8CIW

Methylsuccinyl-CoA dehydrogenase from Pseudomonas migulae with bound FAD and (2S)-methylsuccinyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Exploring alternative pathways for the in vitro establishment of the HOPAC cycle for synthetic CO 2 fixation.

McLean, R.Schwander, T.Diehl, C.Cortina, N.S.Paczia, N.Zarzycki, J.Erb, T.J.

(2023) Sci Adv 9: eadh4299-eadh4299

  • DOI: https://doi.org/10.1126/sciadv.adh4299
  • Primary Citation of Related Structures:  
    8CIW

  • PubMed Abstract: 

    Nature has evolved eight different pathways for the capture and conversion of CO 2 , including the Calvin-Benson-Bassham cycle of photosynthesis. Yet, these pathways underlie constrains and only represent a fraction of the thousands of theoretically possible solutions. To overcome the limitations of natural evolution, we introduce the HydrOxyPropionyl-CoA/Acrylyl-CoA (HOPAC) cycle, a new-to-nature CO 2 -fixation pathway that was designed through metabolic retrosynthesis around the reductive carboxylation of acrylyl-CoA, a highly efficient principle of CO 2 fixation. We realized the HOPAC cycle in a step-wise fashion and used rational engineering approaches and machine learning-guided workflows to further optimize its output by more than one order of magnitude. Version 4.0 of the HOPAC cycle encompasses 11 enzymes from six different organisms, converting ~3.0 mM CO 2 into glycolate within 2 hours. Our work moves the hypothetical HOPAC cycle from a theoretical design into an established in vitro system that forms the basis for different potential applications.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
(2S)-methylsuccinyl-CoA dehydrogenase
A, B
555Pseudomonas migulaeMutation(s): 0 
Gene Names: SAMN04490194_2123
UniProt
Find proteins for A0A1H5ILA2 (Pseudomonas migulae)
Explore A0A1H5ILA2 
Go to UniProtKB:  A0A1H5ILA2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1H5ILA2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZKK (Subject of Investigation/LOI)
Query on ZKK

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
(2S)-Methylsuccinyl-CoA
C26 H42 N7 O19 P3 S
OUFHQHVVFSERRI-VKBDFPRVSA-N
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
COA
Query on COA

Download Ideal Coordinates CCD File 
J [auth B]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
P6G
Query on P6G

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
FLC
Query on FLC

Download Ideal Coordinates CCD File 
F [auth B]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.805α = 90
b = 169.563β = 90
c = 118.39γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection