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Protein

Putative HMP/thiamine-binding protein YkoF

Gene

ykoF

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Part of the ABC transporter complex YkoCDEF that could transport hydroxymethylpyrimidine (HMP) and/or thiamine. Could also transport other HMP-containing products. Binds thiamine via its HMP moiety.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei17 – 171Thiamine; via amide nitrogen and carbonyl oxygen1 Publication
Binding sitei49 – 491Thiamine1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transport

Enzyme and pathway databases

BioCyciBSUB:BSU13240-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Putative HMP/thiamine-binding protein YkoF
Gene namesi
Name:ykoF
Ordered Locus Names:BSU13240
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 200200Putative HMP/thiamine-binding protein YkoFPRO_0000288884Add
BLAST

Proteomic databases

PaxDbiO34911.

Interactioni

Subunit structurei

Homodimer in vitro. In vivo, may be a part of an ABC transporter complex which is composed of two ATP-binding proteins (YkoD), two transmembrane proteins (YkoC and YkoE) and a solute-binding protein (YkoF) (Probable).2 Publications

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100007336.

Structurei

Secondary structure

1
200
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi11 – 199Combined sources
Helixi24 – 3411Combined sources
Beta strandi40 – 445Combined sources
Beta strandi49 – 535Combined sources
Helixi55 – 7016Combined sources
Beta strandi76 – 849Combined sources
Turni103 – 1108Combined sources
Beta strandi117 – 1237Combined sources
Helixi129 – 14214Combined sources
Beta strandi146 – 1505Combined sources
Beta strandi153 – 1564Combined sources
Helixi160 – 17718Combined sources
Beta strandi179 – 19012Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1S7HX-ray2.20A/B/C/D1-200[»]
1S99X-ray1.65A/B1-200[»]
1SBRX-ray2.30A/B1-200[»]
ProteinModelPortaliO34911.
SMRiO34911. Positions 8-193.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO34911.

Family & Domainsi

Phylogenomic databases

eggNOGiENOG4108X43. Bacteria.
ENOG4111NMW. LUCA.
HOGENOMiHOG000036207.
OMAiQFALYPM.
OrthoDBiEOG63C0W3.

Family and domain databases

Gene3Di3.30.70.930. 2 hits.
InterProiIPR015835. HMP/thiamine-bd.
IPR029756. MTH1187/YkoF-like.
IPR011522. Thiamin/HMP-bd_put_YkoF.
[Graphical view]
PfamiPF07615. Ykof. 2 hits.
[Graphical view]
PIRSFiPIRSF021331. YkoF. 1 hit.
SUPFAMiSSF89957. SSF89957. 1 hit.

Sequencei

Sequence statusi: Complete.

O34911-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEHICGTSRI AGFRFSLYPM TDDFISVIKS ALKKTDTSKV WTKTDHISTV
60 70 80 90 100
LRGSIDHVFD AAKAIYLHAA NSEQHIVMNG TFSIGCPGDT QGDTYLSKGD
110 120 130 140 150
KRVNEDAVRG LKAEAPCQFA LYPMNEPDYM GLIMEAVDIA KAQGTFVQGV
160 170 180 190 200
HYASELDGDA HDVFSTLEAV FRMAEQQTNH ITMTVNLSAN SPSRKNRKQG
Length:200
Mass (Da):22,024
Last modified:January 1, 1998 - v1
Checksum:iA75C6662174F9465
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ002571 Genomic DNA. Translation: CAA05603.1.
AL009126 Genomic DNA. Translation: CAB13181.1.
PIRiB69859.
RefSeqiNP_389207.1. NC_000964.3.
WP_003244962.1. NZ_JNCM01000035.1.

Genome annotation databases

EnsemblBacteriaiCAB13181; CAB13181; BSU13240.
GeneIDi936465.
KEGGibsu:BSU13240.
PATRICi18974409. VBIBacSub10457_1397.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ002571 Genomic DNA. Translation: CAA05603.1.
AL009126 Genomic DNA. Translation: CAB13181.1.
PIRiB69859.
RefSeqiNP_389207.1. NC_000964.3.
WP_003244962.1. NZ_JNCM01000035.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1S7HX-ray2.20A/B/C/D1-200[»]
1S99X-ray1.65A/B1-200[»]
1SBRX-ray2.30A/B1-200[»]
ProteinModelPortaliO34911.
SMRiO34911. Positions 8-193.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100007336.

Proteomic databases

PaxDbiO34911.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13181; CAB13181; BSU13240.
GeneIDi936465.
KEGGibsu:BSU13240.
PATRICi18974409. VBIBacSub10457_1397.

Phylogenomic databases

eggNOGiENOG4108X43. Bacteria.
ENOG4111NMW. LUCA.
HOGENOMiHOG000036207.
OMAiQFALYPM.
OrthoDBiEOG63C0W3.

Enzyme and pathway databases

BioCyciBSUB:BSU13240-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO34911.
PROiO34911.

Family and domain databases

Gene3Di3.30.70.930. 2 hits.
InterProiIPR015835. HMP/thiamine-bd.
IPR029756. MTH1187/YkoF-like.
IPR011522. Thiamin/HMP-bd_put_YkoF.
[Graphical view]
PfamiPF07615. Ykof. 2 hits.
[Graphical view]
PIRSFiPIRSF021331. YkoF. 1 hit.
SUPFAMiSSF89957. SSF89957. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence of the Bacillus subtilis genome between xlyA and ykoR."
    Devine K.M.
    Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms."
    Rodionov D.A., Vitreschak A.G., Mironov A.A., Gelfand M.S.
    J. Biol. Chem. 277:48949-48959(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN HMP TRANSPORT.
  4. "Isolation and characterization of new thiamine-deregulated mutants of Bacillus subtilis."
    Schyns G., Potot S., Geng Y., Barbosa T.M., Henriques A., Perkins J.B.
    J. Bacteriol. 187:8127-8136(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN HMP/THIAMINE TRANSPORT.
    Strain: 168 / PY79.
  5. "The structure and ligand binding properties of the B. subtilis YkoF gene product, a member of a novel family of thiamin/HMP-binding proteins."
    Devedjiev Y., Surendranath Y., Derewenda U., Gabrys A., Cooper D.R., Zhang R.G., Lezondra L., Joachimiak A., Derewenda Z.S.
    J. Mol. Biol. 343:395-406(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH THIAMINE, SUBUNIT.
  6. "2.2-A crystal structure of protein ykoF from Bacillus subtilis."
    Midwest center for structural genomics (MCSG)
    Submitted (JAN-2005) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiYKOF_BACSU
AccessioniPrimary (citable) accession number: O34911
Secondary accession number(s): Q796L7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 29, 2007
Last sequence update: January 1, 1998
Last modified: June 8, 2016
This is version 81 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. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  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.