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P94531 (IABF1_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 86. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Intracellular exo-alpha-(1->5)-L-arabinofuranosidase 1
Short name=ABF
EC=3.2.1.55
Alternative name(s):
Intracellular arabinan exo-alpha-(1->5)-L-arabinosidase
Short name=Arabinosidase
Gene names
Name:abfA
Ordered Locus Names:BSU28720
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus ›

Protein attributes

Sequence length500 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.7

Catalytic activity

Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides. Ref.7

Pathway

Glycan metabolism; L-arabinan degradation.

Subunit structure

Homohexamer; trimer of dimers Probable. Ref.7

Subcellular location

Cytoplasm Ref.7.

Induction

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. Ref.5 Ref.6

Disruption phenotype

Cells lacking this gene retain 38% of arabinofuranosidase activity, and the double mutant abfA/abf2 is inactive. Ref.7

Sequence similarities

Belongs to the glycosyl hydrolase 51 family.

Biophysicochemical properties

Kinetic parameters:

KM=0.36 mM for linear alpha-1,5-L-arabinan (at pH 6.6 and 37 degrees Celsius) Ref.7

KM=0.49 mM for p-nitrophenyl-alpha-L-arabinofuranoside (pNP-Araf) (at pH 6.6 and 37 degrees Celsius)

KM=0.78 mM for arabinobiose (at pH 6.6 and 37 degrees Celsius)

KM=1.1 mM for arabinotriose (at pH 6.6 and 37 degrees Celsius)

KM=4.4 mM for sugar beet arabinan (branched) (at pH 6.6 and 37 degrees Celsius)

Vmax=317 µmol/min/mg enzyme with pNP-Araf as substrate (at pH 6.6 and 37 degrees Celsius)

pH dependence:

Optimum pH is 8.

Temperature dependence:

Optimum temperature is 50 degrees Celsius.

Ontologies

Keywords
   Biological processCarbohydrate metabolism
   Cellular componentCytoplasm
   Molecular functionGlycosidase
Hydrolase
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processL-arabinose metabolic process

Inferred from electronic annotation. Source: InterPro

   Molecular_functionalpha-N-arabinofuranosidase activity

Inferred from electronic annotation. Source: EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 500500Intracellular exo-alpha-(1->5)-L-arabinofuranosidase 1
PRO_0000057701

Regions

Region172 – 1732Substrate binding By similarity

Sites

Active site1731Proton donor/acceptor By similarity
Active site2921Nucleophile By similarity
Binding site271Substrate By similarity
Binding site721Substrate; via amide nitrogen By similarity
Binding site2441Substrate By similarity
Binding site2921Substrate By similarity
Binding site3491Substrate By similarity
Site2961Important for substrate recognition By similarity
Site3491Important for substrate recognition By similarity

Experimental info

Sequence conflict1141A → P in CAA99595. Ref.2

Sequences

Sequence LengthMass (Da)Tools
P94531 [UniParc].

Last modified July 7, 2009. Version 2.
Checksum: 3EEA8F8ADA3D705A

FASTA50057,034
        10         20         30         40         50         60 
MKKARMIVDK EYKIGEVDKR IYGSFIEHMG RAVYEGIYEP DHPEADEDGF RKDVQSLIKE 

        70         80         90        100        110        120 
LQVPIIRYPG GNFLSGYNWE DGVGPVENRP RRLDLAWQTT ETNEVGTNEF LSWAKKVNTE 

       130        140        150        160        170        180 
VNMAVNLGTR GIDAARNLVE YCNHPKGSYW SDLRRSHGYE QPYGIKTWCL GNEMDGPWQI 

       190        200        210        220        230        240 
GHKTADEYGR LAAETAKVMK WVDPSIELVA CGSSNSGMPT FIDWEAKVLE HTYEHVDYIS 

       250        260        270        280        290        300 
LHTYYGNRDN NLPNYLARSM DLDHFIKSVA ATCDYVKAKT RSKKTINLSL DEWNVWYHSN 

       310        320        330        340        350        360 
EADKKVEPWI TARPILEDIY NFEDALLVGS LLITMLQHAD RVKIACLAQL VNVIAPIMTE 

       370        380        390        400        410        420 
KGGEAWRQPI FYPYMHASVY GRGESLKPLI SSPKYDCSDF TDVPYVDAAV VYSEEEETLT 

       430        440        450        460        470        480 
IFAVNKAEDQ METEISLRGF ESYQIAEHIV LEHQDIKATN QHNRKNVVPH SNGSSSVSEN 

       490        500 
GLTAHFTPLS WNVIRLKKQS

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		X89810 Genomic DNA. Translation: CAA61937.1.
Z75208 Genomic DNA. Translation: CAA99595.1.
AL009126 Genomic DNA. Translation: CAB14832.2.
PIRC69580.
RefSeqNP_390750.2. NC_000964.3.

3D structure databases

ProteinModelPortalP94531.
SMRP94531. Positions 3-498.
ModBaseSearch...

Protein-protein interaction databases

STRING224308.BSU28720.

Protein family/group databases

CAZyGH51. Glycoside Hydrolase Family 51.

Proteomic databases

PaxDbP94531.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB14832; CAB14832; BSU28720.
GeneID937509.
KEGGbsu:BSU28720.
PATRIC18977636. VBIBacSub10457_3006.

Organism-specific databases

GenoListBSU28720. [Micado]

Phylogenomic databases

eggNOGCOG3534.
HOGENOMHOG000236895.
KOK01209.
ProtClustDBCLSK2539632.

Enzyme and pathway databases

BioCycBSUB:BSU28720-MONOMER.
MetaCyc:BSU28720-MONOMER.
UniPathwayUPA00667.

Family and domain databases

Gene3D3.20.20.80. 1 hit.
InterProIPR010720. Alpha-L-AF_C.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PfamPF06964. Alpha-L-AF_C. 1 hit.
[Graphical view]
SMARTSM00813. Alpha-L-AF_C. 1 hit.
[Graphical view]
SUPFAMSSF51445. Glyco_hydro_cat. 1 hit.
ProtoNetSearch...

Entry information

Entry nameIABF1_BACSU
AccessionPrimary (citable) accession number: P94531
Secondary accession number(s): O05096
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: July 7, 2009
Last modified: May 1, 2013
This is version 86 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Glycosyl hydrolases

Classification of glycosyl hydrolase families and list of entries

Bacillus subtilis

Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents