7TCW | pdb_00007tcw

Methanobactin biosynthetic protein complex of MbnB and MbnC from Methylosinus trichosporium OB3b, H210S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 
    0.265 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

A mixed-valent Fe(II)Fe(III) species converts cysteine to an oxazolone/thioamide pair in methanobactin biosynthesis.

Park, Y.J.Jodts, R.J.Slater, J.W.Reyes, R.M.Winton, V.J.Montaser, R.A.Thomas, P.M.Dowdle, W.B.Ruiz, A.Kelleher, N.L.Bollinger Jr., J.M.Krebs, C.Hoffman, B.M.Rosenzweig, A.C.

(2022) Proc Natl Acad Sci U S A 119: e2123566119-e2123566119

  • DOI: https://doi.org/10.1073/pnas.2123566119

  • PubMed Abstract: 

    SignificanceMethanobactins (Mbns), copper-binding peptidic compounds produced by some bacteria, are candidate therapeutics for human diseases of copper overload. The paired oxazolone-thioamide bidentate ligands of methanobactins are generated from cysteine residues in a precursor peptide, MbnA, by the MbnBC enzyme complex. MbnBC activity depends on the presence of iron and oxygen, but the catalytically active form has not been identified. Here, we provide evidence that a dinuclear Fe(II)Fe(III) center in MbnB, which is the only representative of a >13,000-member protein family to be characterized, is responsible for this reaction. These findings expand the known roles of diiron enzymes in biology and set the stage for mechanistic understanding, and ultimately engineering, of the MbnBC biosynthetic complex.


  • Organizational Affiliation
    • Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208.

Macromolecule Content 

  • Total Structure Weight: 107.63 kDa 
  • Atom Count: 7,556 
  • Modeled Residue Count: 915 
  • Deposited Residue Count: 926 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Methanobactin biosynthesis cassette protein MbnB
A, B
268Methylosinus trichosporium OB3bMutation(s): 4 
Gene Names: mbnBCQW49_07160
UniProt
Find proteins for A0A2D2D5M1 (Methylosinus trichosporium (strain ATCC 35070 / NCIMB 11131 / UNIQEM 75 / OB3b))
Explore A0A2D2D5M1 
Go to UniProtKB:  A0A2D2D5M1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D2D5M1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Methanobactin biosynthesis cassette protein MbnC
C, D
195Methylosinus trichosporium OB3bMutation(s): 3 
Gene Names: mbnCCQW49_07155
UniProt
Find proteins for A0A2D2CY73 (Methylosinus trichosporium (strain ATCC 35070 / NCIMB 11131 / UNIQEM 75 / OB3b))
Explore A0A2D2CY73 
Go to UniProtKB:  A0A2D2CY73
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D2CY73
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE
(Subject of Investigation/LOI)

Query on FE



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
I [auth B],
J [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free:  0.265 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.411α = 90
b = 215.18β = 90
c = 215.146γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118035

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description