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Q9XBQ3

- IABF_GEOSE

UniProt

Q9XBQ3 - IABF_GEOSE

Protein

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

Gene

abfA

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 61 (01 Oct 2014)
      Sequence version 4 (23 Jan 2007)
      Previous versions | rss
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    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 aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.4 Publications

    Catalytic activityi

    Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.2 Publications

    Enzyme regulationi

    Strongly inhibited by Hg2+.1 Publication

    Kineticsi

    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).

    1. KM=0.35 mM for 2,5-dinitro-arabinofuranosyl4 Publications
    2. KM=0.42 mM for p-nitrophenyl alpha-L-arabinofuranoside (pNP-Araf) (at 60 degrees Celsius and at pH 6)4 Publications
    3. KM=0.53 mM for 3,4-dinitro-arabinofuranosyl4 Publications
    4. KM=0.65 mM for 4-nitro-arabinofuranosyl4 Publications
    5. KM=4.4 mM for 3,4-dinitro-xylopyranosyl4 Publications
    6. KM=8 mM for 2,5-dinitro-xylopyranosyl4 Publications
    7. KM=15.3 mM for 2-nitro-xylopyranosyl4 Publications

    Vmax=749 µmol/min/mg enzyme (at 60 degrees Celsius and at pH 6)4 Publications

    pH dependencei

    Optimum pH is 5.5-6.0.4 Publications

    Temperature dependencei

    Optimum temperature is 70 degrees Celsius.4 Publications

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei29 – 291Substrate
    Binding sitei74 – 741Substrate; via amide nitrogen
    Active sitei175 – 1751Proton donor/acceptor
    Binding sitei246 – 2461Substrate
    Active sitei294 – 2941Nucleophile
    Binding sitei294 – 2941Substrate
    Sitei298 – 2981Important for substrate recognitionCurated
    Binding sitei351 – 3511SubstrateBy similarity
    Sitei351 – 3511Important for substrate recognitionCurated

    GO - Molecular functioni

    1. alpha-L-arabinofuranosidase activity Source: UniProtKB-EC

    GO - Biological processi

    1. arabinan catabolic process Source: UniProtKB-UniPathway
    2. L-arabinose metabolic process Source: InterPro

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism

    Enzyme and pathway databases

    UniPathwayiUPA00667.

    Protein family/group databases

    CAZyiGH51. Glycoside Hydrolase Family 51.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Intracellular exo-alpha-(1->5)-L-arabinofuranosidase (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
    OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
    Taxonomic identifieri1422 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi175 – 1751E → 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. 3 Publications
    Mutagenesisi294 – 2941E → A: Abolishes catalytic activity, but the binding affinity shows only a small change. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 502501Intracellular exo-alpha-(1->5)-L-arabinofuranosidasePRO_0000057700Add
    BLAST

    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.1 Publication

    Interactioni

    Subunit structurei

    Homohexamer; trimer of dimers.3 Publications

    Structurei

    Secondary structure

    1
    502
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 94
    Beta strandi14 – 185
    Helixi21 – 244
    Beta strandi25 – 273
    Turni37 – 393
    Beta strandi51 – 533
    Helixi54 – 629
    Beta strandi67 – 715
    Helixi74 – 785
    Helixi81 – 844
    Helixi88 – 903
    Beta strandi94 – 963
    Turni97 – 1004
    Beta strandi101 – 1033
    Helixi109 – 11911
    Beta strandi122 – 1276
    Helixi134 – 14512
    Beta strandi148 – 1503
    Helixi151 – 1588
    Beta strandi169 – 1746
    Helixi187 – 20418
    Beta strandi209 – 2124
    Turni221 – 2244
    Helixi225 – 23410
    Helixi235 – 2373
    Beta strandi239 – 2479
    Helixi254 – 2585
    Helixi261 – 28222
    Beta strandi289 – 2979
    Helixi302 – 3054
    Beta strandi312 – 3143
    Helixi324 – 33916
    Turni340 – 3434
    Beta strandi344 – 3507
    Beta strandi352 – 3565
    Beta strandi358 – 3614
    Beta strandi367 – 3693
    Helixi373 – 38210
    Beta strandi385 – 3884
    Beta strandi391 – 3933
    Beta strandi403 – 41513
    Turni416 – 4194
    Beta strandi420 – 4278
    Beta strandi430 – 4323
    Beta strandi434 – 4396
    Beta strandi447 – 4548
    Beta strandi473 – 4753
    Beta strandi479 – 4813
    Beta strandi484 – 4896
    Beta strandi491 – 50010

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1PZ2X-ray2.00A/B1-502[»]
    1PZ3X-ray1.75A/B1-502[»]
    1QW8X-ray1.80A/B1-502[»]
    1QW9X-ray1.20A/B1-502[»]
    ProteinModelPortaliQ9XBQ3.
    SMRiQ9XBQ3. Positions 5-501.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9XBQ3.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni174 – 1752Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the glycosyl hydrolase 51 family.Curated

    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.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q9XBQ3-1 [UniParc]FASTAAdd to Basket

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    MATKKATMII EKDFKIAEID KRIYGSFIEH LGRAVYGGIY EPGHPQADEN    50
    GFRQDVIELV KELQVPIIRY PGGNFVSGYN WEDGVGPKEQ RPRRLDLAWK 100
    SVETNEIGLN EFMDWAKMVG AEVNMAVNLG TRGIDAARNL VEYCNHPSGS 150
    YYSDLRIAHG YKEPHKIKTW CLGNEMDGPW QIGHKTAVEY GRIACEAAKV 200
    MKWVDPTIEL VVCGSSNRNM PTFAEWEATV LDHTYDHVDY ISLHQYYGNR 250
    DNDTANYLAL SLEMDDFIRS VVAIADYVKA KKRSKKTIHL SFDEWNVWYH 300
    SNEADKLIEP WTVAPPLLED IYNFEDALLV GCMLITLMKH ADRVKIACLA 350
    QLVNVIAPIM TEKNGPAWKQ TIYYPFMHAS VYGRGVALHP VISSPKYDSK 400
    DFTDVPYLES IAVYNEEKEE VTIFAVNRDM EDALLLECDV RSFEDYRVIE 450
    HIVLEHDNVK QTNSAQSSPV VPHRNGDAQL SDRKVSATLP KLSWNVIRLG 500
    KR 502
    Length:502
    Mass (Da):57,212
    Last modified:January 23, 2007 - v4
    Checksum:i37C048AE29DBB230
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF159625 Genomic DNA. Translation: AAD45520.2.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF159625 Genomic DNA. Translation: AAD45520.2 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1PZ2 X-ray 2.00 A/B 1-502 [» ]
    1PZ3 X-ray 1.75 A/B 1-502 [» ]
    1QW8 X-ray 1.80 A/B 1-502 [» ]
    1QW9 X-ray 1.20 A/B 1-502 [» ]
    ProteinModelPortali Q9XBQ3.
    SMRi Q9XBQ3. Positions 5-501.
    ModBasei Search...
    MobiDBi Search...

    Protein family/group databases

    CAZyi GH51. Glycoside Hydrolase Family 51.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    UniPathwayi UPA00667 .

    Miscellaneous databases

    EvolutionaryTracei Q9XBQ3.

    Family and domain databases

    Gene3Di 3.20.20.80. 1 hit.
    InterProi IPR010720. Alpha-L-AF_C.
    IPR013781. Glyco_hydro_catalytic_dom.
    IPR017853. Glycoside_hydrolase_SF.
    [Graphical view ]
    Pfami PF06964. Alpha-L-AF_C. 1 hit.
    [Graphical view ]
    SMARTi SM00813. Alpha-L-AF_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51445. SSF51445. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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.

    Entry informationi

    Entry nameiIABF_GEOSE
    AccessioniPrimary (citable) accession number: Q9XBQ3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 26, 2002
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 61 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. Glycosyl hydrolases
      Classification of glycosyl hydrolase families and list of entries
    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

    External Data

    Dasty 3