA],
FR [auth BA],
FS [auth BA],
FT [auth BA],
GF [auth AA],
GQ [auth BA],
GR [auth BA],
GS [auth BA],
GT [auth BA],
HF [auth AA],
HQ [auth BA],
HR [auth BA],
HS [auth BA],
HT [auth BA],
IF [auth AA],
IQ [auth BA],
IR [auth BA],
IS [auth BA],
IT [auth BA],
JF [auth AA],
JQ [auth BA],
JR [auth BA],
JS [auth BA],
JT [auth BA],
KF [auth AA],
KQ [auth BA],
KR [auth BA],
KS [auth BA],
KT [auth BA],
LF [auth AA],
LP [auth BA],
LQ [auth BA],
LR [auth BA],
LS [auth BA],
MF [auth AA],
MP [auth BA],
MQ [auth BA],
MR [auth BA],
MS [auth BA],
MT [auth BB],
NE [auth AA],
NF [auth AA],
NP [auth BA],
NQ [auth BA],
NR [auth BA],
NS [auth BA],
OE [auth AA],
OF [auth AA],
OP [auth BA],
OQ [auth BA],
OR [auth BA],
OS [auth BA],
OT [auth BC],
PE [auth AA],
PF [auth AA],
PP [auth BA],
PQ [auth BA],
PR [auth BA],
PS [auth BA],
QE [auth AA],
QF [auth AA],
QP [auth BA],
QQ [auth BA],
QR [auth BA],
QS [auth BA],
RE [auth AA],
RF [auth AA],
RP [auth BA],
RQ [auth BA],
RR [auth BA],
RS [auth BA],
RT [auth BD],
SE [auth AA],
SF [auth AA],
SP [auth BA],
SQ [auth BA],
SR [auth BA],
SS [auth BA],
TE [auth AA],
TF [auth AA],
TP [auth BA],
TQ [auth BA],
TR [auth BA],
TS [auth BA],
UE [auth AA],
UF [auth AA],
UP [auth BA],
UQ [auth BA],
UR [auth BA],
US [auth BA],
VE [auth AA],
VF [auth AA],
VP [auth BA],
VQ [auth BA],
VR [auth BA],
VS [auth BA],
WE [auth AA],
WF [auth AA],
WP [auth BA],
WQ [auth BA],
WR [auth BA],
WS [auth BA],
WT [auth BM],
XE [auth AA],
XF [auth AA],
XP [auth BA],
XQ [auth BA],
XR [auth BA],
XS [auth BA],
YE [auth AA],
YF [auth AA],
YP [auth BA],
YQ [auth BA],
YR [auth BA],
YS [auth BA],
ZE [auth AA],
ZP [auth BA],
ZQ [auth BA],
ZR [auth BA],
ZS [auth BA]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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