1LU9

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylobacterium extorquens AM1

• PDB DOI: https://doi.org/10.2210/pdb1LU9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methylorubrum extorquens AM1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-05-22 Released: 2002-09-11 
• Deposition Author(s): Ermler, U., Hagemeier, C.H., Roth, A., Demmer, U., Grabarse, W., Warkentin, E., Vorholt, J.A.

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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 

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

• PubMed: 12176390 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60528 Frankfurt am Main, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 88.92 kDa 
• Atom Count: 7,803 
• Modelled Residue Count: 861 
• Deposited Residue Count: 861 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylene Tetrahydromethanopterin Dehydrogenase	A, B, C	287	Methylorubrum extorquens AM1	Mutation(s): 0  Gene Names: mtdA EC: 1.5.1.5 (PDB Primary Data), 1.5.1 (UniProt)
UniProt
Find proteins for P55818 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore P55818  Go to UniProtKB:  P55818

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 = 133.13	α = 90
b = 85.24	β = 113.81
c = 92.37	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
SHARP	phasing
DM	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-09-11 
Deposition Author(s): Ermler, U., Hagemeier, C.H., Roth, A., Demmer, U., Grabarse, W., Warkentin, E., Vorholt, J.A.

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
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references