6OM4

The structure of Microcin C7 biosynthetic enzyme MccB in complex with N-formylated MccA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by theN-formyl of the peptide precursor.

Dong, S.H.Kulikovsky, A.Zukher, I.Estrada, P.Dubiley, S.Severinov, K.Nair, S.K.

(2019) Chem Sci 10: 2391-2395

  • DOI: https://doi.org/10.1039/c8sc03173h
  • Primary Citation of Related Structures:  
    6OM4

  • PubMed Abstract: 

    Microcin C7 (McC) is a peptide antibiotic modified by a linkage of the terminal isoAsn amide to AMP via a phosphoramidate bond. Post-translational modification on this ribosomally produced heptapeptide precursor is carried out by MccB, which consumes two equivalents of ATP to generate the N-P linkage. We demonstrate that MccB only efficiently processes the precursor heptapeptide that retains the N -formylated initiator Met (fMet). Binding studies and kinetic measurements evidence the role of the N -formyl moiety. Structural data show that the N -formyl peptide binding results in an ordering of residues in the MccB "crossover loop", which dictates specificity in homologous ubiquitin activating enzymes. The N -formyl peptide exhibits substrate inhibition, and cannot be displaced from MccB by the desformyl counterpart. Such substrate inhibition may be a strategy to avert unwanted McC buildup and avert toxicity in the cytoplasm of producing organisms.


  • Organizational Affiliation

    Department of Biochemistry , University of Illinois at Urbana-Champaign , Illinois , USA . Email: snair@illinois.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MccB protein
A, B
348Escherichia coliMutation(s): 0 
Gene Names: mccB
UniProt
Find proteins for Q47506 (Escherichia coli)
Explore Q47506 
Go to UniProtKB:  Q47506
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47506
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Microcin C7
C, D
7Escherichia coliMutation(s): 0 
UniProt
Find proteins for Q47505 (Escherichia coli)
Explore Q47505 
Go to UniProtKB:  Q47505
Entity Groups  
UniProt GroupQ47505
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ND7
Query on ND7

Download Ideal Coordinates CCD File 
M [auth C],
N [auth D]
5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine
C10 H15 N6 O6 P
LDEMREUBLBGZBO-KQYNXXCUSA-N
POP
Query on POP

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth A],
J [auth B],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
C, D
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.094α = 90
b = 76.059β = 90
c = 131.902γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHENIXmodel building
BUCCANEERmodel building
PHENIXphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesAI117210

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description