8APQ

CaMct - Mesaconyl-CoA C1:C4 CoA Transferase of Chloroflexus aurantiacus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for a Cork-Up Mechanism of the Intra-Molecular Mesaconyl-CoA Transferase.

Pfister, P.Zarzycki, J.Erb, T.J.

(2023) Biochemistry 62: 75-84

  • DOI: https://doi.org/10.1021/acs.biochem.2c00532
  • Primary Citation of Related Structures:  
    8APQ, 8APR

  • PubMed Abstract: 

    Mesaconyl-CoA transferase (Mct) is one of the key enzymes of the 3-hydroxypropionate (3HP) bi-cycle for autotrophic CO 2 fixation. Mct is a family III/Frc family CoA transferase that catalyzes an unprecedented intra-molecular CoA transfer from the C1-carboxyl group to the C4-carboxyl group of mesaconate at catalytic efficiencies >10 6 M -1 s -1 . Here, we show that the reaction of Mct proceeds without any significant release of free CoA or the transfer to external acceptor acids. Mct catalyzes intra-molecular CoA transfers at catalytic efficiencies that are at least more than 6 orders of magnitude higher compared to inter-molecular CoA transfers, demonstrating that the enzyme exhibits exquisite control over its reaction. To understand the molecular basis of the intra-molecular CoA transfer in Mct, we solved crystal structures of the enzyme from Chloroflexus aurantiacus in its apo form, as well as in complex with mesaconyl-CoA and several covalently enzyme-bound intermediates of CoA and mesaconate at the catalytically active residue Asp165. Based on these structures, we propose a reaction mechanism for Mct that is similar to inter-molecular family III/Frc family CoA transferases. However, in contrast to the latter that undergo opening and closing cycles during the reaction to exchange substrates, the central cavity of Mct remains sealed ("corked-up") by the CoA moiety, strongly favoring the intra-molecular CoA transfer between the C1 and the C4 position of mesaconate.


  • Organizational Affiliation

    Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-methylfumaryl-CoA isomerase
A, B, C, D, E
A, B, C, D, E, F
430Chloroflexus aurantiacus J-10-flMutation(s): 0 
Gene Names: mctCaur_0175
EC: 5.4.1.3
UniProt
Find proteins for A9WC36 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Explore A9WC36 
Go to UniProtKB:  A9WC36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9WC36
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OA9 (Subject of Investigation/LOI)
Query on OA9

Download Ideal Coordinates CCD File 
G [auth A]Mesaconyl Coenzme A
C26 H40 N7 O19 P3 S
LVBVWNJPMXCQJE-CBBDEUQJSA-N
COA (Subject of Investigation/LOI)
Query on COA

Download Ideal Coordinates CCD File 
H [auth B],
J [auth C],
L [auth D],
N [auth E],
P [auth F]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
MEZ (Subject of Investigation/LOI)
Query on MEZ

Download Ideal Coordinates CCD File 
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
(2E)-2-METHYLBUT-2-ENEDIOIC ACID
C5 H6 O4
HNEGQIOMVPPMNR-NSCUHMNNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.84α = 90
b = 193.84β = 90
c = 251.97γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
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: 2023-01-11
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description