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Protein

Protein YdcF

Gene

ydcF

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Binds S-adenosyl-L-methionine (AdoMet).

Enzyme and pathway databases

BioCyciEcoCyc:EG12110-MONOMER.
ECOL316407:JW1411-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein YdcF
Gene namesi
Name:ydcF
Ordered Locus Names:b1414, JW1411
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12110. ydcF.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 266266Protein YdcFPRO_0000168929Add
BLAST

Proteomic databases

EPDiP34209.
PaxDbiP34209.
PRIDEiP34209.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi4261553. 9 interactions.
DIPiDIP-11642N.
IntActiP34209. 2 interactions.
STRINGi511145.b1414.

Structurei

Secondary structure

1
266
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi11 – 2515Combined sources
Turni29 – 324Combined sources
Beta strandi38 – 447Combined sources
Helixi48 – 6114Combined sources
Beta strandi65 – 684Combined sources
Helixi75 – 839Combined sources
Helixi88 – 903Combined sources
Helixi98 – 10811Combined sources
Helixi114 – 1163Combined sources
Beta strandi117 – 1204Combined sources
Helixi126 – 13813Combined sources
Beta strandi147 – 1504Combined sources
Turni153 – 1553Combined sources
Helixi156 – 16712Combined sources
Beta strandi175 – 1784Combined sources
Beta strandi186 – 1894Combined sources
Beta strandi192 – 1976Combined sources
Helixi205 – 21915Combined sources
Beta strandi225 – 2273Combined sources
Turni228 – 2314Combined sources
Helixi241 – 25111Combined sources
Helixi254 – 2629Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3CA8X-ray1.80A/B1-266[»]
ProteinModelPortaliP34209.
SMRiP34209. Positions 5-265.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP34209.

Family & Domainsi

Sequence similaritiesi

To S.coelicolor SCO4629.Curated

Phylogenomic databases

eggNOGiENOG4107DB1. Bacteria.
COG1434. LUCA.
HOGENOMiHOG000120552.
InParanoidiP34209.
OMAiILCQDAT.
OrthoDBiEOG6WDSF7.
PhylomeDBiP34209.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
InterProiIPR003848. DUF218.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PfamiPF02698. DUF218. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P34209-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNITPFPTLS PATIDAINVI GQWLAQDDFS GEVPYQADCV ILAGNAVMPT
60 70 80 90 100
IDAACKIARD QQIPLLISGG IGHSTTFLYS AIAQHPHYNT IRTTGRAEAT
110 120 130 140 150
ILADIAHQFW HIPHEKIWIE DQSTNCGENA RFSIALLNQA VERVHTAIVV
160 170 180 190 200
QDPTMQRRTM ATFRRMTGDN PDAPRWLSYP GFVPQLGNNA DSVIFINQLQ
210 220 230 240 250
GLWPVERYLS LLTGELPRLR DDSDGYGPRG RDFIVHVDFP AEVIHAWQTL
260
KHDAVLIEAM ESRSLR
Length:266
Mass (Da):29,706
Last modified:November 1, 1997 - v3
Checksum:iDA59CFB3D34728A5
GO

Sequence cautioni

The sequence AAA24246.1 differs from that shown. Reason: Frameshift at positions 8 and 23. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti97 – 971A → R in AAA24246 (Ref. 1) Curated
Sequence conflicti217 – 26650PRLRD…SRSLR → RVYAMIAMATVPAGEILSFT LIFRQKSSMHGKR (Ref. 1) CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L09068 Genomic DNA. Translation: AAA24246.1. Frameshift.
U00096 Genomic DNA. Translation: AAC74496.1.
AP009048 Genomic DNA. Translation: BAA15030.1.
PIRiA64893.
RefSeqiNP_415932.1. NC_000913.3.
WP_001027942.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74496; AAC74496; b1414.
BAA15030; BAA15030; BAA15030.
GeneIDi946215.
KEGGiecj:JW1411.
eco:b1414.
PATRICi32118114. VBIEscCol129921_1477.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L09068 Genomic DNA. Translation: AAA24246.1. Frameshift.
U00096 Genomic DNA. Translation: AAC74496.1.
AP009048 Genomic DNA. Translation: BAA15030.1.
PIRiA64893.
RefSeqiNP_415932.1. NC_000913.3.
WP_001027942.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3CA8X-ray1.80A/B1-266[»]
ProteinModelPortaliP34209.
SMRiP34209. Positions 5-265.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261553. 9 interactions.
DIPiDIP-11642N.
IntActiP34209. 2 interactions.
STRINGi511145.b1414.

Proteomic databases

EPDiP34209.
PaxDbiP34209.
PRIDEiP34209.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74496; AAC74496; b1414.
BAA15030; BAA15030; BAA15030.
GeneIDi946215.
KEGGiecj:JW1411.
eco:b1414.
PATRICi32118114. VBIEscCol129921_1477.

Organism-specific databases

EchoBASEiEB2033.
EcoGeneiEG12110. ydcF.

Phylogenomic databases

eggNOGiENOG4107DB1. Bacteria.
COG1434. LUCA.
HOGENOMiHOG000120552.
InParanoidiP34209.
OMAiILCQDAT.
OrthoDBiEOG6WDSF7.
PhylomeDBiP34209.

Enzyme and pathway databases

BioCyciEcoCyc:EG12110-MONOMER.
ECOL316407:JW1411-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP34209.
PROiP34209.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
InterProiIPR003848. DUF218.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PfamiPF02698. DUF218. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A third gene with high homology to gap gene in the Escherichia coli chromosome."
    Hidalgo E., Limon A., Aguilar J.
    Submitted (NOV-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "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.
  5. "Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography."
    Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B.
    Electrophoresis 20:2181-2195(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: B / BL21.
  6. "The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta-fold characteristic of nucleotide-utilizing enzymes."
    Chao K.L., Lim K., Lehmann C., Doseeva V., Howard A.J., Schwarz F.P., Herzberg O.
    Proteins 72:506-509(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), SUBUNIT, S-ADENOSYL-L-METHIONINE BINDING.

Entry informationi

Entry nameiYDCF_ECOLI
AccessioniPrimary (citable) accession number: P34209
Secondary accession number(s): P77578
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: November 1, 1997
Last modified: March 16, 2016
This is version 108 of the entry and version 3 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

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.