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Protein

PKHD-type hydroxylase YbiX

Gene

ybiX

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

Functioni

Cofactori

Protein has several cofactor binding sites:
  • Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity
  • L-ascorbateBy similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi96 – 961IronBy similarity
Metal bindingi98 – 981IronBy similarity
Metal bindingi158 – 1581IronBy similarity
Binding sitei168 – 16812-oxoglutarateSequence analysis

GO - Molecular functioni

GO - Biological processi

  • cellular iron ion homeostasis Source: EcoCyc
  • cellular response to DNA damage stimulus Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Ligandi

Iron, Metal-binding, Vitamin C

Enzyme and pathway databases

BioCyciEcoCyc:G6413-MONOMER.
ECOL316407:JW5105-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
PKHD-type hydroxylase YbiX (EC:1.14.11.-)
Gene namesi
Name:ybiX
Ordered Locus Names:b0804, JW5105
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13316. ybiX.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 225225PKHD-type hydroxylase YbiXPRO_0000206676Add
BLAST

Proteomic databases

PaxDbiP75779.
PRIDEiP75779.

Interactioni

Protein-protein interaction databases

BioGridi4259955. 2 interactions.
STRINGi511145.b0804.

Structurei

3D structure databases

ProteinModelPortaliP75779.
SMRiP75779. Positions 1-225.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini78 – 177100Fe2OG dioxygenaseAdd
BLAST

Sequence similaritiesi

Contains 1 Fe2OG dioxygenase domain.Curated

Phylogenomic databases

eggNOGiENOG4107E2E. Bacteria.
COG3128. LUCA.
HOGENOMiHOG000236239.
InParanoidiP75779.
KOiK07336.
OMAiPPLFNCY.
OrthoDBiEOG6Z0Q8H.
PhylomeDBiP75779.

Family and domain databases

HAMAPiMF_00657. Hydroxyl_YbiX.
InterProiIPR005123. Oxoglu/Fe-dep_dioxygenase.
IPR023550. PKHD_hydroxylase.
IPR006620. Pro_4_hyd_alph.
[Graphical view]
PfamiPF13640. 2OG-FeII_Oxy_3. 1 hit.
[Graphical view]
SMARTiSM00702. P4Hc. 1 hit.
[Graphical view]
PROSITEiPS51471. FE2OG_OXY. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P75779-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMYHIPGVLS PQDVARFREQ LEQAEWVDGR VTTGAQGAQV KNNQQVDTRS
60 70 80 90 100
TLYAALQNEV LNAVNQHALF FAAALPRTLS TPLFNRYQNN ETYGFHVDGA
110 120 130 140 150
VRSHPQNGWM RTDLSATLFL SDPQSYDGGE LVVNDTFGQH RVKLPAGDLV
160 170 180 190 200
LYPSSSLHCV TPVTRGVRVA SFMWIQSMIR DDKKRAMLFE LDNNIQSLKS
210 220
RYGESEEILS LLNLYHNLLR EWSEI
Length:225
Mass (Da):25,529
Last modified:April 27, 2001 - v2
Checksum:i001CB789CC498421
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73891.2.
AP009048 Genomic DNA. Translation: BAA35470.2.
PIRiD64817.
RefSeqiNP_415325.4. NC_000913.3.
WP_000990177.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73891; AAC73891; b0804.
BAA35470; BAA35470; BAA35470.
GeneIDi947502.
KEGGiecj:JW5105.
eco:b0804.
PATRICi32116811. VBIEscCol129921_0831.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73891.2.
AP009048 Genomic DNA. Translation: BAA35470.2.
PIRiD64817.
RefSeqiNP_415325.4. NC_000913.3.
WP_000990177.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP75779.
SMRiP75779. Positions 1-225.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259955. 2 interactions.
STRINGi511145.b0804.

Proteomic databases

PaxDbiP75779.
PRIDEiP75779.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73891; AAC73891; b0804.
BAA35470; BAA35470; BAA35470.
GeneIDi947502.
KEGGiecj:JW5105.
eco:b0804.
PATRICi32116811. VBIEscCol129921_0831.

Organism-specific databases

EchoBASEiEB3100.
EcoGeneiEG13316. ybiX.

Phylogenomic databases

eggNOGiENOG4107E2E. Bacteria.
COG3128. LUCA.
HOGENOMiHOG000236239.
InParanoidiP75779.
KOiK07336.
OMAiPPLFNCY.
OrthoDBiEOG6Z0Q8H.
PhylomeDBiP75779.

Enzyme and pathway databases

BioCyciEcoCyc:G6413-MONOMER.
ECOL316407:JW5105-MONOMER.

Miscellaneous databases

PROiP75779.

Family and domain databases

HAMAPiMF_00657. Hydroxyl_YbiX.
InterProiIPR005123. Oxoglu/Fe-dep_dioxygenase.
IPR023550. PKHD_hydroxylase.
IPR006620. Pro_4_hyd_alph.
[Graphical view]
PfamiPF13640. 2OG-FeII_Oxy_3. 1 hit.
[Graphical view]
SMARTiSM00702. P4Hc. 1 hit.
[Graphical view]
PROSITEiPS51471. FE2OG_OXY. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  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.

Entry informationi

Entry nameiYBIX_ECOLI
AccessioniPrimary (citable) accession number: P75779
Secondary accession number(s): Q9R7S1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: April 27, 2001
Last modified: January 20, 2016
This is version 118 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.