Go to basket

Tree Display

AceDB Schema

XML Display


Family Report for: RutD


Family RutD
Block X
Parent Family : Abhydrolase_6

RutD is encoded within the Rut operon which allows growth on pyrimidines as sole nitrogen source. The function of this protein is not known, but it is necessary for growth on pyrimidines, and cells lacking RutD produce much less of the Rut pathway intermediate malonic semialdehyde than normal. It is thought that RutD increases the rate of spontaneous hydrolysis of the toxic intermediate aminoacrylate to malonic semialdehyde. The closest relative family is Carboxymethylbutenolide_lactonase. The structure of E. Coli RutD by Knapik et al. revealed a new active site for an alphabeta hydrolase: The nucleophile residue is Histidine located in a pentapptide GHALG. (a similar pentapeptide GHALD with alanine as nucleophile has been found in an un related family Methylketone synthase 1 in hydroxylnitrile lyase Auldridge et al.)

IPR019913 (Pyrimidine utilisation protein RutD)
PF12697 (Abhydrolase_6)
no EC number

Peptide in
Nucleotide in
Alignment with Multalin
|Text only/graphic display
Seed alignment with MAFFT
|No colour/coloured with Mview
Alignment with MAFFT
|No colour/coloured with Mview
|Graphical display, obtained with the dnd file produced by Clustalw

    Title: A multi-faceted analysis of RutD reveals a novel family of alpha/beta hydrolases
    Knapik AA, Petkowski JJ, Otwinowski Z, Cymborowski MT, Cooper DR, Majorek KA, Chruszcz M, Krajewska WM, Minor W
    Ref: Proteins, 80:2359, 2012 : PubMed


    Title: The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems.
    Kim KS, Pelton JG, Inwood WB, Andersen U, Kustu S, Wemmer DE
    Ref: Journal of Bacteriology, 192:4089, 2010 : PubMed


    Title: A previously undescribed pathway for pyrimidine catabolism
    Loh KD, Gyaneshwar P, Markenscoff Papadimitriou E, Fong R, Kim KS, Parales R, Zhou Z, Inwood W, Kustu S
    Ref: Proc Natl Acad Sci U S A, 103:5114, 2006 : PubMed


Other Papers

No structure scheme yet for this family

Structures in RutD family (1)

Genes Proteins in RutD family (30)

No fragments
Substrates of some enzymes in the RutD family (1)

No Inhibitor

Send your questions or comments to :
Mail to: Nicolas Lenfant, Thierry Hotelier, Yves Bourne, Pascale Marchot and Arnaud Chatonnet.
Please cite: Lenfant 2013 Nucleic.Acids.Res. or Marchot Chatonnet 2012 Prot.Pept Lett.
For technical information about these pages see:
ESTHER Home Page and ACEDB Home Page
AcePerl Lincoln Stein Home Page

Acknowledgements and disclaimer