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.)


Interpro : IPR019913 Pyrimidine utilisation protein RutD

PIRSF : PIRSF000875 3-oxoadipate enol-lactonase

Pdoc : No Pdoc

Pfam : PF12697 Abhydrolase_6

Prints : No Print

EC Number : No EC Number


Peptide in Fasta
Nucleotide in Fasta
Alignment with Multalin Text only
Seed alignment with MAFFT No colour
Alignment with MAFFT No colour
Dendrogram The dnd file

Structures (1)

Genes Proteins in RutD family (30)

No fragment of genes

Structures in RutD family (1)

Substrates in RutD family (1)

No Inhibitor

References (3)

Title : A multi-faceted analysis of RutD reveals a novel family of alpha\/beta hydrolases - Knapik_2012_Proteins_80_2359
Author(s) : Knapik AA , Petkowski JJ , Otwinowski Z , Cymborowski MT , Cooper DR , Majorek KA , Chruszcz M , Krajewska WM , Minor W
Ref : Proteins , 80 :2359 , 2012
PubMedID: 22641504
Gene_locus related to this paper: ecoli-rutD

Title : The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems. - Kim_2010_J.Bacteriol_192_4089
Author(s) : Kim KS , Pelton JG , Inwood WB , Andersen U , Kustu S , Wemmer DE
Ref : Journal of Bacteriology , 192 :4089 , 2010
PubMedID: 20400551
Gene_locus related to this paper: ecoli-rutD

Title : A previously undescribed pathway for pyrimidine catabolism - Loh_2006_Proc.Natl.Acad.Sci.U.S.A_103_5114
Author(s) : 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
PubMedID: 16540542
Gene_locus related to this paper: ecoli-rutD