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Protein

Putative reactive intermediate deaminase TdcF

Gene

tdcF

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

Functioni

May be a post-translational regulator that controls the metabolic fate of L-threonine or the potentially toxic intermediate 2-ketobutyrate.

Pathwayi: L-threonine degradation via propanoate pathway

This protein is involved in the pathway L-threonine degradation via propanoate pathway, which is part of Amino-acid degradation.
View all proteins of this organism that are known to be involved in the pathway L-threonine degradation via propanoate pathway and in Amino-acid degradation.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei120 – 1201Substrate

GO - Molecular functioni

  • hydrolase activity Source: UniProtKB-KW
  • identical protein binding Source: EcoCyc

GO - Biological processi

  • L-threonine catabolic process to propionate Source: UniProtKB-UniPathway
  • threonine metabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciEcoCyc:G7626-MONOMER.
ECOL316407:JW5521-MONOMER.
UniPathwayiUPA00052.

Names & Taxonomyi

Protein namesi
Recommended name:
Putative reactive intermediate deaminase TdcF (EC:3.5.4.-)
Gene namesi
Name:tdcF
Synonyms:yhaR
Ordered Locus Names:b3113, JW5521
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12757. tdcF.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 129129Putative reactive intermediate deaminase TdcFPRO_0000170316Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei58 – 581N6-(pyridoxal phosphate)lysineBy similarity

Proteomic databases

EPDiP0AGL2.
PaxDbiP0AGL2.

Interactioni

Subunit structurei

Homotrimer.1 Publication

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

DIPiDIP-48213N.
STRINGi511145.b3113.

Structurei

Secondary structure

1
129
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 53Combined sources
Beta strandi8 – 103Combined sources
Beta strandi14 – 163Combined sources
Beta strandi19 – 224Combined sources
Beta strandi24 – 296Combined sources
Turni37 – 393Combined sources
Helixi46 – 6318Combined sources
Helixi68 – 703Combined sources
Beta strandi71 – 799Combined sources
Helixi81 – 833Combined sources
Helixi84 – 9714Combined sources
Beta strandi104 – 1096Combined sources
Helixi114 – 1163Combined sources
Beta strandi118 – 1269Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2UYJX-ray2.35A/B/C1-129[»]
2UYKX-ray1.60A/B/C1-129[»]
2UYNX-ray1.60A/B/C1-129[»]
2UYPX-ray2.44A/B/C1-129[»]
ProteinModelPortaliP0AGL2.
SMRiP0AGL2. Positions 2-128.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AGL2.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni105 – 1073Substrate binding

Sequence similaritiesi

Belongs to the RutC family.Curated

Phylogenomic databases

eggNOGiENOG4105KME. Bacteria.
COG0251. LUCA.
HOGENOMiHOG000267215.
InParanoidiP0AGL2.
KOiK09022.
OMAiGMVFTSG.
OrthoDBiEOG6QVRPF.
PhylomeDBiP0AGL2.

Family and domain databases

Gene3Di3.30.1330.40. 1 hit.
InterProiIPR013813. Endoribo_LPSP/chorism_mut-like.
IPR006056. RidA.
IPR019897. RidA_CS.
IPR006175. YjgF/YER057c/UK114.
[Graphical view]
PANTHERiPTHR11803. PTHR11803. 1 hit.
PfamiPF01042. Ribonuc_L-PSP. 1 hit.
[Graphical view]
SUPFAMiSSF55298. SSF55298. 1 hit.
TIGRFAMsiTIGR00004. TIGR00004. 1 hit.
PROSITEiPS01094. UPF0076. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0AGL2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKIIETQRA PGAIGPYVQG VDLGSMVFTS GQIPVCPQTG EIPADVQDQA
60 70 80 90 100
RLSLENVKAI VVAAGLSVGD IIKMTVFITD LNDFATINEV YKQFFDEHQA
110 120
TYPTRSCVQV ARLPKDVKLE IEAIAVRSA
Length:129
Mass (Da):14,007
Last modified:December 20, 2005 - v1
Checksum:iD5159CB729CDDB7B
GO

Sequence cautioni

The sequence AAA57917.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18997 Genomic DNA. Translation: AAA57917.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76148.2.
AP009048 Genomic DNA. Translation: BAE77161.1.
PIRiF65100.
RefSeqiNP_417583.4. NC_000913.3.
WP_000719990.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76148; AAC76148; b3113.
BAE77161; BAE77161; BAE77161.
GeneIDi947624.
KEGGiecj:JW5521.
eco:b3113.
PATRICi32121642. VBIEscCol129921_3207.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18997 Genomic DNA. Translation: AAA57917.1. Different initiation.
U00096 Genomic DNA. Translation: AAC76148.2.
AP009048 Genomic DNA. Translation: BAE77161.1.
PIRiF65100.
RefSeqiNP_417583.4. NC_000913.3.
WP_000719990.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2UYJX-ray2.35A/B/C1-129[»]
2UYKX-ray1.60A/B/C1-129[»]
2UYNX-ray1.60A/B/C1-129[»]
2UYPX-ray2.44A/B/C1-129[»]
ProteinModelPortaliP0AGL2.
SMRiP0AGL2. Positions 2-128.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48213N.
STRINGi511145.b3113.

Proteomic databases

EPDiP0AGL2.
PaxDbiP0AGL2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76148; AAC76148; b3113.
BAE77161; BAE77161; BAE77161.
GeneIDi947624.
KEGGiecj:JW5521.
eco:b3113.
PATRICi32121642. VBIEscCol129921_3207.

Organism-specific databases

EchoBASEiEB2611.
EcoGeneiEG12757. tdcF.

Phylogenomic databases

eggNOGiENOG4105KME. Bacteria.
COG0251. LUCA.
HOGENOMiHOG000267215.
InParanoidiP0AGL2.
KOiK09022.
OMAiGMVFTSG.
OrthoDBiEOG6QVRPF.
PhylomeDBiP0AGL2.

Enzyme and pathway databases

UniPathwayiUPA00052.
BioCyciEcoCyc:G7626-MONOMER.
ECOL316407:JW5521-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AGL2.
PROiP0AGL2.

Family and domain databases

Gene3Di3.30.1330.40. 1 hit.
InterProiIPR013813. Endoribo_LPSP/chorism_mut-like.
IPR006056. RidA.
IPR019897. RidA_CS.
IPR006175. YjgF/YER057c/UK114.
[Graphical view]
PANTHERiPTHR11803. PTHR11803. 1 hit.
PfamiPF01042. Ribonuc_L-PSP. 1 hit.
[Graphical view]
SUPFAMiSSF55298. SSF55298. 1 hit.
TIGRFAMsiTIGR00004. TIGR00004. 1 hit.
PROSITEiPS01094. UPF0076. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "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.
  3. "Novel keto acid formate-lyase and propionate kinase enzymes are components of an anaerobic pathway in Escherichia coli that degrades L-threonine to propionate."
    Hesslinger C., Fairhurst S.A., Sawers G.
    Mol. Microbiol. 27:477-492(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE NAME.
  4. "The crystal structure of Escherichia coli TdcF, a member of the highly conserved YjgF/YER057c/UK114 family."
    Burman J.D., Stevenson C.E., Sawers R.G., Lawson D.M.
    BMC Struct. Biol. 7:30-30(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, SUBUNIT.

Entry informationi

Entry nameiTDCF_ECOLI
AccessioniPrimary (citable) accession number: P0AGL2
Secondary accession number(s): P42631, Q2M995
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: March 16, 2016
This is version 86 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.