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Protein

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

Gene

Cthe_2548

Organism
Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (Ruminiclostridium thermocellum)
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 small oligosaccharides as alpha-(1->5)-linked arabinobiose/arabinotriose, but does not display significant activity against linear non-substituted arabinan. It is also highly efficient in the cleavage of alpha-(1->3)-linked arabinoside of xylobiose and of the alpha-(1->3)-linked arabinoside decorations of polymeric wheat arabinoxylan. It exhibits very low activity against 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=5.5 µM for wheat arabinoxylan (at 37 degrees Celsius and at pH 7)1 Publication
  2. KM=0.25 mM for p-nitrophenyl alpha-L-arabinofuranoside (pNP-Araf)(at 37 degrees Celsius and at pH 7)1 Publication
  3. KM=0.55 mM for alpha-(1->5)-linked arabinotriose (at 37 degrees Celsius and at pH 7)1 Publication
  4. KM=0.95 mM for alpha-(1->3)-linked arabinoside of xylobiose (at 37 degrees Celsius and at pH 7)1 Publication

    pH dependencei

    Optimum pH is 6.0.1 Publication

    Temperature dependencei

    Optimum temperature is 60 degrees Celsius.1 Publication

    Pathwayi: L-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 – 271Substrate
    Binding sitei72 – 721Substrate; via amide nitrogen
    Active sitei173 – 1731Proton donor/acceptor1 Publication
    Binding sitei244 – 2441Substrate
    Active sitei292 – 2921Nucleophile1 Publication
    Binding sitei292 – 2921Substrate
    Sitei296 – 2961Important for substrate recognitionBy similarity
    Binding sitei352 – 3521SubstrateBy similarity
    Sitei352 – 3521Important for substrate recognition

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism

    Enzyme and pathway databases

    BioCyciCTHE203119:GIW8-2637-MONOMER.
    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
    Ordered Locus Names:Cthe_2548
    OrganismiClostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (Ruminiclostridium thermocellum)
    Taxonomic identifieri203119 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesRuminococcaceaeRuminiclostridium
    Proteomesi
    • UP000002145 Componenti: Chromosome

    Subcellular locationi

    • Cytoplasm 1 Publication

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi173 – 1731E → A: Absence of arabinofuranosidase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 503503Intracellular exo-alpha-(1->5)-L-arabinofuranosidasePRO_0000422128Add
    BLAST

    Interactioni

    Subunit structurei

    Homohexamer; trimer of dimers.1 Publication

    Protein-protein interaction databases

    STRINGi203119.Cthe_2548.

    Structurei

    Secondary structure

    1
    503
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 86Combined sources
    Beta strandi13 – 164Combined sources
    Helixi19 – 224Combined sources
    Beta strandi23 – 253Combined sources
    Turni35 – 373Combined sources
    Beta strandi49 – 513Combined sources
    Helixi52 – 6110Combined sources
    Beta strandi64 – 696Combined sources
    Helixi74 – 763Combined sources
    Helixi79 – 824Combined sources
    Helixi86 – 883Combined sources
    Beta strandi92 – 943Combined sources
    Turni95 – 984Combined sources
    Beta strandi99 – 1013Combined sources
    Helixi108 – 1169Combined sources
    Beta strandi120 – 1245Combined sources
    Helixi132 – 14312Combined sources
    Beta strandi146 – 1483Combined sources
    Helixi149 – 1568Combined sources
    Beta strandi167 – 1715Combined sources
    Helixi185 – 20218Combined sources
    Beta strandi207 – 2104Combined sources
    Turni219 – 2224Combined sources
    Helixi223 – 23210Combined sources
    Turni233 – 2353Combined sources
    Beta strandi238 – 2458Combined sources
    Helixi252 – 2565Combined sources
    Helixi259 – 28022Combined sources
    Beta strandi287 – 2959Combined sources
    Helixi300 – 3056Combined sources
    Beta strandi307 – 3104Combined sources
    Beta strandi312 – 3154Combined sources
    Helixi325 – 34016Combined sources
    Turni341 – 3444Combined sources
    Beta strandi345 – 3517Combined sources
    Beta strandi353 – 3553Combined sources
    Beta strandi359 – 3613Combined sources
    Beta strandi364 – 3663Combined sources
    Helixi375 – 38410Combined sources
    Beta strandi387 – 3904Combined sources
    Beta strandi393 – 3953Combined sources
    Beta strandi405 – 4095Combined sources
    Beta strandi411 – 4177Combined sources
    Turni418 – 4214Combined sources
    Beta strandi422 – 4287Combined sources
    Beta strandi436 – 4438Combined sources
    Beta strandi450 – 4567Combined sources
    Beta strandi475 – 4773Combined sources
    Beta strandi484 – 4918Combined sources
    Beta strandi496 – 5016Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2C7FX-ray2.70A/B/C/D/E/F1-503[»]
    2C8NX-ray2.90A/B/C/D/E/F1-503[»]
    ProteinModelPortaliA3DIH0.
    SMRiA3DIH0. Positions 2-502.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiA3DIH0.

    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

    eggNOGiENOG4105CZZ. Bacteria.
    COG3534. LUCA.
    HOGENOMiHOG000236895.
    KOiK01209.
    OMAiSGFLEHL.
    OrthoDBiEOG6SJJF9.

    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.

    A3DIH0-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKKARMTVDK DYKIAEIDKR IYGSFVEHLG RAVYDGLYQP GNSKSDEDGF
    60 70 80 90 100
    RKDVIELVKE LNVPIIRYPG GNFVSNYFWE DGVGPVEDRP RRLDLAWKSI
    110 120 130 140 150
    EPNQVGINEF AKWCKKVNAE IMMAVNLGTR GISDACNLLE YCNHPGGSKY
    160 170 180 190 200
    SDMRIKHGVK EPHNIKVWCL GNEMDGPWQV GHKTMDEYGR IAEETARAMK
    210 220 230 240 250
    MIDPSIELVA CGSSSKDMPT FPQWEATVLD YAYDYVDYIS LHQYYGNKEN
    260 270 280 290 300
    DTADFLAKSD DLDDFIRSVI ATCDYIKAKK RSKKDIYLSF DEWNVWYHSN
    310 320 330 340 350
    NEDANIMQNE PWRIAPPLLE DIYTFEDALL VGLMLITLMK HADRIKIACL
    360 370 380 390 400
    AQLINVIAPI VTERNGGAAW RQTIFYPFMH ASKYGRGIVL QPVINSPLHD
    410 420 430 440 450
    TSKHEDVTDI ESVAIYNEEK EEVTIFAVNR NIHEDIVLVS DVRGMKDYRL
    460 470 480 490 500
    LEHIVLEHQD LKIRNSVNGE EVYPKNSDKS SFDDGILTSM LRRASWNVIR

    IGK
    Length:503
    Mass (Da):57,701
    Last modified:March 20, 2007 - v1
    Checksum:i7F030C55B69BF17E
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP000568 Genomic DNA. Translation: ABN53749.1.

    Genome annotation databases

    EnsemblBacteriaiABN53749; ABN53749; Cthe_2548.
    KEGGicth:Cthe_2548.
    PATRICi19519108. VBICloThe47081_2713.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP000568 Genomic DNA. Translation: ABN53749.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2C7FX-ray2.70A/B/C/D/E/F1-503[»]
    2C8NX-ray2.90A/B/C/D/E/F1-503[»]
    ProteinModelPortaliA3DIH0.
    SMRiA3DIH0. Positions 2-502.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi203119.Cthe_2548.

    Protein family/group databases

    CAZyiGH51. Glycoside Hydrolase Family 51.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiABN53749; ABN53749; Cthe_2548.
    KEGGicth:Cthe_2548.
    PATRICi19519108. VBICloThe47081_2713.

    Phylogenomic databases

    eggNOGiENOG4105CZZ. Bacteria.
    COG3534. LUCA.
    HOGENOMiHOG000236895.
    KOiK01209.
    OMAiSGFLEHL.
    OrthoDBiEOG6SJJF9.

    Enzyme and pathway databases

    UniPathwayiUPA00667.
    BioCyciCTHE203119:GIW8-2637-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiA3DIH0.

    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372.
    2. "Structural insight into the ligand specificity of a thermostable family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum."
      Taylor E.J., Smith N.L., Turkenburg J.P., D'Souza S., Gilbert H.J., Davies G.J.
      Biochem. J. 395:31-37(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-173, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, SUBCELLULAR LOCATION, SUBUNIT.

    Entry informationi

    Entry nameiIABF_CLOTH
    AccessioniPrimary (citable) accession number: A3DIH0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 2013
    Last sequence update: March 20, 2007
    Last modified: November 11, 2015
    This is version 58 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    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

    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.