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Protein

Nucleoid-associated protein YbaB

Gene

ybaB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection.UniRule annotation

GO - Molecular functioni

  • DNA binding Source: EcoCyc
Complete GO annotation...

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11100-MONOMER.
ECOL316407:JW0460-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoid-associated protein YbaBUniRule annotation
Gene namesi
Name:ybaBUniRule annotation
Ordered Locus Names:b0471, JW0460
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11100. ybaB.

Subcellular locationi

  • Cytoplasmnucleoid UniRule annotation

GO - Cellular componenti

  • bacterial nucleoid Source: UniProtKB-HAMAP
  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 109109Nucleoid-associated protein YbaBPRO_0000170391Add
BLAST

Proteomic databases

EPDiP0A8B5.
PaxDbiP0A8B5.
PRIDEiP0A8B5.

Interactioni

Subunit structurei

Homodimer.UniRule annotation2 Publications

Protein-protein interaction databases

BioGridi4261967. 28 interactions.
DIPiDIP-48059N.
IntActiP0A8B5. 12 interactions.
MINTiMINT-1219994.
STRINGi511145.b0471.

Structurei

Secondary structure

1
109
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi13 – 153Combined sources
Helixi18 – 2912Combined sources
Beta strandi32 – 376Combined sources
Helixi38 – 403Combined sources
Beta strandi42 – 476Combined sources
Beta strandi52 – 576Combined sources
Helixi59 – 613Combined sources
Helixi66 – 9732Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PUGX-ray2.20A/B/C/D1-109[»]
ProteinModelPortaliP0A8B5.
SMRiP0A8B5. Positions 11-104.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A8B5.

Family & Domainsi

Sequence similaritiesi

Belongs to the YbaB/EbfC family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0718. LUCA.
HOGENOMiHOG000293239.
InParanoidiP0A8B5.
KOiK09747.
OMAiEMGKLTG.
OrthoDBiEOG6DVJWP.
PhylomeDBiP0A8B5.

Family and domain databases

Gene3Di3.30.1310.10. 1 hit.
HAMAPiMF_00274. DNA_YbaB_EbfC.
InterProiIPR004401. YbaB/EbfC.
[Graphical view]
PfamiPF02575. YbaB_DNA_bd. 1 hit.
[Graphical view]
PIRSFiPIRSF004555. UCP004555. 1 hit.
SUPFAMiSSF82607. SSF82607. 1 hit.
TIGRFAMsiTIGR00103. DNA_YbaB_EbfC. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A8B5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFGKGGLGNL MKQAQQMQEK MQKMQEEIAQ LEVTGESGAG LVKVTINGAH
60 70 80 90 100
NCRRVEIDPS LLEDDKEMLE DLVAAAFNDA ARRIEETQKE KMASVSSGMQ

LPPGFKMPF
Length:109
Mass (Da):12,015
Last modified:June 7, 2005 - v1
Checksum:i5E05A853ABDCFABF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M38777 Genomic DNA. Translation: AAA23458.1.
X15761 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAC73573.1.
AP009048 Genomic DNA. Translation: BAE76250.1.
X04487 Genomic DNA. Translation: CAA28176.1.
PIRiA30371. QQECZG.
RefSeqiNP_415004.1. NC_000913.3.
WP_000467098.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73573; AAC73573; b0471.
BAE76250; BAE76250; BAE76250.
GeneIDi945104.
KEGGiecj:JW0460.
eco:b0471.
PATRICi32116099. VBIEscCol129921_0491.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M38777 Genomic DNA. Translation: AAA23458.1.
X15761 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAC73573.1.
AP009048 Genomic DNA. Translation: BAE76250.1.
X04487 Genomic DNA. Translation: CAA28176.1.
PIRiA30371. QQECZG.
RefSeqiNP_415004.1. NC_000913.3.
WP_000467098.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PUGX-ray2.20A/B/C/D1-109[»]
ProteinModelPortaliP0A8B5.
SMRiP0A8B5. Positions 11-104.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261967. 28 interactions.
DIPiDIP-48059N.
IntActiP0A8B5. 12 interactions.
MINTiMINT-1219994.
STRINGi511145.b0471.

Proteomic databases

EPDiP0A8B5.
PaxDbiP0A8B5.
PRIDEiP0A8B5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73573; AAC73573; b0471.
BAE76250; BAE76250; BAE76250.
GeneIDi945104.
KEGGiecj:JW0460.
eco:b0471.
PATRICi32116099. VBIEscCol129921_0491.

Organism-specific databases

EchoBASEiEB1092.
EcoGeneiEG11100. ybaB.

Phylogenomic databases

eggNOGiCOG0718. LUCA.
HOGENOMiHOG000293239.
InParanoidiP0A8B5.
KOiK09747.
OMAiEMGKLTG.
OrthoDBiEOG6DVJWP.
PhylomeDBiP0A8B5.

Enzyme and pathway databases

BioCyciEcoCyc:EG11100-MONOMER.
ECOL316407:JW0460-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0A8B5.
PROiP0A8B5.

Family and domain databases

Gene3Di3.30.1310.10. 1 hit.
HAMAPiMF_00274. DNA_YbaB_EbfC.
InterProiIPR004401. YbaB/EbfC.
[Graphical view]
PfamiPF02575. YbaB_DNA_bd. 1 hit.
[Graphical view]
PIRSFiPIRSF004555. UCP004555. 1 hit.
SUPFAMiSSF82607. SSF82607. 1 hit.
TIGRFAMsiTIGR00103. DNA_YbaB_EbfC. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The recR locus of Escherichia coli K-12: molecular cloning, DNA sequencing and identification of the gene product."
    Mahdi A.A., Lloyd R.G.
    Nucleic Acids Res. 17:6781-6794(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Sequence and expression of the Escherichia coli recR locus."
    Yeung T., Mullin D.A., Chen K.S., Craig E.A., Bardwell J.C.A., Walker J.R.
    J. Bacteriol. 172:6042-6047(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  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. "The adjacent dnaZ and dnaX genes of Escherichia coli are contained within one continuous open reading frame."
    Flower A.M., McHenry C.S.
    Nucleic Acids Res. 14:8091-8101(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-75.
  6. "DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family."
    Cooley A.E., Riley S.P., Kral K., Miller M.C., DeMoll E., Fried M.G., Stevenson B.
    BMC Microbiol. 9:137-137(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: DNA-BINDING, SUBUNIT.
  7. "Structure of E. coli Ybab."
    New York structural genomics research consortium (NYSGRC)
    Submitted (JAN-2005) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiYBAB_ECOLI
AccessioniPrimary (citable) accession number: P0A8B5
Secondary accession number(s): P09994, P17577, Q2MBV6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: March 16, 2016
This is version 93 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.