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Protein

Intracellular exo-alpha-(1->5)-L-arabinofuranosidase 1

Gene

abfA

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

Functioni

Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on arabinotriose, arabinobiose and linear alpha-(1->5)-L-arabinan, and is much less effective on branched sugar beet arabinan.1 Publication

Catalytic activityi

Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.1 Publication

Kineticsi

  1. KM=0.36 mM for linear alpha-1,5-L-arabinan (at pH 6.6 and 37 degrees Celsius)1 Publication
  2. KM=0.49 mM for p-nitrophenyl-alpha-L-arabinofuranoside (pNP-Araf) (at pH 6.6 and 37 degrees Celsius)1 Publication
  3. KM=0.78 mM for arabinobiose (at pH 6.6 and 37 degrees Celsius)1 Publication
  4. KM=1.1 mM for arabinotriose (at pH 6.6 and 37 degrees Celsius)1 Publication
  5. KM=4.4 mM for sugar beet arabinan (branched) (at pH 6.6 and 37 degrees Celsius)1 Publication
  1. Vmax=317 µmol/min/mg enzyme with pNP-Araf as substrate (at pH 6.6 and 37 degrees Celsius)1 Publication

pH dependencei

Optimum pH is 8.1 Publication

Temperature dependencei

Optimum temperature is 50 degrees Celsius.1 Publication

Pathway:iL-arabinan degradation

This protein is involved in the pathway L-arabinan degradation, which is part of Glycan metabolism.
View all proteins of this organism that are known to be involved in the pathway L-arabinan degradation and in Glycan metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei27 – 271SubstrateBy similarity
Binding sitei72 – 721Substrate; via amide nitrogenBy similarity
Active sitei173 – 1731Proton donor/acceptorBy similarity
Binding sitei244 – 2441SubstrateBy similarity
Active sitei292 – 2921NucleophileBy similarity
Binding sitei292 – 2921SubstrateBy similarity
Sitei296 – 2961Important for substrate recognitionBy similarity
Binding sitei349 – 3491SubstrateBy similarity
Sitei349 – 3491Important for substrate recognitionBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Carbohydrate metabolism

Enzyme and pathway databases

BioCyciBSUB:BSU28720-MONOMER.
MetaCyc:BSU28720-MONOMER.
BRENDAi3.2.1.55. 658.
SABIO-RKP94531.
UniPathwayiUPA00667.

Protein family/group databases

CAZyiGH51. Glycoside Hydrolase Family 51.

Names & Taxonomyi

Protein namesi
Recommended name:
Intracellular exo-alpha-(1->5)-L-arabinofuranosidase 1 (EC:3.2.1.55)
Short name:
ABF
Alternative name(s):
Intracellular arabinan exo-alpha-(1->5)-L-arabinosidase
Short name:
Arabinosidase
Gene namesi
Name:abfA
Ordered Locus Names:BSU28720
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU28720. [Micado]

Subcellular locationi

  • Cytoplasm 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene retain 38% of arabinofuranosidase activity, and the double mutant abfA/abf2 is inactive.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 500500Intracellular exo-alpha-(1->5)-L-arabinofuranosidase 1PRO_0000057701Add
BLAST

Proteomic databases

PaxDbiP94531.

Expressioni

Inductioni

Transcription is repressed by glucose and by the binding of AraR to the operon promoter. L-arabinose acts as an inducer by inhibiting the binding of AraR to the DNA, thus allowing expression of the gene (Probable).2 Publications

Interactioni

Subunit structurei

Homohexamer; trimer of dimers.1 Publication

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100015681.

Structurei

3D structure databases

ProteinModelPortaliP94531.
SMRiP94531. Positions 3-498.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni172 – 1732Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the glycosyl hydrolase 51 family.Curated

Phylogenomic databases

eggNOGiCOG3534.
HOGENOMiHOG000236895.
InParanoidiP94531.
KOiK01209.
OMAiSGFLEHL.
OrthoDBiEOG6SJJF9.
PhylomeDBiP94531.

Family and domain databases

Gene3Di3.20.20.80. 1 hit.
InterProiIPR010720. Alpha-L-AF_C.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PfamiPF06964. Alpha-L-AF_C. 1 hit.
[Graphical view]
SMARTiSM00813. Alpha-L-AF_C. 1 hit.
[Graphical view]
SUPFAMiSSF51445. SSF51445. 1 hit.

Sequencei

Sequence statusi: Complete.

P94531-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKARMIVDK EYKIGEVDKR IYGSFIEHMG RAVYEGIYEP DHPEADEDGF
60 70 80 90 100
RKDVQSLIKE LQVPIIRYPG GNFLSGYNWE DGVGPVENRP RRLDLAWQTT
110 120 130 140 150
ETNEVGTNEF LSWAKKVNTE VNMAVNLGTR GIDAARNLVE YCNHPKGSYW
160 170 180 190 200
SDLRRSHGYE QPYGIKTWCL GNEMDGPWQI GHKTADEYGR LAAETAKVMK
210 220 230 240 250
WVDPSIELVA CGSSNSGMPT FIDWEAKVLE HTYEHVDYIS LHTYYGNRDN
260 270 280 290 300
NLPNYLARSM DLDHFIKSVA ATCDYVKAKT RSKKTINLSL DEWNVWYHSN
310 320 330 340 350
EADKKVEPWI TARPILEDIY NFEDALLVGS LLITMLQHAD RVKIACLAQL
360 370 380 390 400
VNVIAPIMTE KGGEAWRQPI FYPYMHASVY GRGESLKPLI SSPKYDCSDF
410 420 430 440 450
TDVPYVDAAV VYSEEEETLT IFAVNKAEDQ METEISLRGF ESYQIAEHIV
460 470 480 490 500
LEHQDIKATN QHNRKNVVPH SNGSSSVSEN GLTAHFTPLS WNVIRLKKQS
Length:500
Mass (Da):57,034
Last modified:July 7, 2009 - v2
Checksum:i3EEA8F8ADA3D705A
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti114 – 1141A → P in CAA99595 (PubMed:8969504).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X89810 Genomic DNA. Translation: CAA61937.1.
Z75208 Genomic DNA. Translation: CAA99595.1.
AL009126 Genomic DNA. Translation: CAB14832.2.
PIRiC69580.
RefSeqiNP_390750.2. NC_000964.3.
WP_004398747.1. NZ_JNCM01000036.1.

Genome annotation databases

EnsemblBacteriaiCAB14832; CAB14832; BSU28720.
GeneIDi937509.
KEGGibsu:BSU28720.
PATRICi18977636. VBIBacSub10457_3006.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X89810 Genomic DNA. Translation: CAA61937.1.
Z75208 Genomic DNA. Translation: CAA99595.1.
AL009126 Genomic DNA. Translation: CAB14832.2.
PIRiC69580.
RefSeqiNP_390750.2. NC_000964.3.
WP_004398747.1. NZ_JNCM01000036.1.

3D structure databases

ProteinModelPortaliP94531.
SMRiP94531. Positions 3-498.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100015681.

Protein family/group databases

CAZyiGH51. Glycoside Hydrolase Family 51.

Proteomic databases

PaxDbiP94531.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14832; CAB14832; BSU28720.
GeneIDi937509.
KEGGibsu:BSU28720.
PATRICi18977636. VBIBacSub10457_3006.

Organism-specific databases

GenoListiBSU28720. [Micado]

Phylogenomic databases

eggNOGiCOG3534.
HOGENOMiHOG000236895.
InParanoidiP94531.
KOiK01209.
OMAiSGFLEHL.
OrthoDBiEOG6SJJF9.
PhylomeDBiP94531.

Enzyme and pathway databases

UniPathwayiUPA00667.
BioCyciBSUB:BSU28720-MONOMER.
MetaCyc:BSU28720-MONOMER.
BRENDAi3.2.1.55. 658.
SABIO-RKP94531.

Family and domain databases

Gene3Di3.20.20.80. 1 hit.
InterProiIPR010720. Alpha-L-AF_C.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PfamiPF06964. Alpha-L-AF_C. 1 hit.
[Graphical view]
SMARTiSM00813. Alpha-L-AF_C. 1 hit.
[Graphical view]
SUPFAMiSSF51445. SSF51445. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression."
    Sa-Nogueira I.M.G., Nogueira T.V., Soares S., de Lencastre H.
    Microbiology 143:957-969(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "The dnaB-pheA (256 degrees-240 degrees) region of the Bacillus subtilis chromosome containing genes responsible for stress responses, the utilization of plant cell walls and primary metabolism."
    Wipat A., Carter N., Brignell C.S., Guy J.B., Piper K., Sanders J., Emmerson P.T., Harwood C.R.
    Microbiology 142:3067-3078(1996) [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. "From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later."
    Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A., Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.
    Microbiology 155:1758-1775(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION TO 114.
  5. "Mode of action of AraR, the key regulator of L-arabinose metabolism in Bacillus subtilis."
    Mota L.J., Tavares P., Sa-Nogueira I.M.G.
    Mol. Microbiol. 33:476-489(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: TRANSCRIPTIONAL REGULATION.
  6. "Transcriptional regulation of genes encoding arabinan-degrading enzymes in Bacillus subtilis."
    Raposo M.P., Inacio J.M., Mota L.J., de Sa-Nogueira I.
    J. Bacteriol. 186:1287-1296(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
    Strain: 168.
  7. "Two distinct arabinofuranosidases contribute to arabino-oligosaccharide degradation in Bacillus subtilis."
    Inacio J.M., Correia I.L., de Sa-Nogueira I.
    Microbiology 154:2719-2729(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, DISRUPTION PHENOTYPE, SUBUNIT.

Entry informationi

Entry nameiIABF1_BACSU
AccessioniPrimary (citable) accession number: P94531
Secondary accession number(s): O05096
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: July 7, 2009
Last modified: June 24, 2015
This is version 98 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. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. Glycosyl hydrolases
    Classification of glycosyl hydrolase families and list of entries
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.