3C3D

Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and phosphate. Northeast Structural Genomics Consortium target MaR46


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1074/jbc.M710352200
  • Primary Citation of Related Structures:  

  • 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 l ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-phospho-L-lactate transferase
A, B, C, D
311Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)Mutation(s): 0 
Gene Names: cofD
EC: 2.7.8.28
Find proteins for Q8PVT6 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Go to UniProtKB:  Q8PVT6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FO1
Query on FO1

Download SDF File 
Download CCD File 
A, B, C, D
1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol
7,8-didemethyl-8-hydroxy-5-deazariboflavin
C16 H17 N3 O7
AUEILLWDYUBWCM-XQQFMLRXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FO1Kd: 1380000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 185.278α = 90.00
b = 185.278β = 90.00
c = 67.789γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
RESOLVEphasing
SCALEPACKdata scaling
SnBphasing
ADSCdata collection
HKL-2000data reduction
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance