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Protein

Exo-1,4-beta-xylosidase xlnD

Gene

xlnD

Organism
Aspergillus niger
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Xylan 1,4-beta-xylosidase involved in the hydrolysis of xylan, a major structural heterogeneous polysaccharide found in plant biomass representing the second most abundant polysaccharide in the biosphere, after cellulose.3 Publications

Catalytic activityi

Hydrolysis of (1->4)-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini.

Kineticsi

  1. KM=255 µM for pNP-beta-D-xylopyranoside2 Publications

    pH dependencei

    Optimum pH is 3.2.2 Publications

    Temperature dependencei

    Optimum temperature is 60 degrees Celsius. Has a high thermal denaturation point. The Tmax of the protein was estimated to be 78.2 degrees Celsius.2 Publications

    Pathwayi: xylan degradation

    This protein is involved in the pathway xylan degradation, which is part of Glycan degradation.
    View all proteins of this organism that are known to be involved in the pathway xylan degradation and in Glycan degradation.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei315 – 3151By similarity

    GO - Molecular functioni

    GO - Biological processi

    • xylan catabolic process Source: CACAO
    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism, Polysaccharide degradation, Xylan degradation

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16902.
    BRENDAi3.2.1.37. 518.
    UniPathwayiUPA00114.

    Protein family/group databases

    CAZyiGH3. Glycoside Hydrolase Family 3.
    mycoCLAPiXYL3D_ASPNG.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exo-1,4-beta-xylosidase xlnD (EC:3.2.1.37)
    Alternative name(s):
    1,4-beta-D-xylan xylohydrolase xlnD
    Beta-xylosidase A
    Beta-xylosidase xlnD
    Xylobiase xlnD
    Gene namesi
    Name:xlnD
    Synonyms:xylA
    OrganismiAspergillus niger
    Taxonomic identifieri5061 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaPezizomycotinaEurotiomycetesEurotiomycetidaeEurotialesAspergillaceaeAspergillus

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Secreted

    Pathology & Biotechi

    Protein family/group databases

    Allergomei3129. Asp n 14.0101.
    82. Asp n 14.

    Chemistry

    ChEMBLiCHEMBL4728.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2626Sequence analysisAdd
    BLAST
    Chaini27 – 804778Exo-1,4-beta-xylosidase xlnDPRO_0000393290Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi29 – 291N-linked (GlcNAc...)Sequence analysis
    Glycosylationi124 – 1241N-linked (GlcNAc...)Sequence analysis
    Glycosylationi148 – 1481N-linked (GlcNAc...)Sequence analysis
    Glycosylationi242 – 2421N-linked (GlcNAc...)Sequence analysis
    Glycosylationi251 – 2511N-linked (GlcNAc...)Sequence analysis
    Glycosylationi357 – 3571N-linked (GlcNAc...)Sequence analysis
    Glycosylationi390 – 3901N-linked (GlcNAc...)Sequence analysis
    Glycosylationi413 – 4131N-linked (GlcNAc...)Sequence analysis
    Glycosylationi444 – 4441N-linked (GlcNAc...)Sequence analysis
    Glycosylationi455 – 4551N-linked (GlcNAc...)Sequence analysis
    Glycosylationi573 – 5731N-linked (GlcNAc...)Sequence analysis
    Glycosylationi576 – 5761N-linked (GlcNAc...)Sequence analysis
    Glycosylationi665 – 6651N-linked (GlcNAc...)Sequence analysis
    Glycosylationi696 – 6961N-linked (GlcNAc...)Sequence analysis
    Glycosylationi718 – 7181N-linked (GlcNAc...)Sequence analysis

    Keywords - PTMi

    Glycoprotein

    Proteomic databases

    PaxDbiO00089.

    Expressioni

    Inductioni

    Expression is under the control of the xylanolytic transcriptional activator xlnR and the repressor creA.2 Publications

    Interactioni

    Protein-protein interaction databases

    STRINGi5061.CADANGAP00000967.

    Chemistry

    BindingDBiO00089.

    Structurei

    3D structure databases

    ProteinModelPortaliO00089.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the glycosyl hydrolase 3 family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiCOG1472. LUCA.

    Family and domain databases

    Gene3Di3.20.20.300. 1 hit.
    3.40.50.1700. 1 hit.
    InterProiIPR026891. Fn3-like.
    IPR026892. Glyco_hydro_3.
    IPR002772. Glyco_hydro_3_C.
    IPR001764. Glyco_hydro_3_N.
    IPR017853. Glycoside_hydrolase_SF.
    [Graphical view]
    PANTHERiPTHR30620. PTHR30620. 1 hit.
    PfamiPF14310. Fn3-like. 1 hit.
    PF00933. Glyco_hydro_3. 1 hit.
    PF01915. Glyco_hydro_3_C. 1 hit.
    [Graphical view]
    SMARTiSM01217. Fn3_like. 1 hit.
    [Graphical view]
    SUPFAMiSSF51445. SSF51445. 1 hit.
    SSF52279. SSF52279. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    O00089-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAHSMSRPVA ATAAALLALA LPQALAQANT SYVDYNIEAN PDLYPLCIET
    60 70 80 90 100
    IPLSFPDCQN GPLRSHLICD ETATPYDRAA SLISLFTLDE LIANTGNTGL
    110 120 130 140 150
    GVSRLGLPAY QVWSEALHGL DRANFSDSGA YNWATSFPQP ILTTAALNRT
    160 170 180 190 200
    LIHQIASIIS TQGRAFNNAG RYGLDVYAPN INTFRHPVWG RGQETPGEDV
    210 220 230 240 250
    SLAAVYAYEY ITGIQGPDPE SNLKLAATAK HYAGYDIENW HNHSRLGNDM
    260 270 280 290 300
    NITQQDLSEY YTPQFHVAAR DAKVQSVMCA YNAVNGVPAC ADSYFLQTLL
    310 320 330 340 350
    RDTFGFVDHG YVSSDCDAAY NIYNPHGYAS SQAAAAAEAI LAGTDIDCGT
    360 370 380 390 400
    TYQWHLNESI AAGDLSRDDI EQGVIRLYTT LVQAGYFDSN TTKANNPYRD
    410 420 430 440 450
    LSWSDVLETD AWNISYQAAT QGIVLLKNSN NVLPLTEKAY PPSNTTVALI
    460 470 480 490 500
    GPWANATTQL LGNYYGNAPY MISPRAAFEE AGYKVNFAEG TGISSTSTSG
    510 520 530 540 550
    FAAALSAAQS ADVIIYAGGI DNTLEAEALD RESIAWPGNQ LDLIQKLASA
    560 570 580 590 600
    AGKKPLIVLQ MGGGQVDSSS LKNNTNVSAL LWGGYPGQSG GFALRDIITG
    610 620 630 640 650
    KKNPAGRLVT TQYPASYAEE FPATDMNLRP EGDNPGQTYK WYTGEAVYEF
    660 670 680 690 700
    GHGLFYTTFA ESSSNTTTKE VKLNIQDILS QTHEDLASIT QLPVLNFTAN
    710 720 730 740 750
    IRNTGKLESD YTAMVFANTS DAGPAPYPKK WLVGWDRLGE VKVGETRELR
    760 770 780 790 800
    VPVEVGSFAR VNEDGDWVVF PGTFELALNL ERKVRVKVVL EGEEEVVLKW

    PGKE
    Length:804
    Mass (Da):87,211
    Last modified:January 1, 1998 - v2
    Checksum:i440D875498C79DF0
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti37 – 371I → V in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti72 – 721T → S in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti130 – 1301A → S in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti220 – 2201E → D in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti275 – 2751Q → H in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti285 – 2851N → D in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti361 – 3611A → T in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti372 – 3721Q → K in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti402 – 4021S → T in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti509 – 5091Q → R in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti550 – 5501A → S in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti553 – 5531K → S in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti578 – 5781S → T in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti685 – 6851D → E in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti702 – 7021R → K in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti729 – 7291K → V in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti740 – 7401E → D in AAD13106 (PubMed:11722900).Curated
    Sequence conflicti769 – 7691V → L in AAD13106 (PubMed:11722900).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z84377 Genomic DNA. Translation: CAB06417.1.
    AF108944 mRNA. Translation: AAD13106.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z84377 Genomic DNA. Translation: CAB06417.1.
    AF108944 mRNA. Translation: AAD13106.1.

    3D structure databases

    ProteinModelPortaliO00089.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi5061.CADANGAP00000967.

    Chemistry

    BindingDBiO00089.
    ChEMBLiCHEMBL4728.

    Protein family/group databases

    Allergomei3129. Asp n 14.0101.
    82. Asp n 14.
    CAZyiGH3. Glycoside Hydrolase Family 3.
    mycoCLAPiXYL3D_ASPNG.

    Proteomic databases

    PaxDbiO00089.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Phylogenomic databases

    eggNOGiCOG1472. LUCA.

    Enzyme and pathway databases

    UniPathwayiUPA00114.
    BioCyciMetaCyc:MONOMER-16902.
    BRENDAi3.2.1.37. 518.

    Family and domain databases

    Gene3Di3.20.20.300. 1 hit.
    3.40.50.1700. 1 hit.
    InterProiIPR026891. Fn3-like.
    IPR026892. Glyco_hydro_3.
    IPR002772. Glyco_hydro_3_C.
    IPR001764. Glyco_hydro_3_N.
    IPR017853. Glycoside_hydrolase_SF.
    [Graphical view]
    PANTHERiPTHR30620. PTHR30620. 1 hit.
    PfamiPF14310. Fn3-like. 1 hit.
    PF00933. Glyco_hydro_3. 1 hit.
    PF01915. Glyco_hydro_3_C. 1 hit.
    [Graphical view]
    SMARTiSM01217. Fn3_like. 1 hit.
    [Graphical view]
    SUPFAMiSSF51445. SSF51445. 1 hit.
    SSF52279. SSF52279. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "beta-Xylosidase activity, encoded by xlnD, is essential for complete hydrolysis of xylan by Aspergillus niger but not for induction of the xylanolytic enzyme spectrum."
      van Peij N.N., Brinkmann J., Vrsanska M., Visser J., de Graaff L.H.
      Eur. J. Biochem. 245:164-173(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
    2. "Degradation of xylan to D-xylose by recombinant Saccharomyces cerevisiae coexpressing the Aspergillus niger beta-xylosidase (xlnD) and the Trichoderma reesei xylanase II (xyn2) genes."
      La Grange D.C., Pretorius I.S., Claeyssens M., van Zyl W.H.
      Appl. Environ. Microbiol. 67:5512-5519(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: ATCC 90196 / Alo MP-22.
    3. "The transcriptional activator XlnR regulates both xylanolytic and endoglucanase gene expression in Aspergillus niger."
      van Peij N.N., Gielkens M.M., de Vries R.P., Visser J., de Graaff L.H.
      Appl. Environ. Microbiol. 64:3615-3619(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    4. "CreA modulates the XlnR-induced expression on xylose of Aspergillus niger genes involved in xylan degradation."
      de Vries R.P., Visser J., de Graaff L.H.
      Res. Microbiol. 150:281-285(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    5. "Heterologous expression of Aspergillus niger beta-D-xylosidase (XlnD): characterization on lignocellulosic substrates."
      Selig M.J., Knoshaug E.P., Decker S.R., Baker J.O., Himmel M.E., Adney W.S.
      Appl. Biochem. Biotechnol. 146:57-68(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, IDENTIFICATION BY MASS SPECTROMETRY.

    Entry informationi

    Entry nameiXYND_ASPNG
    AccessioniPrimary (citable) accession number: O00089
    Secondary accession number(s): O93933
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 23, 2010
    Last sequence update: January 1, 1998
    Last modified: May 11, 2016
    This is version 79 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Documents

    1. Glycosyl hydrolases
      Classification of glycosyl hydrolase families and list of entries
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    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.