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

Beta-1,3-xylanase XYL4

Gene

xyl4

Organism
Vibrio sp.
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the hydrolysis of beta-1,3-xylan into oligosaccharides, mainly xylobiose, xylotriose and xylotetraose. Converts beta-1,3-xylotriose into xylose and xylobiose, converts beta-1,3-xylotetraose mainly into xylotriose and xylose, converts beta-1,3-xylopentaose into xylobiose and xylotriose. Does not hydrolyze beta-1,4-xylan, beta-1,4-mannan, beta-1,4-glucan, beta-1,3-xylobiose or p-nitrophenyl-beta-xyloside.1 Publication

Catalytic activityi

Random hydrolysis of (1->3)-beta-D-glycosidic linkages in (1->3)-beta-D-xylans.1 Publication

Enzyme regulationi

Completely inhibited by Hg2+, partially inhibited by Mn2+, Cu2+ and Pb2+. Unaffected by Ca2+, Mg2+ and EDTA.1 Publication

Kineticsi

  1. KM=7.4 mM for beta-1,3-xylotetraose1 Publication
  2. KM=7.5 mM for beta-1,3-xylopentaose1 Publication

    pH dependencei

    Optimum pH is 7.0-7.5.1 Publication

    Temperature dependencei

    Optimum temperature is 37 degrees Celsius. Inactive above 60 degrees Celsius.1 Publication

    GO - Molecular functioni

    • polysaccharide binding Source: UniProtKB
    • xylan endo-1,3-beta-xylosidase activity Source: UniProtKB

    GO - Biological processi

    • cellulose catabolic process Source: UniProtKB-KW
    • xylan catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism, Cellulose degradation, Polysaccharide degradation, Xylan degradation

    Enzyme and pathway databases

    BRENDAi3.2.1.32. 12038.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Beta-1,3-xylanase XYL41 Publication (EC:3.2.1.32)
    Alternative name(s):
    Beta-1,3-xylanaseImported
    Gene namesi
    Name:xyl4Imported
    OrganismiVibrio sp.
    Taxonomic identifieri678 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi138 – 1381E → D: Very low catalytic activity. 1 Publication
    Mutagenesisi138 – 1381E → Q: Complete loss of catalytic activity. 1 Publication
    Mutagenesisi234 – 2341E → D: Very low catalytic activity. 1 Publication
    Mutagenesisi234 – 2341E → Q: Complete loss of catalytic activity. 1 Publication
    Mutagenesisi268 – 2681E → Q: Catalytic activity reduced by 30%. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2222Sequence AnalysisAdd
    BLAST
    Chaini23 – 576554Beta-1,3-xylanase XYL4Sequence AnalysisPRO_0000403220Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi368 ↔ 452By similarity
    Disulfide bondi399 ↔ 404By similarity
    Disulfide bondi490 ↔ 574By similarity
    Disulfide bondi521 ↔ 526By similarity

    Keywords - PTMi

    Disulfide bond

    Structurei

    Secondary structure

    1
    576
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni24 – 274Combined sources
    Beta strandi30 – 4011Combined sources
    Helixi41 – 5111Combined sources
    Beta strandi56 – 638Combined sources
    Turni64 – 663Combined sources
    Beta strandi70 – 723Combined sources
    Beta strandi74 – 785Combined sources
    Helixi83 – 897Combined sources
    Beta strandi93 – 1008Combined sources
    Helixi105 – 1095Combined sources
    Turni110 – 1134Combined sources
    Helixi114 – 12512Combined sources
    Beta strandi131 – 1355Combined sources
    Helixi142 – 1443Combined sources
    Helixi148 – 16518Combined sources
    Turni168 – 1703Combined sources
    Beta strandi171 – 1766Combined sources
    Helixi189 – 1913Combined sources
    Helixi195 – 1973Combined sources
    Beta strandi199 – 2079Combined sources
    Helixi208 – 2114Combined sources
    Helixi214 – 22613Combined sources
    Beta strandi230 – 2356Combined sources
    Turni242 – 2454Combined sources
    Turni251 – 2533Combined sources
    Helixi262 – 2687Combined sources
    Helixi270 – 27910Combined sources
    Turni280 – 2834Combined sources
    Beta strandi284 – 2907Combined sources
    Helixi294 – 2963Combined sources
    Helixi298 – 3003Combined sources
    Turni302 – 3065Combined sources
    Helixi314 – 3163Combined sources
    Helixi318 – 32811Combined sources
    Helixi340 – 3434Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2DDXX-ray0.86A23-349[»]
    3VPLX-ray1.20A23-349[»]
    ProteinModelPortaliD5MP61.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiD5MP61.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni363 – 45391Carbohydrate binding module (CBM) 1Add
    BLAST
    Regioni487 – 57488Carbohydrate binding module (CBM) 2Add
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi453 – 48432Gly-richSequence AnalysisAdd
    BLAST

    Domaini

    The carbohydrate binding modules (CBM) bind to insoluble beta-1,3-xylan, but not to insoluble beta-1,4-xylan, beta-1,4-glucan, beta-1,4-mannan, curdlan, chitin, or soluble polysaccharides.

    Sequence similaritiesi

    Belongs to the glycosyl hydrolase 26 family.1 Publication

    Keywords - Domaini

    Repeat, Signal

    Family and domain databases

    Gene3Di3.20.20.80. 1 hit.
    InterProiIPR021016. Beta-xylanase.
    IPR013781. Glyco_hydro_catalytic_dom.
    IPR017853. Glycoside_hydrolase_SF.
    [Graphical view]
    PfamiPF11606. AlcCBM31. 2 hits.
    [Graphical view]
    SUPFAMiSSF51445. SSF51445. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    D5MP61-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKRTYLSLIA AGVMSLSVSA WSLDGVLVPE SGILVSVGQD VDSVNDYASA
    60 70 80 90 100
    LGTIPAGVTN YVGIVNLDGL NSDADAGAGR NNIAELANAY PTSALVVGVS
    110 120 130 140 150
    MNGEVDAVAS GRYNANIDTL LNTLAGYDRP VYLRWAYEVD GPWNGHSPSG
    160 170 180 190 200
    IVTSFQYVHD RIIALGHQAK ISLVWQVASY CPTPGGQLDQ WWPGSEYVDW
    210 220 230 240 250
    VGLSYFAPQD CNWDRVNEAA QFARSKGKPL FLNESTPQRY QVADLTYSAD
    260 270 280 290 300
    PAKGTNRQSK TSQQLWDEWF APYFQFMSDN SDIVKGFTYI NADWDSQWRW
    310 320 330 340 350
    AAPYNEGYWG DSRVQANALI KSNWQQEIAK GQYINHSETL FETLGYGSTG
    360 370 380 390 400
    GGDNGGGDNG GTNPPEPCNE EFGYRYVSDS TIEVFHKNNG WSAEWNYVCL
    410 420 430 440 450
    NGLCLQGEIK NGEYVKQFDA QLGSTYGIEF KVADGESQFI TDKSVTFENK
    460 470 480 490 500
    QCGSTGTPGG GDNGSGGDNG GDNGSGGDNG SGGGTDPSQC SADFGYNYRS
    510 520 530 540 550
    DTEIEVFHKD LGWSASWNYI CLDDYCVPGD KSGDSYNRSF NATLGSDYKI
    560 570
    TFKVEDSASQ FITEKNITFV NTSCAQ
    Length:576
    Mass (Da):62,591
    Last modified:July 13, 2010 - v1
    Checksum:iE04449C5F703884D
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB121027 Genomic DNA. Translation: BAD51934.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB121027 Genomic DNA. Translation: BAD51934.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2DDXX-ray0.86A23-349[»]
    3VPLX-ray1.20A23-349[»]
    ProteinModelPortaliD5MP61.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    BRENDAi3.2.1.32. 12038.

    Miscellaneous databases

    EvolutionaryTraceiD5MP61.

    Family and domain databases

    Gene3Di3.20.20.80. 1 hit.
    InterProiIPR021016. Beta-xylanase.
    IPR013781. Glyco_hydro_catalytic_dom.
    IPR017853. Glycoside_hydrolase_SF.
    [Graphical view]
    PfamiPF11606. AlcCBM31. 2 hits.
    [Graphical view]
    SUPFAMiSSF51445. SSF51445. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Molecular cloning and characterization of a novel beta-1,3-xylanase possessing two putative carbohydrate-binding modules from a marine bacterium Vibrio sp. strain AX-4."
      Kiyohara M., Sakaguchi K., Yamaguchi K., Araki T., Nakamura T., Ito M.
      Biochem. J. 388:949-957(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF GLU-138; GLU-234 AND GLU-268.
      Strain: AX-4Imported.
    2. "Characterization and application of carbohydrate-binding modules of beta-1,3-xylanase XYL4."
      Kiyohara M., Sakaguchi K., Yamaguchi K., Araki T., Ito M.
      J. Biochem. 146:633-641(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: CBM31 DOMAIN.
      Strain: AX-41 Publication.
    3. "Atomic resolution analysis of beta-1,3-xylanase catalytic module from Vibrio sp. AX-4."
      Sakaguchi K., Kawamura T., Watanabe N., Kiyohara M., Yamaguchi K., Ito M., Tanaka I.
      Submitted (FEB-2006) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (0.86 ANGSTROMS) OF 23-349 IN COMPLEX WITH MAGNESIUM.
      Strain: AX-41 Publication.

    Entry informationi

    Entry namei3XYN1_VIBSX
    AccessioniPrimary (citable) accession number: D5MP61
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 11, 2011
    Last sequence update: July 13, 2010
    Last modified: April 1, 2015
    This is version 18 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

    Documents

    1. Glycosyl hydrolases
      Classification of glycosyl hydrolase families and list of entries
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.