Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)DescriptionActionsGraphical viewLength
    Binding sitei27Substrate1
    Binding sitei72Substrate; via amide nitrogen1
    Active sitei173Proton donor/acceptor1 Publication1
    Binding sitei244Substrate1
    Active sitei292Nucleophile1 Publication1
    Binding sitei292Substrate1
    Sitei296Important for substrate recognitionBy similarity1
    Binding sitei352SubstrateBy similarity1
    Sitei352Important for substrate recognition1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    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
    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)DescriptionActionsGraphical viewLength
    Mutagenesisi173E → A: Absence of arabinofuranosidase activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004221281 – 503Intracellular exo-alpha-(1->5)-L-arabinofuranosidaseAdd BLAST503

    Interactioni

    Subunit structurei

    Homohexamer; trimer of dimers.1 Publication

    Protein-protein interaction databases

    STRINGi203119.Cthe_2548.

    Structurei

    Secondary structure

    1503
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 8Combined sources6
    Beta strandi13 – 16Combined sources4
    Helixi19 – 22Combined sources4
    Beta strandi23 – 25Combined sources3
    Turni35 – 37Combined sources3
    Beta strandi49 – 51Combined sources3
    Helixi52 – 61Combined sources10
    Beta strandi64 – 69Combined sources6
    Helixi74 – 76Combined sources3
    Helixi79 – 82Combined sources4
    Helixi86 – 88Combined sources3
    Beta strandi92 – 94Combined sources3
    Turni95 – 98Combined sources4
    Beta strandi99 – 101Combined sources3
    Helixi108 – 116Combined sources9
    Beta strandi120 – 124Combined sources5
    Helixi132 – 143Combined sources12
    Beta strandi146 – 148Combined sources3
    Helixi149 – 156Combined sources8
    Beta strandi167 – 171Combined sources5
    Helixi185 – 202Combined sources18
    Beta strandi207 – 210Combined sources4
    Turni219 – 222Combined sources4
    Helixi223 – 232Combined sources10
    Turni233 – 235Combined sources3
    Beta strandi238 – 245Combined sources8
    Helixi252 – 256Combined sources5
    Helixi259 – 280Combined sources22
    Beta strandi287 – 295Combined sources9
    Helixi300 – 305Combined sources6
    Beta strandi307 – 310Combined sources4
    Beta strandi312 – 315Combined sources4
    Helixi325 – 340Combined sources16
    Turni341 – 344Combined sources4
    Beta strandi345 – 351Combined sources7
    Beta strandi353 – 355Combined sources3
    Beta strandi359 – 361Combined sources3
    Beta strandi364 – 366Combined sources3
    Helixi375 – 384Combined sources10
    Beta strandi387 – 390Combined sources4
    Beta strandi393 – 395Combined sources3
    Beta strandi405 – 409Combined sources5
    Beta strandi411 – 417Combined sources7
    Turni418 – 421Combined sources4
    Beta strandi422 – 428Combined sources7
    Beta strandi436 – 443Combined sources8
    Beta strandi450 – 456Combined sources7
    Beta strandi475 – 477Combined sources3
    Beta strandi484 – 491Combined sources8
    Beta strandi496 – 501Combined sources6

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiA3DIH0.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni172 – 173Substrate bindingBy similarity2

    Sequence similaritiesi

    Belongs to the glycosyl hydrolase 51 family.Curated

    Phylogenomic databases

    eggNOGiENOG4105CZZ. Bacteria.
    COG3534. LUCA.
    HOGENOMiHOG000236895.
    KOiK01209.
    OMAiSGFLEHL.
    OrthoDBiPOG091H07CN.

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2C7FX-ray2.70A/B/C/D/E/F1-503[»]
    2C8NX-ray2.90A/B/C/D/E/F1-503[»]
    ProteinModelPortaliA3DIH0.
    SMRiA3DIH0.
    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.
    OrthoDBiPOG091H07CN.

    Enzyme and pathway databases

    UniPathwayiUPA00667.

    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...

    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 2, 2016
    This is version 61 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.