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Protein

L-arabinose-binding periplasmic protein

Gene

araF

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

Functioni

Involved in the high-affinity L-arabinose membrane transport system. Binds with high affinity to arabinose, but can also bind D-galactose (approximately 2-fold reduction) and D-fucose (approximately 40-fold reduction).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei87 – 871The binding site for the sugar molecule has not yet been established, but C-87 may be involved

GO - Molecular functioni

  • monosaccharide binding Source: EcoCyc
  • monosaccharide-transporting ATPase activity Source: EcoCyc

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Sugar transport, Transport

Enzyme and pathway databases

BioCyciEcoCyc:ARAF-MONOMER.
ECOL316407:JW1889-MONOMER.
MetaCyc:ARAF-MONOMER.
RETL1328306-WGS:GSTH-3770-MONOMER.

Protein family/group databases

TCDBi3.A.1.2.2. the atp-binding cassette (abc) superfamily.

Names & Taxonomyi

Protein namesi
Recommended name:
L-arabinose-binding periplasmic protein
Short name:
ABP
Gene namesi
Name:araF
Ordered Locus Names:b1901, JW1889
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10057. araF.

Subcellular locationi

GO - Cellular componenti

  • outer membrane-bounded periplasmic space Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi277 – 2771P → G: Improves binding to galactose.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 23232 PublicationsAdd
BLAST
Chaini24 – 329306L-arabinose-binding periplasmic proteinPRO_0000031720Add
BLAST

Proteomic databases

EPDiP02924.
PaxDbiP02924.
PRIDEiP02924.

Interactioni

Protein-protein interaction databases

BioGridi4261850. 13 interactions.
IntActiP02924. 5 interactions.
STRINGi511145.b1901.

Structurei

Secondary structure

1
329
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi26 – 338Combined sources
Helixi38 – 5417Combined sources
Beta strandi56 – 627Combined sources
Helixi66 – 7813Combined sources
Beta strandi83 – 875Combined sources
Helixi91 – 933Combined sources
Helixi94 – 10310Combined sources
Beta strandi107 – 1137Combined sources
Beta strandi128 – 1314Combined sources
Helixi133 – 15119Combined sources
Helixi155 – 1573Combined sources
Beta strandi158 – 1647Combined sources
Helixi169 – 18517Combined sources
Helixi189 – 1913Combined sources
Beta strandi192 – 1965Combined sources
Beta strandi198 – 2014Combined sources
Helixi202 – 21312Combined sources
Beta strandi220 – 2256Combined sources
Helixi229 – 24113Combined sources
Helixi246 – 2483Combined sources
Beta strandi249 – 2568Combined sources
Helixi257 – 2593Combined sources
Helixi260 – 2634Combined sources
Beta strandi265 – 2673Combined sources
Beta strandi270 – 2767Combined sources
Helixi279 – 29618Combined sources
Beta strandi302 – 3065Combined sources
Beta strandi310 – 3134Combined sources
Turni314 – 3163Combined sources
Helixi317 – 3237Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ABEX-ray1.70A24-329[»]
1ABFX-ray1.90A24-329[»]
1APBX-ray1.76A24-329[»]
1BAPX-ray1.75A24-329[»]
2WRZX-ray2.20A/B24-329[»]
5ABPX-ray1.80A24-329[»]
6ABPX-ray1.67A24-329[»]
7ABPX-ray1.67A24-329[»]
8ABPX-ray1.49A24-329[»]
9ABPX-ray1.97A24-329[»]
ProteinModelPortaliP02924.
SMRiP02924. Positions 25-329.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP02924.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105DMK. Bacteria.
COG1879. LUCA.
HOGENOMiHOG000220638.
KOiK10537.
OMAiNDIPGAL.
OrthoDBiEOG60PH89.
PhylomeDBiP02924.

Family and domain databases

InterProiIPR026266. AraF.
IPR001761. Peripla_BP/Lac1_sug-bd_dom.
IPR028082. Peripla_BP_I.
[Graphical view]
PfamiPF00532. Peripla_BP_1. 1 hit.
[Graphical view]
PIRSFiPIRSF002816. AraF. 1 hit.
SUPFAMiSSF53822. SSF53822. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P02924-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHKFTKALAA IGLAAVMSQS AMAENLKLGF LVKQPEEPWF QTEWKFADKA
60 70 80 90 100
GKDLGFEVIK IAVPDGEKTL NAIDSLAASG AKGFVICTPD PKLGSAIVAK
110 120 130 140 150
ARGYDMKVIA VDDQFVNAKG KPMDTVPLVM MAATKIGERQ GQELYKEMQK
160 170 180 190 200
RGWDVKESAV MAITANELDT ARRRTTGSMD ALKAAGFPEK QIYQVPTKSN
210 220 230 240 250
DIPGAFDAAN SMLVQHPEVK HWLIVGMNDS TVLGGVRATE GQGFKAADII
260 270 280 290 300
GIGINGVDAV SELSKAQATG FYGSLLPSPD VHGYKSSEML YNWVAKDVEP
310 320
PKFTEVTDVV LITRDNFKEE LEKKGLGGK
Length:329
Mass (Da):35,541
Last modified:November 1, 1997 - v2
Checksum:iA79D167EA92B0C64
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti194 – 1941Q → E in CAA29476 (PubMed:2445996).Curated
Sequence conflicti281 – 2811V → L in CAA29476 (PubMed:2445996).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06091 Genomic DNA. Translation: CAA29476.1.
U00096 Genomic DNA. Translation: AAC74971.1.
AP009048 Genomic DNA. Translation: BAA15721.1.
K00420 Genomic DNA. Translation: AAA23472.1.
PIRiE64953. JGECA.
RefSeqiNP_416414.1. NC_000913.3.
WP_000548675.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74971; AAC74971; b1901.
BAA15721; BAA15721; BAA15721.
GeneIDi946409.
KEGGiecj:JW1889.
eco:b1901.
PATRICi32119127. VBIEscCol129921_1981.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06091 Genomic DNA. Translation: CAA29476.1.
U00096 Genomic DNA. Translation: AAC74971.1.
AP009048 Genomic DNA. Translation: BAA15721.1.
K00420 Genomic DNA. Translation: AAA23472.1.
PIRiE64953. JGECA.
RefSeqiNP_416414.1. NC_000913.3.
WP_000548675.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ABEX-ray1.70A24-329[»]
1ABFX-ray1.90A24-329[»]
1APBX-ray1.76A24-329[»]
1BAPX-ray1.75A24-329[»]
2WRZX-ray2.20A/B24-329[»]
5ABPX-ray1.80A24-329[»]
6ABPX-ray1.67A24-329[»]
7ABPX-ray1.67A24-329[»]
8ABPX-ray1.49A24-329[»]
9ABPX-ray1.97A24-329[»]
ProteinModelPortaliP02924.
SMRiP02924. Positions 25-329.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261850. 13 interactions.
IntActiP02924. 5 interactions.
STRINGi511145.b1901.

Protein family/group databases

TCDBi3.A.1.2.2. the atp-binding cassette (abc) superfamily.

Proteomic databases

EPDiP02924.
PaxDbiP02924.
PRIDEiP02924.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74971; AAC74971; b1901.
BAA15721; BAA15721; BAA15721.
GeneIDi946409.
KEGGiecj:JW1889.
eco:b1901.
PATRICi32119127. VBIEscCol129921_1981.

Organism-specific databases

EchoBASEiEB0055.
EcoGeneiEG10057. araF.

Phylogenomic databases

eggNOGiENOG4105DMK. Bacteria.
COG1879. LUCA.
HOGENOMiHOG000220638.
KOiK10537.
OMAiNDIPGAL.
OrthoDBiEOG60PH89.
PhylomeDBiP02924.

Enzyme and pathway databases

BioCyciEcoCyc:ARAF-MONOMER.
ECOL316407:JW1889-MONOMER.
MetaCyc:ARAF-MONOMER.
RETL1328306-WGS:GSTH-3770-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP02924.
PROiP02924.

Family and domain databases

InterProiIPR026266. AraF.
IPR001761. Peripla_BP/Lac1_sug-bd_dom.
IPR028082. Peripla_BP_I.
[Graphical view]
PfamiPF00532. Peripla_BP_1. 1 hit.
[Graphical view]
PIRSFiPIRSF002816. AraF. 1 hit.
SUPFAMiSSF53822. SSF53822. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "High-affinity L-arabinose transport operon. Nucleotide sequence and analysis of gene products."
    Scripture J.B., Voelker C., Miller S., O'Donnell R.T., Polgar L., Rade J., Horazdovsky B.F., Hogg R.W.
    J. Mol. Biol. 197:37-46(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: BEK 180.
  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. "The nucleotide sequences defining the signal peptides of the galactose-binding protein and the arabinose-binding protein."
    Scripture J.B., Hogg R.W.
    J. Biol. Chem. 258:10853-10855(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-37.
  6. "Amino acid sequence of the L-arabinose-binding protein from Escherichia coli B/r."
    Hogg R.W., Hermodson M.A.
    J. Biol. Chem. 252:5135-5141(1977) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 24-329.
    Strain: B/R.
  7. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
    Link A.J., Robison K., Church G.M.
    Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 24-35.
    Strain: K12 / EMG2.
  8. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  9. "L-arabinose-binding protein-sugar complex at 2.4-A resolution. Stereochemistry and evidence for a structural change."
    Newcomer M.E., Gilliland G.L., Quiocho F.A.
    J. Biol. Chem. 256:13213-13217(1981) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 24-329.
  10. "The 2.8-A resolution structure of the L-arabinose-binding protein from Escherichia coli. Polypeptide chain folding, domain similarity, and probable location of sugar-binding site."
    Quiocho F.A., Gilliland G.L., Phillips G.N. Jr.
    J. Biol. Chem. 252:5142-5149(1977) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 24-329.
  11. "A Pro to Gly mutation in the hinge of the arabinose-binding protein enhances binding and alters specificity. Sugar-binding and crystallographic studies."
    Vermersch P.S., Tesmer J.J.G., Lemon D.D., Quiocho F.A.
    J. Biol. Chem. 265:16592-16603(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 24-329 OF MUTANT GLY-277.

Entry informationi

Entry nameiARAF_ECOLI
AccessioniPrimary (citable) accession number: P02924
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: November 1, 1997
Last modified: March 16, 2016
This is version 143 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

3D-structure, Complete proteome, Direct protein sequencing, 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.