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Q9XBQ3 (IABF_GEOSE) Reviewed, UniProtKB/Swiss-Prot

Last modified October 16, 2013. Version 59. 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

Names and origin

Protein namesRecommended name:
Intracellular exo-alpha-(1->5)-L-arabinofuranosidase

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
OrganismGeobacillus stearothermophilus (Bacillus stearothermophilus)
Taxonomic identifier1422 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

Protein attributes

Sequence length502 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
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 aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides. Ref.2 Ref.3 Ref.4 Ref.6

Catalytic activity

Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides. Ref.4 Ref.6

Enzyme regulation

Strongly inhibited by Hg2+. Ref.2

Pathway

Glycan metabolism; L-arabinan degradation.

Subunit structure

Homohexamer; trimer of dimers Probable. Ref.2 Ref.5 Ref.6

Subcellular location

Cytoplasm By similarity.

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.2

Sequence similarities

Belongs to the glycosyl hydrolase 51 family.

Biophysicochemical properties

Kinetic parameters:

Apparently, AbfA can accommodate xylopyranose in the active site, but without the necessary distortion required for the efficient catalysis of six-membered rings. This explains in part its lower specificity towards the xylopyranosidic substrates (PubMes:14517232).

KM=0.35 mM for 2,5-dinitro-arabinofuranosyl Ref.2 Ref.3 Ref.4 Ref.6

KM=0.42 mM for p-nitrophenyl alpha-L-arabinofuranoside (pNP-Araf) (at 60 degrees Celsius and at pH 6)

KM=0.53 mM for 3,4-dinitro-arabinofuranosyl

KM=0.65 mM for 4-nitro-arabinofuranosyl

KM=4.4 mM for 3,4-dinitro-xylopyranosyl

KM=8 mM for 2,5-dinitro-xylopyranosyl

KM=15.3 mM for 2-nitro-xylopyranosyl

Vmax=749 µmol/min/mg enzyme (at 60 degrees Celsius and at pH 6)

pH dependence:

Optimum pH is 5.5-6.0.

Temperature dependence:

Optimum temperature is 70 degrees Celsius.

Ontologies

Keywords
   Biological processCarbohydrate metabolism
   Cellular componentCytoplasm
   Molecular functionGlycosidase
Hydrolase
   Technical term3D-structure
Direct protein sequencing
Gene Ontology (GO)
   Biological_processL-arabinose metabolic process

Inferred from electronic annotation. Source: InterPro

arabinan catabolic process

Inferred from electronic annotation. Source: UniProtKB-UniPathway

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionalpha-L-arabinofuranosidase activity

Inferred from electronic annotation. Source: UniProtKB-EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.2
Chain2 – 502501Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
PRO_0000057700

Regions

Region174 – 1752Substrate binding By similarity

Sites

Active site1751Proton donor/acceptor Ref.3 Ref.4 Ref.6
Active site2941Nucleophile Ref.3 Ref.4 Ref.6
Binding site291Substrate
Binding site741Substrate; via amide nitrogen
Binding site2461Substrate
Binding site2941Substrate
Binding site3511Substrate By similarity
Site2981Important for substrate recognition Probable
Site3511Important for substrate recognition Probable

Experimental info

Mutagenesis1751E → A: Strongly reduced catalytic activity. Increases affinity for substrates. The mutant has an effect on the glycosylation step. The removal of the acid-base catalyst seems to have affected the ionization state of the nucleophile, elevating its pKa, reducing its acidity, and shifting the optimal pH to higher values. Ref.3 Ref.4 Ref.6
Mutagenesis2941E → A: Abolishes catalytic activity, but the binding affinity shows only a small change. Ref.4

Secondary structure

.......................................................................................... 502
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9XBQ3 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: 37C048AE29DBB230

FASTA50257,212
        10         20         30         40         50         60 
MATKKATMII EKDFKIAEID KRIYGSFIEH LGRAVYGGIY EPGHPQADEN GFRQDVIELV 

        70         80         90        100        110        120 
KELQVPIIRY PGGNFVSGYN WEDGVGPKEQ RPRRLDLAWK SVETNEIGLN EFMDWAKMVG 

       130        140        150        160        170        180 
AEVNMAVNLG TRGIDAARNL VEYCNHPSGS YYSDLRIAHG YKEPHKIKTW CLGNEMDGPW 

       190        200        210        220        230        240 
QIGHKTAVEY GRIACEAAKV MKWVDPTIEL VVCGSSNRNM PTFAEWEATV LDHTYDHVDY 

       250        260        270        280        290        300 
ISLHQYYGNR DNDTANYLAL SLEMDDFIRS VVAIADYVKA KKRSKKTIHL SFDEWNVWYH 

       310        320        330        340        350        360 
SNEADKLIEP WTVAPPLLED IYNFEDALLV GCMLITLMKH ADRVKIACLA QLVNVIAPIM 

       370        380        390        400        410        420 
TEKNGPAWKQ TIYYPFMHAS VYGRGVALHP VISSPKYDSK DFTDVPYLES IAVYNEEKEE 

       430        440        450        460        470        480 
VTIFAVNRDM EDALLLECDV RSFEDYRVIE HIVLEHDNVK QTNSAQSSPV VPHRNGDAQL 

       490        500 
SDRKVSATLP KLSWNVIRLG KR 

« Hide

References

[1]Gilead-Gropper S., Gat O., Alchanati I., Yaron S., Bren A., Shoham Y.
Submitted (NOV-2001) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: T-6 / NCIMB 40222.
[2]"Purification and characterization of alpha-L-arabinofuranosidase from Bacillus stearothermophilus T-6."
Gilead S., Shoham Y.
Appl. Environ. Microbiol. 61:170-174(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-51, FUNCTION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, INDUCTION, SUBUNIT.
Strain: T-6 / NCIMB 40222.
[3]"The identification of the acid-base catalyst of alpha-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase."
Shallom D., Belakhov V., Solomon D., Gilead-Gropper S., Baasov T., Shoham G., Shoham Y.
FEBS Lett. 514:163-167(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF GLU-175, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM.
[4]"Detailed kinetic analysis and identification of the nucleophile in alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase."
Shallom D., Belakhov V., Solomon D., Shoham G., Baasov T., Shoham Y.
J. Biol. Chem. 277:43667-43673(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-175 AND GLU-294, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM.
[5]"Crystallization and preliminary X-ray analysis of a family 51 glycoside hydrolase, the alpha-l-arabinofuranosidase from Geobacillus stearothermophilus T-6."
Hovel K., Shallom D., Niefind K., Baasov T., Shoham G., Shoham Y., Schomburg D.
Acta Crystallogr. D 59:913-915(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT.
[6]"Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase."
Hovel K., Shallom D., Niefind K., Belakhov V., Shoham G., Baasov T., Shoham Y., Schomburg D.
EMBO J. 22:4922-4932(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANT ALA-175 IN COMPLEX WITH SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-175, REACTION MECHANISM, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF159625 Genomic DNA. Translation: AAD45520.2.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1PZ2X-ray2.00A/B1-502[»]
1PZ3X-ray1.75A/B1-502[»]
1QW8X-ray1.80A/B1-502[»]
1QW9X-ray1.20A/B1-502[»]
ProteinModelPortalQ9XBQ3.
SMRQ9XBQ3. Positions 5-501.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

CAZyGH51. Glycoside Hydrolase Family 51.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

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. SSF51445. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ9XBQ3.

Entry information

Entry nameIABF_GEOSE
AccessionPrimary (citable) accession number: Q9XBQ3
Entry history
Integrated into UniProtKB/Swiss-Prot: July 26, 2002
Last sequence update: January 23, 2007
Last modified: October 16, 2013
This is version 59 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Glycosyl hydrolases

Classification of glycosyl hydrolase families and list of entries