9HNF | pdb_00009hnf

Beta-keto acid cleavage enzyme from Paracoccus denitrificans with bound acetoacetate and acetyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.192 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Design and implementation of aerobic and ambient CO 2 -reduction as an entry-point for enhanced carbon fixation.

Satanowski, A.Marchal, D.G.Perret, A.Petit, J.L.Bouzon, M.Doring, V.Dubois, I.He, H.Smith, E.N.Pellouin, V.Petri, H.M.Rainaldi, V.Nattermann, M.Burgener, S.Paczia, N.Zarzycki, J.Heinemann, M.Bar-Even, A.Erb, T.J.

(2025) Nat Commun 16: 3134-3134

  • DOI: https://doi.org/10.1038/s41467-025-57549-4
  • Primary Citation of Related Structures:  
    8RIO, 8RIP, 9HNF

  • PubMed Abstract: 

    The direct reduction of CO 2 into one-carbon molecules is key to highly efficient biological CO 2 -fixation. However, this strategy is currently restricted to anaerobic organisms and low redox potentials. In this study, we introduce the CORE cycle, a synthetic metabolic pathway that converts CO 2 to formate at aerobic conditions and ambient CO 2 levels, using only NADPH as a reductant. Combining theoretical pathway design and analysis, enzyme bioprospecting and high-throughput screening, modular assembly and adaptive laboratory evolution, we realize the CORE cycle in vivo and demonstrate that the cycle supports growth of E. coli by supplementing C1-metabolism and serine biosynthesis from CO 2 . We further analyze the theoretical potential of the CORE cycle as a new entry-point for carbon in photorespiration and autotrophy. Overall, our work expands the solution space for biological carbon reduction, offering a promising approach to enhance CO 2 fixation processes such as photosynthesis, and opening avenues for synthetic autotrophy.


  • Organizational Affiliation

    Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, Germany. ari.satanowski@gmail.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-keto-5-aminohexanoate cleavage protein
A, B
334Paracoccus denitrificans PD1222Mutation(s): 0 
Gene Names: Pden_3578
UniProt
Find proteins for A1B802 (Paracoccus denitrificans (strain Pd 1222))
Explore A1B802 
Go to UniProtKB:  A1B802
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1B802
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO (Subject of Investigation/LOI)
Query on ACO

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
AAE (Subject of Investigation/LOI)
Query on AAE

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
ACETOACETIC ACID
C4 H6 O3
WDJHALXBUFZDSR-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.192 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.9α = 90
b = 138.48β = 90
c = 136.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
European CommissionEuropean Union862087

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release