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P45796

- XYND_PAEPO

UniProt

P45796 - XYND_PAEPO

Protein

Arabinoxylan arabinofuranohydrolase

Gene

xynD

Organism
Paenibacillus polymyxa (Bacillus polymyxa)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 85 (01 Oct 2014)
      Sequence version 1 (01 Nov 1995)
      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 By similarity. Preferres wheat flour xylan over oat spelt xylan as substrate. Does not display endoxylanase activity.By similarity1 Publication

    Catalytic activityi

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

    Enzyme regulationi

    Activated by calcium and magnesium. Inhibited by copper.1 Publication

    pH dependencei

    Optimum pH is 6.5.1 Publication

    Temperature dependencei

    Optimum temperature is 55 degrees Celsius.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei49 – 491Proton acceptorBy similarity
    Sitei188 – 1881Important for catalytic activityBy similarity
    Active sitei248 – 2481Proton donorBy similarity
    Binding sitei311 – 3111SubstrateBy similarity
    Metal bindingi382 – 3821Calcium 1; structuralBy similarity
    Metal bindingi384 – 3841Calcium 1; structuralBy similarity
    Metal bindingi406 – 4061Calcium 1; structuralBy similarity
    Metal bindingi407 – 4071Calcium 1; via carbonyl oxygen; structuralBy similarity
    Metal bindingi503 – 5031Calcium 1; structuralBy similarity
    Metal bindingi503 – 5031Calcium 1; via carbonyl oxygen; structuralBy similarity
    Metal bindingi520 – 5201Calcium 2; structural
    Metal bindingi522 – 5221Calcium 2; structural
    Metal bindingi539 – 5391Calcium 2; via carbonyl oxygen; structural
    Metal bindingi544 – 5441Calcium 3; via carbonyl oxygen; structural
    Metal bindingi620 – 6201Calcium 3
    Metal bindingi624 – 6241Calcium 3; via carbonyl oxygen; structural
    Metal bindingi625 – 6251Calcium 3
    Metal bindingi629 – 6291Calcium 2; structural
    Metal bindingi629 – 6291Calcium 2; 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

    BRENDAi3.2.1.8. 7322.
    UniPathwayiUPA00114.

    Protein family/group databases

    CAZyiCBM36. Carbohydrate-Binding Module Family 36.
    CBM6. 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
    OrganismiPaenibacillus polymyxa (Bacillus polymyxa)
    Taxonomic identifieri1406 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesPaenibacillaceaePaenibacillus

    Subcellular locationi

    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 – 635609Arabinoxylan arabinofuranohydrolasePRO_0000012202Add
    BLAST

    Structurei

    Secondary structure

    1
    635
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi517 – 5204
    Helixi521 – 5233
    Beta strandi524 – 5307
    Beta strandi532 – 5343
    Beta strandi536 – 5438
    Beta strandi549 – 58133
    Beta strandi584 – 59512
    Beta strandi597 – 6059
    Beta strandi609 – 61810
    Beta strandi620 – 6234
    Beta strandi626 – 6349

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1UX7X-ray1.50A516-635[»]
    1W0NX-ray0.80A505-635[»]
    ProteinModelPortaliP45796.
    SMRiP45796. Positions 516-635.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP45796.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini379 – 508130CBM6 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini517 – 634118CBM6 2PROSITE-ProRule annotationAdd
    BLAST

    Domaini

    The C-terminal CBM6 domain shows calcium-dependent xylo-oligosaccharide and xylan binding. It binds, next to the structural calcium ion, a second calcium ion that, in addition to its coordination sites on the protein, completes its heptacoordination through coordination to the bound xylose moiety.

    Sequence similaritiesi

    Belongs to the glycosyl hydrolase 43 family.Curated
    Contains 2 CBM6 (carbohydrate binding type-6) domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat, Signal

    Family and domain databases

    Gene3Di2.115.10.20. 1 hit.
    2.60.120.260. 2 hits.
    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. 2 hits.
    PF04616. Glyco_hydro_43. 1 hit.
    [Graphical view]
    SMARTiSM00606. CBD_IV. 1 hit.
    [Graphical view]
    SUPFAMiSSF49785. SSF49785. 2 hits.
    SSF75005. SSF75005. 1 hit.
    PROSITEiPS51175. CBM6. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P45796-1 [UniParc]FASTAAdd to Basket

    « Hide

    MIRKCLVLFL SFALLLSVFP MLNVDAANRP LAKIPGNSNP LMDHKLGADP    50
    YSLVYDGRVY IFMSSDTYVY NKDGSIKEND FSALDRIQVI SSTDMVNWTD 100
    HGTIPVAGAN NKNSGRGIAK WASNSWAPAV AHKKINGRDK FFLYFANGGA 150
    GIGVLTADTP IGPWTDPLGK ALVTHSTPGM AGVTWLFDPA VLVDDDGTGY 200
    LYSGGGIPNE SDPASIANPK TARVIKLGAD MTSVIGSATT IDAPYLFEDS 250
    GIHKYNGKYY YSYCINFAGT HPQQYPAGEI GYMVSDNPMG PFTYKGHFLK 300
    NPYTFFGVGG NNHHAVFNFK NEWYVVYHAQ TVSKAQIGAG KGYRSPHINK 350
    LVHKEDGSIS EVQGNMTGIA QLSNMNPYTR VEAETIAWQA GVTTEPTQAS 400
    GGPISNLNVT NIHNGDWIAV GKADFGSAGA KTFKANVATN VGGNIEVRLD 450
    SETGPLVGSL KVPSTGGMQT WREVETTINN ATGVHNIYLV FTGSGSGNLL 500
    NLDAWQFTPN TGGNTITKVE AENMKIGGTY AGKISAPFDG VALYANADYV 550
    SYSQYFANST HNISVRGASS NAGTAKVDLV IGGVTVGSFN FTGKTPTVQT 600
    LSNITHATGD QEIKLALTSD DGTWDAYVDF IEFSL 635
    Length:635
    Mass (Da):67,914
    Last modified:November 1, 1995 - v1
    Checksum:iF9DEC69967323316
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X57094 Genomic DNA. Translation: CAA40378.1.
    PIRiS19011.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X57094 Genomic DNA. Translation: CAA40378.1 .
    PIRi S19011.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1UX7 X-ray 1.50 A 516-635 [» ]
    1W0N X-ray 0.80 A 505-635 [» ]
    ProteinModelPortali P45796.
    SMRi P45796. Positions 516-635.
    ModBasei Search...
    MobiDBi Search...

    Protein family/group databases

    CAZyi CBM36. Carbohydrate-Binding Module Family 36.
    CBM6. Carbohydrate-Binding Module Family 6.
    GH43. Glycoside Hydrolase Family 43.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    UniPathwayi UPA00114 .
    BRENDAi 3.2.1.8. 7322.

    Miscellaneous databases

    EvolutionaryTracei P45796.

    Family and domain databases

    Gene3Di 2.115.10.20. 1 hit.
    2.60.120.260. 2 hits.
    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. 2 hits.
    PF04616. Glyco_hydro_43. 1 hit.
    [Graphical view ]
    SMARTi SM00606. CBD_IV. 1 hit.
    [Graphical view ]
    SUPFAMi SSF49785. SSF49785. 2 hits.
    SSF75005. SSF75005. 1 hit.
    PROSITEi PS51175. CBM6. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Two beta-glycanase genes are clustered in Bacillus polymyxa: molecular cloning, expression, and sequence analysis of genes encoding a xylanase and an endo-beta-(1,3)-(1,4)-glucanase."
      Gosalbes M.J., Perez-Gonzalez J.A., Gonzalez R., Navarro A.
      J. Bacteriol. 173:7705-7710(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 842 / DSM 36 / JCM 2507 / NBRC 15309 / NCIMB 8158 / NCTC 10343 / NRRL B-4317 / VKM B-514.
    2. "Purification and characterization of an arabinofuranosidase from Bacillus polymyxa expressed in Bacillus subtilis."
      Morales P., Sendra J.M., Perez-Gonzalez J.A.
      Appl. Microbiol. Biotechnol. 44:112-117(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 27-46, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
      Strain: CECT 153 / NCTC 4747 / NRRL NRS-1237.
    3. "Ab initio structure determination and functional characterization of CBM36; a new family of calcium-dependent carbohydrate binding modules."
      Jamal-Talabani S., Boraston A.B., Turkenburg J.P., Tarbouriech N., Ducros V.M.-A., Davies G.J.
      Structure 12:1177-1187(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (0.8 ANGSTROMS) OF 505-635 IN COMPLEX WITH XYLOTRIOSE.
      Strain: ATCC 842 / DSM 36 / JCM 2507 / NBRC 15309 / NCIMB 8158 / NCTC 10343 / NRRL B-4317 / VKM B-514.

    Entry informationi

    Entry nameiXYND_PAEPO
    AccessioniPrimary (citable) accession number: P45796
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: November 1, 1995
    Last modified: October 1, 2014
    This is version 85 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, 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