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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

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei138Proton donorPROSITE-ProRule annotation1
    Active sitei234NucleophilePROSITE-ProRule annotation1

    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)DescriptionActionsGraphical viewLength
    Mutagenesisi138E → D: Very low catalytic activity. 1 Publication1
    Mutagenesisi138E → Q: Complete loss of catalytic activity. 1 Publication1
    Mutagenesisi234E → D: Very low catalytic activity. 1 Publication1
    Mutagenesisi234E → Q: Complete loss of catalytic activity. 1 Publication1
    Mutagenesisi268E → Q: Catalytic activity reduced by 30%. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 22Sequence analysisAdd BLAST22
    ChainiPRO_000040322023 – 576Beta-1,3-xylanase XYL4Sequence analysisAdd BLAST554

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Disulfide bondi368 ↔ 452By similarity
    Disulfide bondi399 ↔ 404By similarity
    Disulfide bondi490 ↔ 574By similarity
    Disulfide bondi521 ↔ 526By similarity

    Keywords - PTMi

    Disulfide bond

    Structurei

    Secondary structure

    1576
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Turni24 – 27Combined sources4
    Beta strandi30 – 40Combined sources11
    Helixi41 – 51Combined sources11
    Beta strandi56 – 63Combined sources8
    Turni64 – 66Combined sources3
    Beta strandi70 – 72Combined sources3
    Beta strandi74 – 78Combined sources5
    Helixi83 – 89Combined sources7
    Beta strandi93 – 100Combined sources8
    Helixi105 – 109Combined sources5
    Turni110 – 113Combined sources4
    Helixi114 – 125Combined sources12
    Beta strandi131 – 135Combined sources5
    Helixi142 – 144Combined sources3
    Helixi148 – 165Combined sources18
    Turni168 – 170Combined sources3
    Beta strandi171 – 176Combined sources6
    Helixi189 – 191Combined sources3
    Helixi195 – 197Combined sources3
    Beta strandi199 – 207Combined sources9
    Helixi208 – 211Combined sources4
    Helixi214 – 226Combined sources13
    Beta strandi230 – 235Combined sources6
    Turni242 – 245Combined sources4
    Turni251 – 253Combined sources3
    Helixi262 – 268Combined sources7
    Helixi270 – 279Combined sources10
    Turni280 – 283Combined sources4
    Beta strandi284 – 290Combined sources7
    Helixi294 – 296Combined sources3
    Helixi298 – 300Combined sources3
    Turni302 – 306Combined sources5
    Helixi314 – 316Combined sources3
    Helixi318 – 328Combined sources11
    Helixi340 – 343Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2DDXX-ray0.86A23-349[»]
    3VPLX-ray1.20A23-349[»]
    ProteinModelPortaliD5MP61.
    SMRiD5MP61.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiD5MP61.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini23 – 293GH26PROSITE-ProRule annotationAdd BLAST271

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni363 – 453Carbohydrate binding module (CBM) 1Add BLAST91
    Regioni487 – 574Carbohydrate binding module (CBM) 2Add BLAST88

    Compositional bias

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Compositional biasi453 – 484Gly-richSequence analysisAdd BLAST32

    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.PROSITE-ProRule annotation1 Publication
    Contains 1 GH26 (glycosyl hydrolase family 26) domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat, Signal

    Family and domain databases

    Gene3Di3.20.20.80. 1 hit.
    InterProiIPR021016. Beta-xylanase.
    IPR022790. GH26_dom.
    IPR013781. Glyco_hydro_catalytic_dom.
    IPR017853. Glycoside_hydrolase_SF.
    [Graphical view]
    PfamiPF11606. AlcCBM31. 2 hits.
    [Graphical view]
    SUPFAMiSSF51445. SSF51445. 1 hit.
    PROSITEiPS51764. GH26. 1 hit.
    [Graphical view]

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2DDXX-ray0.86A23-349[»]
    3VPLX-ray1.20A23-349[»]
    ProteinModelPortaliD5MP61.
    SMRiD5MP61.
    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.
    IPR022790. GH26_dom.
    IPR013781. Glyco_hydro_catalytic_dom.
    IPR017853. Glycoside_hydrolase_SF.
    [Graphical view]
    PfamiPF11606. AlcCBM31. 2 hits.
    [Graphical view]
    SUPFAMiSSF51445. SSF51445. 1 hit.
    PROSITEiPS51764. GH26. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    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: November 2, 2016
    This is version 21 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

    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.