6U48

E. coli 50S with phazolicin (PHZ) bound in exit tunnel


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition.

Travin, D.Y.Watson, Z.L.Metelev, M.Ward, F.R.Osterman, I.A.Khven, I.M.Khabibullina, N.F.Serebryakova, M.Mergaert, P.Polikanov, Y.S.Cate, J.H.D.Severinov, K.

(2019) Nat Commun 10: 4563-4563

  • DOI: 10.1038/s41467-019-12589-5
  • Primary Citation of Related Structures:  
    6U48

  • PubMed Abstract: 
  • Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a┬árapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing peptides (LAPs) comprise a subclass of RiPPs that display outstanding diversity of mechanisms of action while sharing common structural features ...

    Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a rapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing peptides (LAPs) comprise a subclass of RiPPs that display outstanding diversity of mechanisms of action while sharing common structural features. Here, we report the discovery of a new LAP biosynthetic gene cluster in the genome of Rhizobium Pop5, which encodes the precursor peptide and modification machinery of phazolicin (PHZ) - an extensively modified peptide exhibiting narrow-spectrum antibacterial activity against some symbiotic bacteria of leguminous plants. The cryo-EM structure of the Escherichia coli 70S-PHZ complex reveals that the drug interacts with the 23S rRNA and uL4/uL22 proteins and obstructs ribosomal exit tunnel in a way that is distinct from other compounds. We show that the uL4 loop sequence determines the species-specificity of antibiotic action. PHZ expands the known diversity of LAPs and may be used in the future as biocontrol agent for agricultural needs.


    Organizational Affiliation

    Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, USA. severik@waksman.rutgers.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL2 CC271Escherichia coliMutation(s): 0 
Find proteins for A0A1X3I1Y9 (Escherichia coli M056)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL3 CD209Escherichia coliMutation(s): 0 
Find proteins for A0A1X3JBR5 (Escherichia coli H386)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL4 CE201Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL5 CF177Escherichia coliMutation(s): 0 
Find proteins for V8K465 (Escherichia coli LAU-EC10)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL6 CG176Escherichia coliMutation(s): 0 
Find proteins for A0A080FKA9 (Escherichia coli 1-392-07_S4_C3)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein bL9 CH149Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL11 CJ134Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL13 CK142Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL14 CL122Escherichia coliMutation(s): 0 
Find proteins for A0A140N3H4 (Escherichia coli (strain B / BL21-DE3))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL15 CM144Escherichia coliMutation(s): 0 
Gene Names: 
rplOA8C65_19395A9R57_24660ACU57_21045AM464_09135AUQ13_22145BANRA_01932BANRA_03684BHS87_18545BJJ90_02210BMA87_18510BON75_18850BON98_13310BUE81_25610BvCms2454_01416BvCmsHHP001_00334BvCmsHHP019_04131BvCmsHHP056_02703BvCmsKSP026_02554BvCmsSINP011_02480BW690_10710BZL31_22885C5F72_02595C5F73_02860C5N07_23575C9E25_20065C9Z39_20710CA593_09735CG692_20270CI693_13520CI694_01990CIG45_22410D0X26_24495D2185_22985D3821_17755D3O91_20305D3Y67_24390D4638_19455D4718_17880D9C99_17930D9D20_21995D9D44_22490D9G29_15635D9G69_20945D9H68_17710D9J52_19090D9Z28_15390DAH37_14685DBQ99_03415DJ503_19770DL326_22310DNC98_19095DT034_22410DTL43_21000E2119_19640E2134_21880E2135_06185E4A44_21305E4K51_21490E4K55_21420E4K60_18985E4K61_20025E5P22_10480E5P28_20875EA213_19860EAI42_04990EAI52_16365EC1094V2_354EC3234A_55c00230EC3426_04459ECTO6_00449ED307_17010EEP23_17135EG808_17075EI021_21030EI028_20740EI032_18995EI041_20035EIZ93_12470EL75_0396EL79_0415EL80_0407ELT20_19170EPT01_19765ERS085365_03907ERS085416_03881ERS139211_03685ERS150873_04051EXX71_21335EYD11_02080F1E19_19655F9040_18095FRV13_20015FV293_22465FWK02_06270G5632_17770G5688_20025GHR40_07050GKF39_20550GKF74_18130GKF86_20070GKF89_18470GP671_20580GP689_20785GP954_00945GP979_02005GQE33_22230GQE34_14255GQE64_20420GQM17_19915GRW05_09060GRW27_21285GRW42_19350GRW57_03540GRW80_20585GRW81_21150NCTC10963_00456NCTC11022_03475NCTC11126_02772NCTC12650_00710NCTC13216_01351NCTC9045_00567NCTC9062_02686NCTC9117_00757NCTC9706_02738PGD_00585RK56_021420SAMEA3472047_03862SAMEA3472080_04748SAMEA3484427_04887SAMEA3484429_04875SAMEA3752559_00346SAMEA3753300_02227

Find proteins for A0A037Y8L6 (Escherichia coli)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL16 CN136Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein bL17 CO120Escherichia coliMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein uL18 CP116Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein bL19 CQ114Escherichia coliMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein bL20 CR117Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein bL21 CS103Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein uL22 CT110Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL23 CU93Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL24 CV102Escherichia coliMutation(s): 0 
Find proteins for A0A0G3K7Z5 (Escherichia coli PCN033)
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Entity ID: 22
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50S ribosomal protein bL25 CW94Escherichia coliMutation(s): 0 
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Entity ID: 23
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50S ribosomal protein bL27 CX75Escherichia coliMutation(s): 0 
Find proteins for A0A1X3JCC7 (Escherichia coli H386)
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Entity ID: 24
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50S ribosomal protein bL28 CY77Escherichia coliMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein uL29 CZ62Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein uL30 C058Escherichia coliMutation(s): 0 
Find proteins for A0A073UEE9 (Escherichia coli 5-366-08_S1_C1)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein bL32 C156Escherichia coliMutation(s): 0 
Find proteins for V0ZMP5 (Escherichia coli 908573)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein bL33 C250Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein bL34 C346Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein bL35 C464Escherichia coliMutation(s): 0 
Find proteins for I2RJ64 (Escherichia coli 1.2741)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein bL36 C538Escherichia coliMutation(s): 0 
Find proteins for A0A0E2L017 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
phazolicin A22Rhizobium sp. Pop5Mutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S rRNACA2904Escherichia coli
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S rRNACB118Escherichia coli
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
MEQ
Query on MEQ
CDL-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4
CNL-PEPTIDE LINKINGC6 H14 N4 O3ARG
BB9
Query on BB9
APEPTIDE LINKINGC3 H5 N O2 SCYS
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 32
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002365
Query on PRD_002365
AphazolicinPeptide-like /  Antimicrobial

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM R01-114454
National Science Foundation (NSF, United States)United States1106400

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 2.0: 2019-11-27
    Changes: Author supporting evidence, Polymer sequence
  • Version 2.1: 2020-04-01
    Changes: Database references
  • Version 2.2: 2020-08-12
    Changes: Structure summary