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D5MP61

- 3XYN1_VIBSX

UniProt

D5MP61 - 3XYN1_VIBSX

Protein

Beta-1,3-xylanase XYL4

Gene

xyl4

Organism
Vibrio sp.
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 16 (01 Oct 2014)
      Sequence version 1 (13 Jul 2010)
      Previous versions | rss
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    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

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

    GO - Biological processi

    1. cellulose catabolic process Source: UniProtKB-KW
    2. xylan catabolic process Source: UniProtKB

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism, Cellulose degradation, Polysaccharide degradation, Xylan degradation

    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 – 274
    Beta strandi30 – 4011
    Helixi41 – 5111
    Beta strandi56 – 638
    Turni64 – 663
    Beta strandi70 – 723
    Beta strandi74 – 785
    Helixi83 – 897
    Beta strandi93 – 1008
    Helixi105 – 1095
    Turni110 – 1134
    Helixi114 – 12512
    Beta strandi131 – 1355
    Helixi142 – 1443
    Helixi148 – 16518
    Turni168 – 1703
    Beta strandi171 – 1766
    Helixi189 – 1913
    Helixi195 – 1973
    Beta strandi199 – 2079
    Helixi208 – 2114
    Helixi214 – 22613
    Beta strandi230 – 2356
    Turni242 – 2454
    Turni251 – 2533
    Helixi262 – 2687
    Helixi270 – 27910
    Turni280 – 2834
    Beta strandi284 – 2907
    Helixi294 – 2963
    Helixi298 – 3003
    Turni302 – 3065
    Helixi314 – 3163
    Helixi318 – 32811
    Helixi340 – 3434

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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

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    MKRTYLSLIA AGVMSLSVSA WSLDGVLVPE SGILVSVGQD VDSVNDYASA    50
    LGTIPAGVTN YVGIVNLDGL NSDADAGAGR NNIAELANAY PTSALVVGVS 100
    MNGEVDAVAS GRYNANIDTL LNTLAGYDRP VYLRWAYEVD GPWNGHSPSG 150
    IVTSFQYVHD RIIALGHQAK ISLVWQVASY CPTPGGQLDQ WWPGSEYVDW 200
    VGLSYFAPQD CNWDRVNEAA QFARSKGKPL FLNESTPQRY QVADLTYSAD 250
    PAKGTNRQSK TSQQLWDEWF APYFQFMSDN SDIVKGFTYI NADWDSQWRW 300
    AAPYNEGYWG DSRVQANALI KSNWQQEIAK GQYINHSETL FETLGYGSTG 350
    GGDNGGGDNG GTNPPEPCNE EFGYRYVSDS TIEVFHKNNG WSAEWNYVCL 400
    NGLCLQGEIK NGEYVKQFDA QLGSTYGIEF KVADGESQFI TDKSVTFENK 450
    QCGSTGTPGG GDNGSGGDNG GDNGSGGDNG SGGGTDPSQC SADFGYNYRS 500
    DTEIEVFHKD LGWSASWNYI CLDDYCVPGD KSGDSYNRSF NATLGSDYKI 550
    TFKVEDSASQ FITEKNITFV NTSCAQ 576
    Length:576
    Mass (Da):62,591
    Last modified:July 13, 2010 - v1
    Checksum:iE04449C5F703884D
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB121027 Genomic DNA. Translation: BAD51934.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB121027 Genomic DNA. Translation: BAD51934.1 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2DDX X-ray 0.86 A 23-349 [» ]
    3VPL X-ray 1.20 A 23-349 [» ]
    ProteinModelPortali D5MP61.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei D5MP61.

    Family and domain databases

    Gene3Di 3.20.20.80. 1 hit.
    InterProi IPR021016. Beta-xylanase.
    IPR013781. Glyco_hydro_catalytic_dom.
    IPR017853. Glycoside_hydrolase_SF.
    [Graphical view ]
    Pfami PF11606. AlcCBM31. 2 hits.
    [Graphical view ]
    SUPFAMi SSF51445. SSF51445. 1 hit.
    ProtoNeti Search...

    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: October 1, 2014
    This is version 16 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