3IQF

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of the hydride transfer mechanism in F(420)-dependent methylenetetrahydromethanopterin dehydrogenase

Ceh, K.Demmer, U.Warkentin, E.Moll, J.Thauer, R.K.Shima, S.Ermler, U.

(2009) Biochemistry 48: 10098-10105

  • DOI: 10.1021/bi901104d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • F(420)-dependent methylenetetrahydromethanopterin (methylene-H(4)MPT) dehydrogenase (Mtd) of Methanopyrus kandleri is an enzyme of the methanogenic energy metabolism that catalyzes the reversible hydride transfer between methenyl-H(4)MPT(+) and methy ...

    F(420)-dependent methylenetetrahydromethanopterin (methylene-H(4)MPT) dehydrogenase (Mtd) of Methanopyrus kandleri is an enzyme of the methanogenic energy metabolism that catalyzes the reversible hydride transfer between methenyl-H(4)MPT(+) and methylene-H(4)MPT using coenzyme F(420) as hydride carrier. We determined the structures of the Mtd-methylene-H(4)MPT, Mtd-methenyl-H(4)MPT(+), and the Mtd-methenyl-H(4)MPT(+)-F(420)H(2) complexes at 2.1, 2.0, and 1.8 A resolution, respectively. The pterin-imidazolidine-phenyl ring system is present in a new extended but not planar conformation which is virtually identical in methenyl-H(4)MPT(+) and methylene-H(4)MPT at the current resolution. Both substrates methenyl-H(4)MPT(+) and F(420)H(2) bind in a face to face arrangement to an active site cleft, thereby ensuring a direct hydride transfer between their C14a and C5 atoms, respectively. The polypeptide scaffold does not reveal any significant conformational change upon binding of the bulky substrates but in turn changes the conformations of the substrate rings either to avoid clashes between certain ring atoms or to adjust the rings involved in hydride transfer for providing an optimal catalytic efficiency.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
F420-dependent methylenetetrahydromethanopterin dehydrogenase
A, B, C, D, E, F, G, H, I, J, K, L
283Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)Mutation(s): 0 
Gene Names: mtd
EC: 1.5.98.1
Find proteins for P94951 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938))
Go to UniProtKB:  P94951
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
E4M
Query on E4M

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol
C31 H44 N6 O16 P
RANKJVUGLXUXOL-CAFBYHECSA-O
 Ligand Interaction
CA
Query on CA

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B, E, I, J, K, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 103.400α = 90.00
b = 167.100β = 113.60
c = 122.500γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance