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 
  • R-Value Observed: 0.195 

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:  
    2P5X, 4HEB, 4LU1, 4JHC

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maf-like protein YceFAB215Escherichia coli K-12Mutation(s): 0 
Gene Names: yceFb1087JW5155
EC: 3.6.1
Find proteins for P0A729 (Escherichia coli (strain K12))
Explore P0A729 
Go to UniProtKB:  P0A729
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.413α = 90
b = 52.856β = 90
c = 128.948γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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