7VG5

10,5-methenyltetrahydrofolate cyclohydrolase from Methylobacterium extorquens AM1 with tetrahydrofolate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 

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Literature

Structural insight into a molecular mechanism of methenyltetrahydrofolate cyclohydrolase from Methylobacterium extorquens AM1.

Kim, S.Lee, S.H.Kim, I.K.Seo, H.Kim, K.J.

(2022) Int J Biol Macromol 202: 234-240

  • DOI: https://doi.org/10.1016/j.ijbiomac.2022.01.072
  • Primary Citation of Related Structures:  
    7VG4, 7VG5

  • PubMed Abstract: 

    Bioconversion of the C1 compounds into value-added products is one of the CO 2 -reducing strategies. In particular, because CO 2 can be easily converted into formate, the efficient and direct bioconversion of CO 2 through formate assimilation is attracting attention. The tetrahydrofolate (THF) cycle is the highly efficient reconstructed formate assimilation pathway, and 5,10-methenyltetrahydrofolate cyclohydrolase (FchA) is an essential enzyme involved in the THF cycle. In this study, a kinetic analysis of FchA from Methylobacterium extorquens AM1 (MeFchA) was performed and revealed that the enzyme has much higher cyclization than hydrolyzation activity, making it an optimal enzyme for formate assimilation. The crystal structure of MeFchA in the apo- and the THF-complexed forms was also determined, revealing that the substrate-binding site of the enzyme has three differently charged regions to stabilize the three differently charged moieties of the formyl-THF substrate. The residues involved in the substrate binding were also verified through site-directed mutagenesis. This study provides a biochemical and structural basis for the molecular mechanism underlying formate assimilation.


  • Organizational Affiliation

    School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methenyltetrahydrofolate cyclohydrolase
A, B
216Methylorubrum extorquens AM1Mutation(s): 0 
Gene Names: fchAMexAM1_META1p1729
EC: 3.5.4.9
UniProt
Find proteins for Q49135 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Explore Q49135 
Go to UniProtKB:  Q49135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ49135
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.322α = 90
b = 49.513β = 97.38
c = 64.071γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science, ICT and Future Planning (MSIP)Korea, Republic Of2021M3D3A1A01079480_2021-5

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description