6GRG

E. coli Microcin synthetase McbBCD complex with pro-MccB17, ADP and phosphate bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison.

Ghilarov, D.Stevenson, C.E.M.Travin, D.Y.Piskunova, J.Serebryakova, M.Maxwell, A.Lawson, D.M.Severinov, K.

(2019) Mol Cell 73: 749-762.e5

  • DOI: https://doi.org/10.1016/j.molcel.2018.11.032
  • Primary Citation of Related Structures:  
    6GOS, 6GRG, 6GRH, 6GRI

  • PubMed Abstract: 

    The introduction of azole heterocycles into a peptide backbone is the principal step in the biosynthesis of numerous compounds with therapeutic potential. One of them is microcin B17, a bacterial topoisomerase inhibitor whose activity depends on the conversion of selected serine and cysteine residues of the precursor peptide to oxazoles and thiazoles by the McbBCD synthetase complex. Crystal structures of McbBCD reveal an octameric B 4 C 2 D 2 complex with two bound substrate peptides. Each McbB dimer clamps the N-terminal recognition sequence, while the C-terminal heterocycle of the modified peptide is trapped in the active site of McbC. The McbD and McbC active sites are distant from each other, which necessitates alternate shuttling of the peptide substrate between them, while remaining tethered to the McbB dimer. An atomic-level view of the azole synthetase is a starting point for deeper understanding and control of biosynthesis of a large group of ribosomally synthesized natural products.


  • Organizational Affiliation

    Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Cracow, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriocin microcin B1768Escherichia coli str. K-12 substr. MG1655Mutation(s): 6 
Gene Names: mcbA
UniProt
Find proteins for P05834 (Escherichia coli)
Explore P05834 
Go to UniProtKB:  P05834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05834
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Microcin B17-processing protein McbBB [auth 1],
C [auth 2]
295Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: mcbB
UniProt
Find proteins for P23184 (Escherichia coli)
Explore P23184 
Go to UniProtKB:  P23184
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23184
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Microcin B17-processing protein McbCD [auth C]272Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: mcbC
UniProt
Find proteins for P23185 (Escherichia coli)
Explore P23185 
Go to UniProtKB:  P23185
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23185
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Microcin B17-processing protein McbDE [auth D]396Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: mcbD
UniProt
Find proteins for P23186 (Escherichia coli)
Explore P23186 
Go to UniProtKB:  P23186
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23186
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
K [auth 2]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
FMN
Query on FMN

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F [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
ADP
Query on ADP

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N [auth D]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4
Query on SO4

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H [auth 1]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4
Query on PO4

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O [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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I [auth 1]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

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G [auth 1],
J [auth 2]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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L [auth 2],
M [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

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S [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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P [auth D],
Q [auth D],
R [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
F6N
Query on F6N
A
PEPTIDE LINKINGC5 H6 N2 O3GLY, SER
F75
Query on F75
A
PEPTIDE LINKINGC5 H6 N2 O2 SGLY, CYS
OTZ
Query on OTZ
A
PEPTIDE LINKINGC8 H7 N3 O3 SGLY, SER, CYS
TOZ
Query on TOZ
A
PEPTIDE LINKINGC8 H7 N3 O3 SGLY, CYS, SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.64α = 90
b = 83.28β = 91.43
c = 86.79γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionPolandMarie Sklodowska-Curie grant agreement No 665778
Russian Foundation for Basic ResearchRussian FederationRFBR-Royal Society International Exchanges Scheme (KO165410043/IE160246)
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P012523/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J004561/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description