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Protein

Putative aminoacrylate hydrolase RutD

Gene

rutD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

May increase the rate of spontaneous hydrolysis of aminoacrylate to malonic semialdehyde. Required to remove a toxic intermediate produce in vivo, but not in vitro in the pyrimidine nitrogen degradation.1 Publication

Catalytic activityi

(Z)-3-aminoacrylate + H2O = malonate semialdehyde + NH3.

GO - Molecular functioni

GO - Biological processi

  • nitrogen utilization Source: UniProtKB
  • pyrimidine nucleobase catabolic process Source: EcoCyc
  • uracil catabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Enzyme and pathway databases

BioCyciEcoCyc:G6520-MONOMER.
ECOL316407:JW0994-MONOMER.

Protein family/group databases

ESTHERiecoli-rutD. RutD.

Names & Taxonomyi

Protein namesi
Recommended name:
Putative aminoacrylate hydrolase RutD (EC:3.5.1.-)
Alternative name(s):
Aminohydrolase
Gene namesi
Name:rutD
Synonyms:ycdJ
Ordered Locus Names:b1009, JW0994
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13856. rutD.

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene form less than the normal amount of malonic semialdehyde because a portion of the 3-carbon intermediate is diverted out of the Rut pathway.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 266266Putative aminoacrylate hydrolase RutDPRO_0000168800Add
BLAST

Proteomic databases

PaxDbiP75895.

Expressioni

Inductioni

Up-regulated by the nitrogen regulatory protein C (NtrC also called GlnG) and repressed by RutR.2 Publications

Interactioni

Protein-protein interaction databases

BioGridi4262210. 24 interactions.
STRINGi511145.b1009.

Structurei

3D structure databases

ProteinModelPortaliP75895.
SMRiP75895. Positions 1-266.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG41074FZ. Bacteria.
COG0596. LUCA.
HOGENOMiHOG000028072.
InParanoidiP75895.
KOiK09023.
OMAiHREAACK.
OrthoDBiEOG632D20.
PhylomeDBiP75895.

Family and domain databases

Gene3Di3.40.50.1820. 1 hit.
HAMAPiMF_00832. RutD.
InterProiIPR029058. AB_hydrolase.
IPR000073. AB_hydrolase_1.
IPR019913. Pyrimidine_utilisation_RutD.
[Graphical view]
PfamiPF00561. Abhydrolase_1. 1 hit.
[Graphical view]
PRINTSiPR00111. ABHYDROLASE.
SUPFAMiSSF53474. SSF53474. 1 hit.
TIGRFAMsiTIGR03611. RutD. 1 hit.

Sequencei

Sequence statusi: Complete.

P75895-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLSLSPPPY ADAPVVVLIS GLGGSGSYWL PQLAVLEQEY QVVCYDQRGT
60 70 80 90 100
GNNPDTLAED YSIAQMAAEL HQALVAAGIE HYAVVGHALG ALVGMQLALD
110 120 130 140 150
YPASVTVLIS VNGWLRINAH TRRCFQVRER LLYSGGAQAW VEAQPLFLYP
160 170 180 190 200
ADWMAARAPR LEAEDALALA HFQGKNNLLR RLNALKRADF SHHADRIRCP
210 220 230 240 250
VQIICASDDL LVPTACSSEL HAALPDSQKM VMPYGGHACN VTDPETFNAL
260
LLNGLASLLH HREAAL
Length:266
Mass (Da):28,898
Last modified:February 1, 1997 - v1
Checksum:i378E13994425E9E2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74094.1.
AP009048 Genomic DNA. Translation: BAA35776.1.
PIRiG64842.
RefSeqiNP_415529.1. NC_000913.3.
WP_000777653.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74094; AAC74094; b1009.
BAA35776; BAA35776; BAA35776.
GeneIDi946586.
KEGGiecj:JW0994.
eco:b1009.
PATRICi32117247. VBIEscCol129921_1047.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74094.1.
AP009048 Genomic DNA. Translation: BAA35776.1.
PIRiG64842.
RefSeqiNP_415529.1. NC_000913.3.
WP_000777653.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP75895.
SMRiP75895. Positions 1-266.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262210. 24 interactions.
STRINGi511145.b1009.

Protein family/group databases

ESTHERiecoli-rutD. RutD.

Proteomic databases

PaxDbiP75895.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74094; AAC74094; b1009.
BAA35776; BAA35776; BAA35776.
GeneIDi946586.
KEGGiecj:JW0994.
eco:b1009.
PATRICi32117247. VBIEscCol129921_1047.

Organism-specific databases

EchoBASEiEB3616.
EcoGeneiEG13856. rutD.

Phylogenomic databases

eggNOGiENOG41074FZ. Bacteria.
COG0596. LUCA.
HOGENOMiHOG000028072.
InParanoidiP75895.
KOiK09023.
OMAiHREAACK.
OrthoDBiEOG632D20.
PhylomeDBiP75895.

Enzyme and pathway databases

BioCyciEcoCyc:G6520-MONOMER.
ECOL316407:JW0994-MONOMER.

Miscellaneous databases

PROiP75895.

Family and domain databases

Gene3Di3.40.50.1820. 1 hit.
HAMAPiMF_00832. RutD.
InterProiIPR029058. AB_hydrolase.
IPR000073. AB_hydrolase_1.
IPR019913. Pyrimidine_utilisation_RutD.
[Graphical view]
PfamiPF00561. Abhydrolase_1. 1 hit.
[Graphical view]
PRINTSiPR00111. ABHYDROLASE.
SUPFAMiSSF53474. SSF53474. 1 hit.
TIGRFAMsiTIGR03611. RutD. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation."
    Zimmer D.P., Soupene E., Lee H.L., Wendisch V.F., Khodursky A.B., Peter B.J., Bender R.A., Kustu S.
    Proc. Natl. Acad. Sci. U.S.A. 97:14674-14679(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  5. Cited for: FUNCTION IN PYRIMIDINE CATABOLISM AND NOMENCLATURE.
    Strain: K12 / MG1655 / ATCC 47076.
  6. "RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines."
    Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A.
    Mol. Microbiol. 66:744-757(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  7. "The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems."
    Kim K.S., Pelton J.G., Inwood W.B., Andersen U., Kustu S., Wemmer D.E.
    J. Bacteriol. 192:4089-4102(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.

Entry informationi

Entry nameiRUTD_ECOLI
AccessioniPrimary (citable) accession number: P75895
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 16, 2002
Last sequence update: February 1, 1997
Last modified: May 11, 2016
This is version 111 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The Rut pathway degrades exogenous pyrimidines as the sole nitrogen source at room temperature but not at 37 degrees Celsius, a restriction that is apparently a consequence of an inadequate ability to remove toxic malonic semialdehyde at the higher temperature (RutE/YdfG function).

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.