9BU9 | pdb_00009bu9

Mixed-valent (2/3) dimanganese SfbO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 
    0.187 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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Literature

O 2 Activation and Enzymatic C-H Bond Activation Mediated by a Dimanganese Cofactor.

Liu, C.Rao, G.Nguyen, J.Britt, R.D.Rittle, J.

(2025) J Am Chem Soc 147: 2148-2157

  • DOI: https://doi.org/10.1021/jacs.4c16271
  • Primary Citation of Related Structures:  
    9BU9, 9BUA

  • PubMed Abstract: 

    Dioxygen (O 2 ) is a potent oxidant used by aerobic organisms for energy transduction and critical biosynthetic processes. Numerous metalloenzymes harness O 2 to mediate C-H bond hydroxylation reactions, but most commonly feature iron or copper ions in their active site cofactors. In contrast, many manganese-activated enzymes─such as glutamine synthetase and isocitrate lyase─perform redox neutral chemical transformations and very few are known to activate O 2 or C-H bonds. Here, we report that the dimanganese-metalated form of the cambialistic monooxygenase SfbO (Mn 2 -SfbO) can efficiently mediate enzymatic C-H bond hydroxylation. The activity of the dimanganese form of SfbO toward substrate hydroxylation is comparable to that of its heterobimetallic Mn/Fe form but exhibits distinct kinetic profiles. Kinetic, spectroscopic, and structural studies invoke a mixed-valent dimanganese cofactor (Mn II Mn III ) in O 2 activation and evidence a stoichiometric role for superoxide in maturing an O 2 -inert Mn II 2 cofactor. Computational studies support a hypothesis wherein superoxide addition to the Mn II 2 cofactor installs a critical bridging hydroxide ligand that stabilizes higher-valent manganese oxidation states. These findings establish the viability of proteinaceous dimanganese cofactors in mediating complex, multistep redox transformations.


  • Organizational Affiliation
    • Department of Chemistry, University of California, Berkeley, California 94720, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amidohydrolase family protein
A, B, C, D
372Litorilinea aerophilaMutation(s): 0 
Gene Names: FKZ61_10105
UniProt
Find proteins for A0A540VG95 (Litorilinea aerophila)
Explore A0A540VG95 
Go to UniProtKB:  A0A540VG95
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A540VG95
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
N [auth B],
Q [auth C],
V [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
K [auth B]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
T [auth D],
U [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
O [auth B]
P [auth B]
R [auth C]
I [auth A],
J [auth A],
O [auth B],
P [auth B],
R [auth C],
S [auth C],
W [auth D],
X [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free:  0.187 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.098α = 90
b = 127.981β = 90
c = 138.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2026-03-11
    Changes: Database references