Enoyl-CoA carboxylases/reductases in complex with ethylmalonyl CoA

Experimental Data Snapshot

  • Resolution: 1.72 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Four amino acids define the CO2binding pocket of enoyl-CoA carboxylases/reductases.

Stoffel, G.M.M.Saez, D.A.DeMirci, H.Vogeli, B.Rao, Y.Zarzycki, J.Yoshikuni, Y.Wakatsuki, S.Vohringer-Martinez, E.Erb, T.J.

(2019) Proc Natl Acad Sci U S A 116: 13964-13969

  • DOI: https://doi.org/10.1073/pnas.1901471116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Carboxylases are biocatalysts that capture and convert carbon dioxide (CO 2 ) under mild conditions and atmospheric concentrations at a scale of more than 400 Gt annually. However, how these enzymes bind and control the gaseous CO 2 molecule during catalysis is only poorly understood. One of the most efficient classes of carboxylating enzymes are enoyl-CoA carboxylases/reductases (Ecrs), which outcompete the plant enzyme RuBisCO in catalytic efficiency and fidelity by more than an order of magnitude. Here we investigated the interactions of CO 2 within the active site of Ecr from Kitasatospora setae Combining experimental biochemistry, protein crystallography, and advanced computer simulations we show that 4 amino acids, N81, F170, E171, and H365, are required to create a highly efficient CO 2 -fixing enzyme. Together, these 4 residues anchor and position the CO 2 molecule for the attack by a reactive enolate created during the catalytic cycle. Notably, a highly ordered water molecule plays an important role in an active site that is otherwise carefully shielded from water, which is detrimental to CO 2 fixation. Altogether, our study reveals unprecedented molecular details of selective CO 2 binding and C-C-bond formation during the catalytic cycle of nature's most efficient CO 2 -fixing enzyme. This knowledge provides the basis for the future development of catalytic frameworks for the capture and conversion of CO 2 in biology and chemistry.

  • Organizational Affiliation

    Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Crotonyl-CoA carboxylase/reductase
A, B, C, D
449Kitasatospora setae KM-6054Mutation(s): 0 
Gene Names: ccr1KSE_56510
Find proteins for E4N096 (Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054))
Explore E4N096 
Go to UniProtKB:  E4N096
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE4N096
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on N9V

Download Ideal Coordinates CCD File 
F [auth A],
L [auth D]
5'-O-[(S)-{[(S)-[(3R)-4-({(1E)-3-[(2-{[(2S)-2-carboxybutanoyl]sulfanyl}ethyl)amino]-3-oxoprop-1-en-1-yl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine 3'-(dihydrogen phosphate)
C26 H40 N7 O19 P3 S
Query on NDP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
M [auth D]
C21 H30 N7 O17 P3
Query on IMD

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
N [auth D]
C3 H5 N2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.72 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.1α = 90
b = 78.7β = 108.1
c = 138.9γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2019-06-26 
  • Deposition Author(s): DeMirci, H.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1231306

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references