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Q45071

- XYND_BACSU

UniProt

Q45071 - XYND_BACSU

Protein

Arabinoxylan arabinofuranohydrolase

Gene

xynD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 91 (01 Oct 2014)
      Sequence version 2 (01 Jun 1998)
      Previous versions | rss
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    Functioni

    Cleaves arabinose units from O-2- or O-3-monosubstituted xylose residues, thereby assisting in arabinoxylan (AX) and short-chain arabinoxylo-oligosaccharide (AXOS) degradation. Is more active on wheat bran AXOS than on wheat water-extractable AX and rye water-extractable AX. Does not display endoxylanase, xylosidase or arabinanase activity.1 Publication

    Catalytic activityi

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

    pH dependencei

    Optimum pH is 5.6. Stable from pH 4.4 to 7.6.1 Publication

    Temperature dependencei

    Optimum temperature is 45 degrees Celsius. Thermostable for 40 min from 4 to 45 degrees Celsius.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei50 – 501Proton acceptor
    Sitei189 – 1891Important for catalytic activity
    Active sitei251 – 2511Proton donor
    Binding sitei314 – 3141Substrate
    Metal bindingi385 – 3851Calcium; structural
    Metal bindingi387 – 3871Calcium; structural
    Metal bindingi409 – 4091Calcium; structural
    Metal bindingi410 – 4101Calcium; via carbonyl oxygen; structural
    Metal bindingi506 – 5061Calcium; structural
    Metal bindingi506 – 5061Calcium; via carbonyl oxygen; structural

    GO - Molecular functioni

    1. alpha-L-arabinofuranosidase activity Source: UniProtKB-EC
    2. carbohydrate binding Source: InterPro
    3. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. xylan catabolic process Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism, Polysaccharide degradation, Xylan degradation

    Keywords - Ligandi

    Calcium, Metal-binding

    Enzyme and pathway databases

    BioCyciBSUB:BSU18160-MONOMER.
    BRENDAi3.2.1.55. 700.
    UniPathwayiUPA00114.

    Protein family/group databases

    CAZyiCBM6. Carbohydrate-Binding Module Family 6.
    GH43. Glycoside Hydrolase Family 43.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Arabinoxylan arabinofuranohydrolase (EC:3.2.1.55)
    Short name:
    AXH
    Alternative name(s):
    AXH-m2,3
    Short name:
    AXH-m23
    Alpha-L-arabinofuranosidase
    Short name:
    AF
    Gene namesi
    Name:xynD
    Ordered Locus Names:BSU18160
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU18160. [Micado]

    Subcellular locationi

    Secreted 1 Publication

    GO - Cellular componenti

    1. extracellular region Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Secreted

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 26261 PublicationAdd
    BLAST
    Chaini27 – 513487Arabinoxylan arabinofuranohydrolasePRO_0000360828Add
    BLAST

    Proteomic databases

    PaxDbiQ45071.

    Interactioni

    Protein-protein interaction databases

    STRINGi224308.BSU18160.

    Structurei

    Secondary structure

    1
    513
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi32 – 343
    Beta strandi49 – 568
    Beta strandi59 – 657
    Beta strandi87 – 10519
    Beta strandi110 – 1123
    Helixi113 – 1164
    Beta strandi127 – 13610
    Beta strandi139 – 14810
    Beta strandi153 – 1608
    Beta strandi168 – 1714
    Beta strandi185 – 1873
    Beta strandi191 – 1944
    Beta strandi200 – 2056
    Helixi216 – 2205
    Beta strandi225 – 2306
    Beta strandi234 – 24411
    Beta strandi249 – 25810
    Beta strandi261 – 2688
    Beta strandi270 – 2723
    Beta strandi282 – 2909
    Beta strandi296 – 3027
    Helixi305 – 3095
    Beta strandi317 – 3226
    Beta strandi325 – 3339
    Helixi334 – 3407
    Beta strandi348 – 3536
    Beta strandi388 – 3947
    Beta strandi396 – 3994
    Beta strandi410 – 4134
    Beta strandi420 – 4278
    Turni429 – 4313
    Beta strandi433 – 4419
    Beta strandi446 – 4549
    Beta strandi459 – 4657
    Beta strandi475 – 4806
    Beta strandi486 – 49510
    Beta strandi497 – 5004
    Beta strandi504 – 5129

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3C7EX-ray2.00A27-513[»]
    3C7FX-ray1.55A27-513[»]
    3C7GX-ray2.02A27-513[»]
    3C7HX-ray2.00A27-513[»]
    3C7OX-ray1.80A27-513[»]
    ProteinModelPortaliQ45071.
    SMRiQ45071. Positions 27-513.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ45071.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini382 – 511130CBM6PROSITE-ProRule annotationAdd
    BLAST

    Domaini

    The CBM6 domain lost its carbohydrate binding capacity.

    Sequence similaritiesi

    Belongs to the glycosyl hydrolase 43 family.Curated
    Contains 1 CBM6 (carbohydrate binding type-6) domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiCOG5498.
    HOGENOMiHOG000292007.
    KOiK15921.
    OMAiSPHINKL.
    OrthoDBiEOG6GXTPP.
    PhylomeDBiQ45071.

    Family and domain databases

    Gene3Di2.115.10.20. 1 hit.
    2.60.120.260. 1 hit.
    InterProiIPR006584. Cellulose-bd_IV.
    IPR005084. CMB_fam6.
    IPR008979. Galactose-bd-like.
    IPR006710. Glyco_hydro_43.
    IPR023296. Glyco_hydro_beta-prop.
    [Graphical view]
    PANTHERiPTHR22925. PTHR22925. 1 hit.
    PfamiPF03422. CBM_6. 1 hit.
    PF04616. Glyco_hydro_43. 1 hit.
    [Graphical view]
    SMARTiSM00606. CBD_IV. 1 hit.
    [Graphical view]
    SUPFAMiSSF49785. SSF49785. 1 hit.
    SSF75005. SSF75005. 1 hit.
    PROSITEiPS51175. CBM6. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q45071-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRKKCSVCLW ILVLLLSCLS GKSAYAATST TIAKHIGNSN PLIDHHLGAD    50
    PVALTYNGRV YIYMSSDDYE YNSNGTIKDN SFANLNRVFV ISSADMVNWT 100
    DHGAIPVAGA NGANGGRGIA KWAGASWAPS IAVKKINGKD KFFLYFANSG 150
    GGIGVLTADS PIGPWTDPIG KPLVTPSTPG MSGVVWLFDP AVFVDDDGTG 200
    YLYAGGGVPG VSNPTQGQWA NPKTARVIKL GPDMTSVVGS ASTIDAPFMF 250
    EDSGLHKYNG TYYYSYCINF GGTHPADKPP GEIGYMTSSS PMGPFTYRGH 300
    FLKNPGAFFG GGGNNHHAVF NFKNEWYVVY HAQTVSSALF GAGKGYRSPH 350
    INKLVHNADG SIQEVAANYA GVTQISNLNP YNRVEAETFA WNGRILTEKS 400
    TAPGGPVNNQ HVTSIQNGDW IAVGNADFGA GGARSFKANV ASTLGGKIEV 450
    RLDSADGKLV GTLNVPSTGG AQTWREIETA VSGATGVHKV FFVFTGTGTG 500
    NLFNFDYWQF TQR 513
    Length:513
    Mass (Da):54,498
    Last modified:June 1, 1998 - v2
    Checksum:i1EBC94AB6CE1490F
    GO

    Mass spectrometryi

    Molecular mass is 52080 Da from positions 27 - 513. Determined by MALDI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL009126 Genomic DNA. Translation: CAB13699.1.
    PIRiH69735.
    RefSeqiNP_389698.1. NC_000964.3.

    Genome annotation databases

    EnsemblBacteriaiCAB13699; CAB13699; BSU18160.
    GeneIDi936433.
    KEGGibsu:BSU18160.
    PATRICi18975467. VBIBacSub10457_1925.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL009126 Genomic DNA. Translation: CAB13699.1 .
    PIRi H69735.
    RefSeqi NP_389698.1. NC_000964.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3C7E X-ray 2.00 A 27-513 [» ]
    3C7F X-ray 1.55 A 27-513 [» ]
    3C7G X-ray 2.02 A 27-513 [» ]
    3C7H X-ray 2.00 A 27-513 [» ]
    3C7O X-ray 1.80 A 27-513 [» ]
    ProteinModelPortali Q45071.
    SMRi Q45071. Positions 27-513.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224308.BSU18160.

    Protein family/group databases

    CAZyi CBM6. Carbohydrate-Binding Module Family 6.
    GH43. Glycoside Hydrolase Family 43.

    Proteomic databases

    PaxDbi Q45071.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB13699 ; CAB13699 ; BSU18160 .
    GeneIDi 936433.
    KEGGi bsu:BSU18160.
    PATRICi 18975467. VBIBacSub10457_1925.

    Organism-specific databases

    GenoListi BSU18160. [Micado ]

    Phylogenomic databases

    eggNOGi COG5498.
    HOGENOMi HOG000292007.
    KOi K15921.
    OMAi SPHINKL.
    OrthoDBi EOG6GXTPP.
    PhylomeDBi Q45071.

    Enzyme and pathway databases

    UniPathwayi UPA00114 .
    BioCyci BSUB:BSU18160-MONOMER.
    BRENDAi 3.2.1.55. 700.

    Miscellaneous databases

    EvolutionaryTracei Q45071.

    Family and domain databases

    Gene3Di 2.115.10.20. 1 hit.
    2.60.120.260. 1 hit.
    InterProi IPR006584. Cellulose-bd_IV.
    IPR005084. CMB_fam6.
    IPR008979. Galactose-bd-like.
    IPR006710. Glyco_hydro_43.
    IPR023296. Glyco_hydro_beta-prop.
    [Graphical view ]
    PANTHERi PTHR22925. PTHR22925. 1 hit.
    Pfami PF03422. CBM_6. 1 hit.
    PF04616. Glyco_hydro_43. 1 hit.
    [Graphical view ]
    SMARTi SM00606. CBD_IV. 1 hit.
    [Graphical view ]
    SUPFAMi SSF49785. SSF49785. 1 hit.
    SSF75005. SSF75005. 1 hit.
    PROSITEi PS51175. CBM6. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "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.
      , 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.
    2. "Proteome analysis of Bacillus subtilis extracellular proteins: a two-dimensional protein electrophoretic study."
      Hirose I., Sano K., Shioda I., Kumano M., Nakamura K., Yamane K.
      Microbiology 146:65-75(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 27-37, SUBCELLULAR LOCATION.
      Strain: 168.
    3. "Recombinant expression and characterization of XynD from Bacillus subtilis subsp. subtilis ATCC 6051: a GH 43 arabinoxylan arabinofuranohydrolase."
      Bourgois T.M., Van Craeyveld V., Van Campenhout S., Courtin C.M., Delcour J.A., Robben J., Volckaert G.
      Appl. Microbiol. Biotechnol. 75:1309-1317(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, MASS SPECTROMETRY.
      Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
    4. "Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family."
      Vandermarliere E., Bourgois T.M., Winn M.D., van Campenhout S., Volckaert G., Delcour J.A., Strelkov S.V., Rabijns A., Courtin C.M.
      Biochem. J. 418:39-47(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF 27-513 IN COMPLEXES WITH XYLOTRIOSE; XYLOTETRAOSE; ARABINOXYLO-OLIGOSACCHARIDES AND CELLOTETRAOSE.
      Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.

    Entry informationi

    Entry nameiXYND_BACSU
    AccessioniPrimary (citable) accession number: Q45071
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 20, 2009
    Last sequence update: June 1, 1998
    Last modified: October 1, 2014
    This is version 91 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. Glycosyl hydrolases
      Classification of glycosyl hydrolase families and list of entries
    3. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    4. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    5. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3