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Protein

D-ribose pyranase

Gene

rbsD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose.By similarity

Catalytic activityi

Beta-D-ribopyranose = beta-D-ribofuranose.

Pathwayi: D-ribose degradation

This protein is involved in step 1 of the subpathway that synthesizes D-ribose 5-phosphate from beta-D-ribopyranose.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. D-ribose pyranase (rbsD)
  2. Ribokinase (rbsK)
This subpathway is part of the pathway D-ribose degradation, which is itself part of Carbohydrate metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-ribose 5-phosphate from beta-D-ribopyranose, the pathway D-ribose degradation and in Carbohydrate metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei20 – 201Proton donorCurated
Binding sitei28 – 281Substrate
Binding sitei98 – 981Substrate

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Carbohydrate metabolism

Enzyme and pathway databases

BioCyciBSUB:BSU35930-MONOMER.
UniPathwayiUPA00916; UER00888.

Names & Taxonomyi

Protein namesi
Recommended name:
D-ribose pyranase (EC:5.4.99.62)
Gene namesi
Name:rbsD
Ordered Locus Names:BSU35930
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi98 – 981H → A: Reduced sugar-binding affinity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 131131D-ribose pyranasePRO_0000097190Add
BLAST

Proteomic databases

PaxDbiP36946.

Interactioni

Subunit structurei

Homodecamer; dimer of pentamers.1 Publication

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100019436.

Structurei

Secondary structure

1
131
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi9 – 179Combined sources
Beta strandi23 – 275Combined sources
Beta strandi37 – 415Combined sources
Helixi51 – 6111Combined sources
Beta strandi64 – 707Combined sources
Helixi72 – 765Combined sources
Helixi78 – 8710Combined sources
Beta strandi89 – 968Combined sources
Helixi98 – 1047Combined sources
Helixi105 – 1073Combined sources
Beta strandi109 – 1135Combined sources
Beta strandi123 – 1275Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1OGCX-ray2.00A/B/C/D/E1-131[»]
1OGDX-ray1.95A/B/C/D/E1-131[»]
1OGEX-ray2.05A/B/C/D/E1-131[»]
1OGFX-ray2.30A/B/C/D/E1-131[»]
ProteinModelPortaliP36946.
SMRiP36946. Positions 1-131.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP36946.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni120 – 1223Substrate binding

Sequence similaritiesi

Belongs to the RbsD / FucU family. RbsD subfamily.Curated

Phylogenomic databases

eggNOGiENOG4105MRB. Bacteria.
COG1869. LUCA.
HOGENOMiHOG000219040.
InParanoidiP36946.
KOiK06726.
OMAiIIRTGEC.
OrthoDBiEOG68SW4G.
PhylomeDBiP36946.

Family and domain databases

Gene3Di3.40.1650.10. 1 hit.
HAMAPiMF_01661. D_rib_pyranase.
InterProiIPR023064. D-ribose_pyranase.
IPR023750. RbsD-like.
IPR007721. RbsD_FucU.
[Graphical view]
PfamiPF05025. RbsD_FucU. 1 hit.
[Graphical view]
SUPFAMiSSF102546. SSF102546. 1 hit.

Sequencei

Sequence statusi: Complete.

P36946-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKHGILNSH LAKILADLGH TDKIVIADAG LPVPDGVLKI DLSLKPGLPA
60 70 80 90 100
FQDTAAVLAE EMAVEKVIAA AEIKASNQEN AKFLENLFSE QEIEYLSHEE
110 120 130
FKLLTKDAKA VIRTGEFTPY ANCILQAGVL F
Length:131
Mass (Da):14,227
Last modified:June 1, 1994 - v1
Checksum:i053F1AC529CC98D1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z25798 Genomic DNA. Translation: CAA81050.1.
Z92953 Genomic DNA. Translation: CAB07464.1.
AL009126 Genomic DNA. Translation: CAB15610.1.
PIRiI40464.
RefSeqiNP_391474.1. NC_000964.3.
WP_003244175.1. NZ_JNCM01000034.1.

Genome annotation databases

EnsemblBacteriaiCAB15610; CAB15610; BSU35930.
GeneIDi936846.
KEGGibsu:BSU35930.
PATRICi18979206. VBIBacSub10457_3765.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z25798 Genomic DNA. Translation: CAA81050.1.
Z92953 Genomic DNA. Translation: CAB07464.1.
AL009126 Genomic DNA. Translation: CAB15610.1.
PIRiI40464.
RefSeqiNP_391474.1. NC_000964.3.
WP_003244175.1. NZ_JNCM01000034.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1OGCX-ray2.00A/B/C/D/E1-131[»]
1OGDX-ray1.95A/B/C/D/E1-131[»]
1OGEX-ray2.05A/B/C/D/E1-131[»]
1OGFX-ray2.30A/B/C/D/E1-131[»]
ProteinModelPortaliP36946.
SMRiP36946. Positions 1-131.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100019436.

Proteomic databases

PaxDbiP36946.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB15610; CAB15610; BSU35930.
GeneIDi936846.
KEGGibsu:BSU35930.
PATRICi18979206. VBIBacSub10457_3765.

Phylogenomic databases

eggNOGiENOG4105MRB. Bacteria.
COG1869. LUCA.
HOGENOMiHOG000219040.
InParanoidiP36946.
KOiK06726.
OMAiIIRTGEC.
OrthoDBiEOG68SW4G.
PhylomeDBiP36946.

Enzyme and pathway databases

UniPathwayiUPA00916; UER00888.
BioCyciBSUB:BSU35930-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP36946.

Family and domain databases

Gene3Di3.40.1650.10. 1 hit.
HAMAPiMF_01661. D_rib_pyranase.
InterProiIPR023064. D-ribose_pyranase.
IPR023750. RbsD-like.
IPR007721. RbsD_FucU.
[Graphical view]
PfamiPF05025. RbsD_FucU. 1 hit.
[Graphical view]
SUPFAMiSSF102546. SSF102546. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Analysis of a ribose transport operon from Bacillus subtilis."
    Woodson K., Devine K.M.
    Microbiology 140:1829-1838(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "The Bacillus subtilis genome from gerBC (311 degrees) to licR (334 degrees)."
    Presecan E., Moszer I., Boursier L., Cruz Ramos H., De La Fuente V., Hullo M.-F., Lelong C., Schleich S., Sekowska A., Song B.H., Villani G., Kunst F., Danchin A., Glaser P.
    Microbiology 143:3313-3328(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  3. "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.
  4. "Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture."
    Kim M.-S., Shin J., Lee W., Lee H.-S., Oh B.-H.
    J. Biol. Chem. 278:28173-28180(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEXES WITH D-RIBOSE AND RIBOSE-5-PHOSPHATE, SUBUNIT, MUTAGENESIS OF HIS-98, REACTION MECHANISM.

Entry informationi

Entry nameiRBSD_BACSU
AccessioniPrimary (citable) accession number: P36946
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: February 17, 2016
This is version 111 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Was originally thought (PubMed:7921236 and PubMed:9353933) to be a high affinity ribose transport protein.Curated

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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.