Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei. Northeast Structural Genomics Consortium target MaR46

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

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Molecular insights into the biosynthesis of the f420 coenzyme.

Forouhar, F.Abashidze, M.Xu, H.Grochowski, L.L.Seetharaman, J.Hussain, M.Kuzin, A.Chen, Y.Zhou, W.Xiao, R.Acton, T.B.Montelione, G.T.Galinier, A.White, R.H.Tong, L.

(2008) J Biol Chem 283: 11832-11840

  • DOI: https://doi.org/10.1074/jbc.M710352200
  • Primary Citation of Related Structures:  
    3C3D, 3C3E, 3CGW

  • PubMed Abstract: 

    Coenzyme F(420), a hydride carrier, is found in Archaea and some bacteria and has crucial roles in methanogenesis, antibiotic biosynthesis, DNA repair, and activation of antitubercular compounds. CofD, 2-phospho-l-lactate transferase, catalyzes the last step in the biosynthesis of F(420)-0 (F(420) without polyglutamate), by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (Fo). CofD is highly conserved among F(420)-producing organisms, and weak sequence homologs are also found in non-F(420)-producing organisms. This superfamily does not share any recognizable sequence conservation with other proteins. Here we report the first crystal structures of CofD, the free enzyme and two ternary complexes, with Fo and P(i) or with Fo and GDP, from Methanosarcina mazei. The active site is located at the C-terminal end of a Rossmann fold core, and three large insertions make significant contributions to the active site and dimer formation. The observed binding modes of Fo and GDP can explain known biochemical properties of CofD and are also supported by our binding assays. The structures provide significant molecular insights into the biosynthesis of the F(420) coenzyme. Large structural differences in the active site region of the non-F(420)-producing CofD homologs suggest that they catalyze a different biochemical reaction.

  • Organizational Affiliation

    Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LPPG:FO 2-phospho-L-lactate transferase311Methanosarcina mazei Go1Mutation(s): 0 
Gene Names: cofDMM_1874
EC: 2.7.8
Find proteins for Q8PVT6 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PVT6 
Go to UniProtKB:  Q8PVT6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PVT6
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.64α = 90
b = 110.64β = 90
c = 75.947γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance