7DZ9

MbnABC complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure and catalytic mechanism of the MbnBC holoenzyme required for methanobactin biosynthesis.

Dou, C.Long, Z.Li, S.Zhou, D.Jin, Y.Zhang, L.Zhang, X.Zheng, Y.Li, L.Zhu, X.Liu, Z.He, S.Yan, W.Yang, L.Xiong, J.Fu, X.Qi, S.Ren, H.Chen, S.Dai, L.Wang, B.Cheng, W.

(2022) Cell Res 32: 302-314

  • DOI: https://doi.org/10.1038/s41422-022-00620-2
  • Primary Citation of Related Structures:  
    7DZ9, 7FC0

  • PubMed Abstract: 

    Methanobactins (Mbns) are a family of copper-binding peptides involved in copper uptake by methanotrophs, and are potential therapeutic agents for treating diseases characterized by disordered copper accumulation. Mbns are produced via modification of MbnA precursor peptides at cysteine residues catalyzed by the core biosynthetic machinery containing MbnB, an iron-dependent enzyme, and MbnC. However, mechanistic details underlying the catalysis of the MbnBC holoenzyme remain unclear. Here, we present crystal structures of MbnABC complexes from two distinct species, revealing that the leader peptide of the substrate MbnA binds MbnC for recruitment of the MbnBC holoenzyme, while the core peptide of MbnA resides in the catalytic cavity created by the MbnB-MbnC interaction which harbors a unique tri-iron cluster. Ligation of the substrate sulfhydryl group to the tri-iron center achieves a dioxygen-dependent reaction for oxazolone-thioamide installation. Structural analysis of the MbnABC complexes together with functional investigation of MbnB variants identified a conserved catalytic aspartate residue as a general base required for MbnBC-mediated MbnA modification. Together, our study reveals the similar architecture and function of MbnBC complexes from different species, demonstrating an evolutionarily conserved catalytic mechanism of the MbnBC holoenzymes.


  • Organizational Affiliation

    Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MbnB260Vibrio caribbeanicus ATCC BAA-2122Mutation(s): 0 
Gene Names: VIBC2010_09967
UniProt
Find proteins for E3BK14 (Vibrio caribbeanicus ATCC BAA-2122)
Explore E3BK14 
Go to UniProtKB:  E3BK14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE3BK14
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
cpMbnB260Vibrio caribbeanicus ATCC BAA-2122Mutation(s): 0 
Gene Names: VIBC2010_09967
UniProt
Find proteins for E3BK14 (Vibrio caribbeanicus ATCC BAA-2122)
Explore E3BK14 
Go to UniProtKB:  E3BK14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE3BK14
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MbnCC [auth D],
F [auth C]
180Vibrio caribbeanicus ATCC BAA-2122Mutation(s): 0 
Gene Names: VIBC2010_09962
UniProt
Find proteins for E3BK13 (Vibrio caribbeanicus ATCC BAA-2122)
Explore E3BK13 
Go to UniProtKB:  E3BK13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE3BK13
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MbnAD [auth E]23Vibrio caribbeanicus ATCC BAA-2122Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
MbnAE [auth F]22Vibrio caribbeanicus ATCC BAA-2122Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.915α = 90
b = 69.065β = 93.59
c = 82.573γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release