4JHC

Crystal structure of the uncharacterized Maf protein YceF from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Biochemical and structural studies of conserved maf proteins revealed nucleotide pyrophosphatases with a preference for modified nucleotides.

Tchigvintsev, A.Tchigvintsev, D.Flick, R.Popovic, A.Dong, A.Xu, X.Brown, G.Lu, W.Wu, H.Cui, H.Dombrowski, L.Joo, J.C.Beloglazova, N.Min, J.Savchenko, A.Caudy, A.A.Rabinowitz, J.D.Murzin, A.G.Yakunin, A.F.

(2013) Chem.Biol. 20: 1386-1398

  • DOI: 10.1016/j.chembiol.2013.09.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Maf (for multicopy associated filamentation) proteins represent a large family of conserved proteins implicated in cell division arrest but whose biochemical activity remains unknown. Here, we show that the prokaryotic and eukaryotic Maf proteins exh ...

    Maf (for multicopy associated filamentation) proteins represent a large family of conserved proteins implicated in cell division arrest but whose biochemical activity remains unknown. Here, we show that the prokaryotic and eukaryotic Maf proteins exhibit nucleotide pyrophosphatase activity against 5-methyl-UTP, pseudo-UTP, 5-methyl-CTP, and 7-methyl-GTP, which represent the most abundant modified bases in all organisms, as well as against canonical nucleotides dTTP, UTP, and CTP. Overexpression of the Maf protein YhdE in E. coli cells increased intracellular levels of dTMP and UMP, confirming that dTTP and UTP are the in vivo substrates of this protein. Crystal structures and site-directed mutagenesis of Maf proteins revealed the determinants of their activity and substrate specificity. Thus, pyrophosphatase activity of Maf proteins toward canonical and modified nucleotides might provide the molecular mechanism for a dual role of these proteins in cell division arrest and house cleaning.


    Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maf-like protein YceF
A, B
215Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yceF
Find proteins for P0A729 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A729
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.413α = 90.00
b = 52.856β = 90.00
c = 128.948γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
JDirectordata collection
HKL-3000data scaling
HKL-3000data reduction
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Database references, Structure summary
  • Version 1.2: 2013-12-18
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description