1Y60

Structure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1 with bound 5,10-methylene tetrahydromethanopterin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

How an enzyme binds the C1-carrier tetrahydromethanopterin: Structure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1

Acharya, P.Goenrich, M.Hagemeier, C.H.Demmer, U.Vorholt, J.A.Thauer, R.K.Ermler, U.

(2005) J.Biol.Chem. 280: 13712-13719

  • DOI: 10.1074/jbc.M412320200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tetrahydromethanopterin (H4 MPT) is a tetrahydrofolate analogue involved as a C1 carrier in the metabolism of various groups of microorganisms. How H4MPT is bound to the respective C1 unit converting enzymes remained elusive. We describe here the str ...

    Tetrahydromethanopterin (H4 MPT) is a tetrahydrofolate analogue involved as a C1 carrier in the metabolism of various groups of microorganisms. How H4MPT is bound to the respective C1 unit converting enzymes remained elusive. We describe here the structure of the homopentameric formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1 established at 2.0 angstrom without and at 1.9 angstrom with methylene-H4MPT bound. Methylene-H4MPT is bound in an "S"-shaped conformation into the cleft formed between two adjacent subunits. Coenzyme binding is accompanied by side chain rearrangements up to 5 angstrom and leads to a rigidification of the C-terminal arm, a formation of a new hydrophobic cluster, and an inversion of the amide side chain of Gln88. Methylene-H4MPT in Fae shows a characteristic kink between the tetrahydropyrazine and the imidazolidine rings of 70 degrees that is more pronounced than that reported for free methylene-H4MPT in solution (50 degrees). Fae is an essential enzyme for energy metabolism and formaldehyde detoxification of this bacterium and catalyzes the formation of methylene-H4MPT from H4MPT and formaldehyde. The molecular mechanism ofthis reaction involving His22 as acid catalyst is discussed.


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Formaldehyde-activating enzyme fae
A, B, C, D, E
169Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)Mutation(s): 0 
Gene Names: fae
EC: 4.2.1.147
Find proteins for Q9FA38 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Go to UniProtKB:  Q9FA38
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H4M
Query on H4M

Download SDF File 
Download CCD File 
B, C, D, E
5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN
C31 H45 N6 O16 P
GBMIGEWJAPFSQI-UQXKJNEMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.860α = 90.00
b = 112.590β = 91.00
c = 72.010γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
EPMRphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance