7FC0

Reconstitution of MbnABC complex from Rugamonas rubra ATCC-43154 (GroupIII)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 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
RrMbnA precosur peptideA,
F [auth D]
29Rugamonas rubraMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Methanobactin biosynthesis cassette protein MbnBB [auth E]264Rugamonas rubraMutation(s): 0 
Gene Names: SAMN02982985_00539
UniProt
Find proteins for A0A1I4IFL0 (Rugamonas rubra)
Explore A0A1I4IFL0 
Go to UniProtKB:  A0A1I4IFL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I4IFL0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Methanobactin biosynthesis cassette protein MbnBC [auth B]263Rugamonas rubraMutation(s): 0 
Gene Names: SAMN02982985_00539
UniProt
Find proteins for A0A1I4IFL0 (Rugamonas rubra)
Explore A0A1I4IFL0 
Go to UniProtKB:  A0A1I4IFL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I4IFL0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Methanobactin biosynthesis cassette protein MbnCD [auth F],
E [auth C]
199Rugamonas rubraMutation(s): 0 
Gene Names: SAMN02982985_00538
UniProt
Find proteins for A0A1I4IFH0 (Rugamonas rubra)
Explore A0A1I4IFH0 
Go to UniProtKB:  A0A1I4IFH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I4IFH0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.968α = 90
b = 173.968β = 90
c = 61.185γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description