RutD
Relationship
Comment
Pyrimidine utilisation protein 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 pentapetide 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.)
Database
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
Sequences
| Peptide in | Fasta |
| Nucleotide in | Fasta |
| Alignment with Multalin | Text only |
| Seed alignment with MAFFT | No colour / coloured with Mview |
| Alignment with MAFFT | No colour / coloured with Mview |
| Dendrogram | The dnd file |
| Structure | Name | Proteins |
|---|---|---|
| 3V48 | Crystal Structure of the putative alpha\/beta hydrolase RutD from E.coli | ecoli-rutD |
| Gene_locus | Name | Species |
|---|---|---|
| 9caul-q0lxe3 | Caulobacter sp. K31 alpha\/beta hydrolase fold-1 | Caulobacter sp. K31 |
| aciad-q6ffz9 | Acinetobacter sp. (strain ADP1) putative hydrolase (alpha\/beta hydrolase superfamily) | Acinetobacter sp. |
| agrrk-rutd | Agrobacterium radiobacter (strain K84 \/ ATCC BAA-868). Aminohydrolase | Agrobacterium radiobacter |
| agrtu-ATU2497 | Agrobacterium tumefaciens (strain C58 \/ ATCC 33970) hydrolase | Agrobacterium tumefaciens |
| azoc5-rutd | Azorhizobium caulinodans (strain ATCC 43989 \/ DSM 5975 \/ JCM 20966 \/ LMG 6465 \/ NBRC 14845 \/ NCIMB 13405 \/ ORS 571). Aminohydrolase | Azorhizobium caulinodans |
| caucr-CC2797 | Caulobacter crescentus\; Caulobacter vibrioides hydrolase, Putative aminoacrylate hydrolase RutD | Caulobacter crescentus |
| caust-rutd | Caulobacter segnis (strain ATCC 21756 \/ DSM 7131 \/ JCM 7823 \/ NBRC 15250 \/ LMG 17158 \/ TK0059) (Mycoplana segnis). Aminohydrolase | Caulobacter segnis |
| crotz-rutd | Cronobacter turicensis (strain DSM 18703 \/ CCUG 55852 \/ LMG 23827 \/ z3032). Aminohydrolase | Cronobacter turicensis |
| ecoli-rutD |  Escherichia coli BchO gene protein rutD Pyrimidine utilization protein D ycdJ rarA |
Escherichia coli |
| ent38-a4w922 | Enterobacter sp. (strain 638) Alpha\/beta hydrolase fold | Enterobacter sp. |
| entcc-rutd | Enterobacter cloacae subsp. cloacae (strain ATCC 13047 \/ DSM 30054 \/ NBRC 13535 \/ NCTC 10005 \/ WDCM 00083 \/ NCDC 279-56). Aminohydrolase | Enterobacter cloacae subsp. cloacae |
| ents8-a7mfy0 | Enterobacter sakazakii (strain ATCC BAA-894) Putative uncharacterized protein | Enterobacter sakazakii |
| klep3-rutd | Klebsiella pneumoniae (strain 342). Putative aminoacrylate hydrolase RutD | Klebsiella pneumoniae |
| klep7-a6t799 | Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 \/ MG 78578) Putative hydrolase | Klebsiella pneumoniae subsp. pneumoniae |
| klevt-rutd | Klebsiella variicola (strain At-22). Putative aminoacrylate hydrolase RutD | Klebsiella variicola |
| metc4-rutd | Methylorubrum extorquens (strain CM4 \/ NCIMB 13688) (Methylobacterium extorquens) Putative aminoacrylate hydrolase RutD | Methylorubrum extorquens |
| metea-rutd | Methylorubrum extorquens (strain ATCC 14718 \/ DSM 1338 \/ JCM 2805 \/ NCIMB 9133 \/ AM1) (Methylobacterium extorquens). Putative aminoacrylate hydrolase RutD | Methylorubrum extorquens |
| meted-rutd | Methylorubrum extorquens (strain DSM 6343 \/ CIP 106787 \/ DM4) (Methylobacterium extorquens). Putative aminoacrylate hydrolase RutD | Methylorubrum extorquens |
| metep-rutd | Methylorubrum extorquens (strain PA1) (Methylobacterium extorquens). Putative aminoacrylate hydrolase RutD | Methylorubrum extorquens |
| metpb-rutd | Methylorubrum populi (strain ATCC BAA-705 \/ NCIMB 13946 \/ BJ001) (Methylobacterium populi). Putative aminoacrylate hydrolase RutD | Methylorubrum populi |
| metrj-rutd | Methylobacterium radiotolerans (strain ATCC 27329 \/ DSM 1819 \/ JCM 2831 \/ NBRC 15690 \/ NCIMB 10815 \/ 0-1). Putative aminoacrylate hydrolase RutD | Methylobacterium radiotolerans |
| panam-rutd | Pantoea ananatis (strain LMG 20103). Putative aminoacrylate hydrolase RutD | Pantoea ananatis |
| pse14-q48mq7 | Pseudomonas syringae pv. phaseolicola (strain 1448A \/ Race 6) hydrolase, alpha\/beta fold family | Pseudomonas syringae pv. phaseolicola |
| psesy-PSPTO1154 | Pseudomonas syringae (pv. tomato) hydrolase, alpha\/beta fold family | Pseudomonas syringae |
| pseu2-q4zxs0 | Pseudomonas syringae pv. syringae (strain B728a) alpha\/beta hydrolase fold | Pseudomonas syringae pv. syringae |
| pseu5-a4vqh7 | Pseudomonas stutzeri (strain A1501) Hydrolase, alpha\/beta fold family | Pseudomonas stutzeri |
| serp5-a8gct3 | Serratia proteamaculans (strain 568) Alpha\/beta hydrolase fold | Serratia proteamaculans |
| shifl-YCDJ | Shigella flexneri, Shigella sonnei, Shigella dysenteriae, Shigella boydii, putative acetyltransferase | Shigella flexneri |
| varps-rutd | Variovorax paradoxus (strain S110). Putative aminoacrylate hydrolase RutD | Variovorax paradoxus |
| yere8-a1jmx1 | Yersinia enterocolitica serotype O:8 \/ biotype 1B (strain 8081) putative hydrolase | Yersinia enterocolitica |
| Substrate | Chemical Nomenclature | Proteins |
|---|---|---|
| Aminoacrylate | (Z)-3-aminoprop-2-enoic acid | ecoli-rutD |
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 |
| Abstract : |
| PubMedSearch : Knapik_2012_Proteins_80_2359 |
| 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 |
| Abstract : |
| PubMedSearch : Kim_2010_J.Bacteriol_192_4089 |
| 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 |
| Abstract : |
| PubMedSearch : Loh_2006_Proc.Natl.Acad.Sci.U.S.A_103_5114 |
| PubMedID: 16540542 |
| Gene_locus related to this paper: ecoli-rutD |