1LU9

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylobacterium extorquens AM1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of methylene-tetrahydromethanopterin dehydrogenase from methylobacterium extorquens AM1.

Ermler, U.Hagemeier, C.H.Roth, A.Demmer, U.Grabarse, W.Warkentin, E.Vorholt, J.A.

(2002) Structure 10: 1127-1137

  • DOI: 10.1016/s0969-2126(02)00802-x
  • Primary Citation of Related Structures:  
    1LU9, 1LUA

  • PubMed Abstract: 
  • NADP-dependent methylene-H(4)MPT dehydrogenase, MtdA, from Methylobacterium extorquens AM1 catalyzes the dehydrogenation of methylene-tetrahydromethanopterin and methylene-tetrahydrofolate with NADP(+) as cosubstrate. The X-ray structure of MtdA with ...

    NADP-dependent methylene-H(4)MPT dehydrogenase, MtdA, from Methylobacterium extorquens AM1 catalyzes the dehydrogenation of methylene-tetrahydromethanopterin and methylene-tetrahydrofolate with NADP(+) as cosubstrate. The X-ray structure of MtdA with and without NADP bound was established at 1.9 A resolution. The enzyme is present as a homotrimer. The alpha,beta fold of the monomer is related to that of methylene-H(4)F dehydrogenases, suggesting a common evolutionary origin. The position of the active site is located within a large crevice built up by the two domains of one subunit and one domain of a second subunit. Methylene-H(4)MPT could be modeled into the cleft, and crucial active site residues such as Phe18, Lys256, His260, and Thr102 were identified. The molecular basis of the different substrate specificities and different catalytic demands of MtdA compared to methylene-H(4)F dehydrogenases are discussed.


    Related Citations: 
    • The NADP-Dependent Methylene Tetrahydromethanopterin Dehydrogenase in Methylobacterium extorquens AM1
      Vorholt, J.A., Chistoserdova, L., Lidstrom, M.E., Thauer, R.K.
      (1998) J Bacteriol 180: 5351

    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60528 Frankfurt am Main, Germany. ulrich.ermler@mpibp-frankfurt.mpg.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methylene Tetrahydromethanopterin DehydrogenaseA, B, C287Methylorubrum extorquens AM1Mutation(s): 0 
Gene Names: mtdAMexAM1_META1p1728
EC: 1.5.1.5 (PDB Primary Data), 1.5.1 (UniProt)
Find proteins for P55818 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Explore P55818 
Go to UniProtKB:  P55818
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.13α = 90
b = 85.24β = 113.81
c = 92.37γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
SHARPphasing
DMmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance