8FUM

AibH1H2 metalated with Fe in the presence of Tris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Enzymatic Hydroxylation of Aliphatic C-H Bonds by a Mn/Fe Cofactor.

Powell, M.M.Rao, G.Britt, R.D.Rittle, J.

(2023) J Am Chem Soc 145: 16526-16537

  • DOI: https://doi.org/10.1021/jacs.3c03419
  • Primary Citation of Related Structures:  
    8FUL, 8FUM, 8FUN, 8FUO

  • PubMed Abstract: 

    The aerobic oxidation of carbon-hydrogen (C-H) bonds in biology is currently known to be accomplished by a limited set of cofactors that typically include heme, nonheme iron, and copper. While manganese cofactors perform difficult oxidation reactions, including water oxidation within Photosystem II, they are generally not known to be used for C-H bond activation, and those that do catalyze this important reaction display limited intrinsic reactivity. Here we report that the 2-aminoisobutyric acid hydroxylase from Rhodococcus wratislaviensis , AibH1H2, requires manganese to functionalize a strong, aliphatic C-H bond (BDE = 100 kcal/mol). Structural and spectroscopic studies of this enzyme reveal a redox-active, heterobimetallic manganese-iron active site at the locus of O 2 activation and substrate coordination. This result expands the known reactivity of biological manganese-iron cofactors, which was previously restricted to single-electron transfer or stoichiometric protein oxidation. Furthermore, the AibH1H2 cofactor is supported by a protein fold distinct from typical bimetallic oxygenases, and bioinformatic analyses identify related proteins abundant in microorganisms. This suggests that many uncharacterized monooxygenases may similarly require manganese to perform oxidative biochemical tasks.


  • Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amidohydrolase
A, C, E, G
392Rhodococcus wratislaviensis NBRC 100605Mutation(s): 0 
Gene Names: Rhow_000804
UniProt
Find proteins for A0A402C2V4 (Rhodococcus wratislaviensis)
Explore A0A402C2V4 
Go to UniProtKB:  A0A402C2V4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A402C2V4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Amidohydrolase
B, F, H
378Rhodococcus wratislaviensis NBRC 100605Mutation(s): 0 
Gene Names: Rhow_000803
UniProt
Find proteins for A0A402C2Q3 (Rhodococcus wratislaviensis)
Explore A0A402C2Q3 
Go to UniProtKB:  A0A402C2Q3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A402C2Q3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Amidohydrolase378Rhodococcus wratislaviensis NBRC 100605Mutation(s): 0 
Gene Names: Rhow_000803
UniProt
Find proteins for A0A402C2Q3 (Rhodococcus wratislaviensis)
Explore A0A402C2Q3 
Go to UniProtKB:  A0A402C2Q3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A402C2Q3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
AA [auth E]
I [auth A]
J [auth A]
MA [auth G]
N [auth B]
AA [auth E],
I [auth A],
J [auth A],
MA [auth G],
N [auth B],
NA [auth G],
S [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
GA [auth F]
HA [auth F]
IA [auth F]
O [auth B]
SA [auth H]
GA [auth F],
HA [auth F],
IA [auth F],
O [auth B],
SA [auth H],
V [auth D],
W [auth D]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth E]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
FE
Query on FE

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CA [auth E]
JA [auth F]
K [auth A]
KA [auth F]
OA [auth G]
CA [auth E],
JA [auth F],
K [auth A],
KA [auth F],
OA [auth G],
P [auth B],
Q [auth B],
T [auth C],
TA [auth H],
UA [auth H],
X [auth D],
Y [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth E]
EA [auth E]
FA [auth E]
L [auth A]
LA [auth F]
DA [auth E],
EA [auth E],
FA [auth E],
L [auth A],
LA [auth F],
M [auth A],
PA [auth G],
QA [auth G],
R [auth B],
RA [auth G],
U [auth C],
VA [auth H],
WA [auth H],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
B, F, H
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.59α = 90
b = 232.64β = 92.77
c = 147.636γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata 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: 2023-04-05
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references