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Protein

Endo-1,4-beta-xylanase A

Gene

xynA1

Organism
Paenibacillus sp. (strain JDR-2)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the depolymerization of methylglucuronoxylan (MeGAXn), a beta-1,4 xylan in which 10% to 20% of the xylose residues are substituted with alpha-1,2-4-O-methylglucuronate (MeGA) residues, which is predominant in hemicellulose fractions of hardwood and crop residues. Generates xylobiose (X2) and aldotetrauronate (MeGAX3) as the predominant products of MeGAXn hydrolysis; these products are then directly assimilated by the bacterium for subsequent metabolism. Thus, allows the bacterium to efficiently use polymeric MeGAXn as a growth substrate.1 Publication

Catalytic activityi

Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.1 Publication

Kineticsi

    1. Vmax=8.0 µmol/min/mg enzyme with sweet gum methylglucuronoxylan as substrate1 Publication

    pH dependencei

    Optimum pH is 6.5 with sweet gum methylglucuronoxylan as substrate.1 Publication

    Temperature dependencei

    Optimum temperature is 45 degrees Celsius with sweet gum methylglucuronoxylan as substrate.1 Publication

    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)DescriptionActionsGraphical viewLength
    Active sitei651Proton donorBy similarity1
    Active sitei706By similarity1
    Active sitei775NucleophilePROSITE-ProRule annotation1

    GO - Molecular functioni

    • carbohydrate binding Source: InterPro
    • endo-1,4-beta-xylanase activity Source: UniProtKB

    GO - Biological processi

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

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism, Polysaccharide degradation, Xylan degradation

    Enzyme and pathway databases

    UniPathwayiUPA00114.

    Protein family/group databases

    CAZyiCBM22. Carbohydrate-Binding Module Family 22.
    CBM9. Carbohydrate-Binding Module Family 9.
    GH10. Glycoside Hydrolase Family 10.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Endo-1,4-beta-xylanase A (EC:3.2.1.8)
    Alternative name(s):
    1,4-beta-D-xylan xylanohydrolase A
    Gene namesi
    Name:xynA1
    Synonyms:xynA
    Ordered Locus Names:Pjdr2_0221
    OrganismiPaenibacillus sp. (strain JDR-2)
    Taxonomic identifieri324057 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesPaenibacillaceaePaenibacillus
    Proteomesi
    • UP000002510 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    • cell wall Source: UniProtKB
    • extracellular region Source: UniProtKB-KW
    Complete GO annotation...

    Keywords - Cellular componenti

    Cell wall, Secreted

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 30Sequence analysisAdd BLAST30
    ChainiPRO_500048460931 – 1462Endo-1,4-beta-xylanase AAdd BLAST1432

    Interactioni

    Protein-protein interaction databases

    STRINGi324057.Pjdr2_0221.

    Structurei

    Secondary structure

    11462
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi520 – 523Combined sources4
    Turni524 – 527Combined sources4
    Beta strandi529 – 534Combined sources6
    Helixi536 – 539Combined sources4
    Helixi541 – 550Combined sources10
    Beta strandi552 – 558Combined sources7
    Helixi562 – 565Combined sources4
    Helixi575 – 586Combined sources12
    Beta strandi590 – 597Combined sources8
    Beta strandi599 – 601Combined sources3
    Helixi604 – 606Combined sources3
    Beta strandi608 – 610Combined sources3
    Beta strandi616 – 618Combined sources3
    Helixi621 – 639Combined sources19
    Helixi640 – 642Combined sources3
    Beta strandi643 – 650Combined sources8
    Helixi664 – 666Combined sources3
    Helixi671 – 676Combined sources6
    Helixi680 – 694Combined sources15
    Beta strandi701 – 707Combined sources7
    Helixi712 – 732Combined sources21
    Turni733 – 735Combined sources3
    Beta strandi741 – 744Combined sources4
    Beta strandi747 – 749Combined sources3
    Helixi754 – 765Combined sources12
    Turni766 – 768Combined sources3
    Beta strandi770 – 779Combined sources10
    Helixi787 – 807Combined sources21
    Helixi808 – 811Combined sources4
    Beta strandi812 – 817Combined sources6
    Helixi822 – 824Combined sources3
    Helixi828 – 830Combined sources3
    Beta strandi833 – 835Combined sources3
    Helixi843 – 849Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3RDKX-ray1.49A/B518-851[»]
    3RO8X-ray1.34A/B/C/D/E/F/G/H518-851[»]
    4E4PX-ray1.92A/B518-851[»]
    ProteinModelPortaliC6CRV0.
    SMRiC6CRV0.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini64 – 165CBM-cenC 1Add BLAST102
    Domaini207 – 319CBM-cenC 2Add BLAST113
    Domaini360 – 490CBM-cenC 3Add BLAST131
    Domaini514 – 851GH10PROSITE-ProRule annotationAdd BLAST338
    Domaini1279 – 1342SLH 1PROSITE-ProRule annotationAdd BLAST64
    Domaini1345 – 1404SLH 2PROSITE-ProRule annotationAdd BLAST60
    Domaini1407 – 1462SLH 3PROSITE-ProRule annotationAdd BLAST56

    Compositional bias

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Compositional biasi186 – 191Poly-Thr6

    Sequence similaritiesi

    Contains 1 GH10 (glycosyl hydrolase family 10) domain.PROSITE-ProRule annotation
    Contains 3 SLH (S-layer homology) domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat, Signal

    Phylogenomic databases

    eggNOGiENOG4105D9F. Bacteria.
    COG3693. LUCA.
    HOGENOMiHOG000049670.
    KOiK01181.
    OMAiNDYNEDN.
    OrthoDBiPOG091H0Y2G.

    Family and domain databases

    Gene3Di2.60.120.260. 3 hits.
    2.60.40.1190. 1 hit.
    3.20.20.80. 1 hit.
    InterProiIPR010502. Carb-bd_dom_fam9.
    IPR003305. CenC_carb-bd.
    IPR008979. Galactose-bd-like.
    IPR001000. GH10.
    IPR031158. GH10_AS.
    IPR013781. Glyco_hydro_catalytic_dom.
    IPR017853. Glycoside_hydrolase_SF.
    IPR001119. SLH_dom.
    [Graphical view]
    PfamiPF06452. CBM9_1. 1 hit.
    PF02018. CBM_4_9. 2 hits.
    PF00331. Glyco_hydro_10. 1 hit.
    PF00395. SLH. 3 hits.
    [Graphical view]
    PRINTSiPR00134. GLHYDRLASE10.
    SMARTiSM00633. Glyco_10. 1 hit.
    [Graphical view]
    SUPFAMiSSF49785. SSF49785. 3 hits.
    SSF51445. SSF51445. 1 hit.
    PROSITEiPS00591. GH10_1. 1 hit.
    PS51760. GH10_2. 1 hit.
    PS51272. SLH. 3 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    C6CRV0-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSRSLKKFVS ILLAAALLIP IGRLAPVAEA AENPTIVYHE DFAIDKGKAI
    60 70 80 90 100
    QSGGASLTQV TGKVFDGNND GSALYVSNRA NTWDAADFKF ADIGLQNGKT
    110 120 130 140 150
    YTVTVKGYVD QDATVPSGAQ AFLQAVDSNN YGFLASANFA AGTAFTLTKE
    160 170 180 190 200
    FTVDTSVSTQ LRVQSSEEGK AVPFYIGDIL ITANPTTTTN TVYHEDFATD
    210 220 230 240 250
    KGKAVQSGGA NLAQVADKVF DGNDDGKALY VSNRANTWDA ADFKFADIGL
    260 270 280 290 300
    QNGKTYTVTV KGYVDQDATV PSGAQAFLQA VDSNNYGFLA SANFAARSAF
    310 320 330 340 350
    TLTKEFTVDT SVSTQLRVQS SEEGKAVPFY IGDILITETV NSGGGQEDPP
    360 370 380 390 400
    RPPALPFNTI TFEDQTAGGF TGRAGTETLT VTNESNHTAD GSYSLKVEGR
    410 420 430 440 450
    TTSWHGPSLR VEKYVDKGYE YKVTAWVKLL SPETSTKLEL ASQVGDGGSA
    460 470 480 490 500
    NYPSLASKTI TAADGWVQLQ GNYRYNSVGG EYLTIYVQSS NATASYYIDD
    510 520 530 540 550
    ISFESTGSGP VGIQKDLAPL KDVYKNDFLI GNAISAEDLE GTRLELLKMH
    560 570 580 590 600
    HDVVTAGNAM KPDALQPTKG NFTFTAADAM IDKVLAEGMK MHGHVLVWHQ
    610 620 630 640 650
    QSPAWLNTKK DDNNNTVPLG RDEALDNLRT HIQTVMKHFG NKVISWDVVN
    660 670 680 690 700
    EAMNDNPSNP ADYKASLRQT PWYQAIGSDY VEQAFLAARE VLDENPSWNI
    710 720 730 740 750
    KLYYNDYNED NQNKATAIYN MVKDINDRYA AAHNGKLLID GVGMQGHYNI
    760 770 780 790 800
    NTNPDNVKLS LEKFISLGVE VSVSELDVTA GNNYTLPENL AVGQAYLYAQ
    810 820 830 840 850
    LFKLYKEHAD HIARVTFWGM DDNTSWRAEN NPLLFDKNLQ AKPAYYGVID
    860 870 880 890 900
    PDKYMEEHAP ESKDANQAEA QYGTPVIDGT VDSIWSNAQA MPVNRYQMAW
    910 920 930 940 950
    QGATGTAKAL WDDQNLYVLI QVSDSQLNKA NENAWEQDSV EVFLDQNNGK
    960 970 980 990 1000
    TTFYQNDDGQ YRVNFDNETS FSPASIAAGF ESQTKKTANS YTVELKIPLT
    1010 1020 1030 1040 1050
    AVTPANQKKL GFDVQINDAT DGARTSVAAW NDTTGNGYQD TSVYGELTLA
    1060 1070 1080 1090 1100
    GKGTGGTGTV GTTVPQTGNV VKNPDGSTTL KPEVKTTNGN AVGTVTGDDL
    1110 1120 1130 1140 1150
    KKALDQAAPA AGGKKQVIID VPLQANAATY AVQLPTQSLK SQDGYQLTAK
    1160 1170 1180 1190 1200
    IANAFIQIPS NMLANTNVTT DQVSIRVAKA SLDNVDAATR ELIGNRPVID
    1210 1220 1230 1240 1250
    LSLVAGGNVI AWNNPTAPVT VAVPYAPTAE ELKHPEHILI WYIDGSGKAT
    1260 1270 1280 1290 1300
    PVPNSRYDAA LGAVVFQTTH FSTYAAVSVF TTFGDLAKVP WAKEAIDAMA
    1310 1320 1330 1340 1350
    SRGVIKGTGE NTFSPAASIK RADFIALLVR ALELHGTGTT DTAMFSDVPA
    1360 1370 1380 1390 1400
    NAYYYNELAV AKQLGIATGF EDNTFKPDSS ISRQDMMVLT TRALAVLGKQ
    1410 1420 1430 1440 1450
    LPAGGSLNAF SDAASVAGYA QDSVAALVKA GVVQGSGSKL APNDQLTRAE
    1460
    AAVILYRIWK LQ
    Length:1,462
    Mass (Da):157,322
    Last modified:September 1, 2009 - v1
    Checksum:iAE29664CDEA3BF3E
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti313S → T in CAI79477 (PubMed:16461704).Curated1
    Sequence conflicti454 – 461SLASKTIT → TPTTQAWQARRLP in CAI79477 (PubMed:16461704).Curated8

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ938162 Genomic DNA. Translation: CAI79477.1.
    CP001656 Genomic DNA. Translation: ACS98901.1.
    RefSeqiWP_012772223.1. NC_012914.1.

    Genome annotation databases

    EnsemblBacteriaiACS98901; ACS98901; Pjdr2_0221.
    KEGGipjd:Pjdr2_0221.
    PATRICi22830917. VBIPaeSp118865_0225.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ938162 Genomic DNA. Translation: CAI79477.1.
    CP001656 Genomic DNA. Translation: ACS98901.1.
    RefSeqiWP_012772223.1. NC_012914.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3RDKX-ray1.49A/B518-851[»]
    3RO8X-ray1.34A/B/C/D/E/F/G/H518-851[»]
    4E4PX-ray1.92A/B518-851[»]
    ProteinModelPortaliC6CRV0.
    SMRiC6CRV0.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi324057.Pjdr2_0221.

    Protein family/group databases

    CAZyiCBM22. Carbohydrate-Binding Module Family 22.
    CBM9. Carbohydrate-Binding Module Family 9.
    GH10. Glycoside Hydrolase Family 10.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiACS98901; ACS98901; Pjdr2_0221.
    KEGGipjd:Pjdr2_0221.
    PATRICi22830917. VBIPaeSp118865_0225.

    Phylogenomic databases

    eggNOGiENOG4105D9F. Bacteria.
    COG3693. LUCA.
    HOGENOMiHOG000049670.
    KOiK01181.
    OMAiNDYNEDN.
    OrthoDBiPOG091H0Y2G.

    Enzyme and pathway databases

    UniPathwayiUPA00114.

    Family and domain databases

    Gene3Di2.60.120.260. 3 hits.
    2.60.40.1190. 1 hit.
    3.20.20.80. 1 hit.
    InterProiIPR010502. Carb-bd_dom_fam9.
    IPR003305. CenC_carb-bd.
    IPR008979. Galactose-bd-like.
    IPR001000. GH10.
    IPR031158. GH10_AS.
    IPR013781. Glyco_hydro_catalytic_dom.
    IPR017853. Glycoside_hydrolase_SF.
    IPR001119. SLH_dom.
    [Graphical view]
    PfamiPF06452. CBM9_1. 1 hit.
    PF02018. CBM_4_9. 2 hits.
    PF00331. Glyco_hydro_10. 1 hit.
    PF00395. SLH. 3 hits.
    [Graphical view]
    PRINTSiPR00134. GLHYDRLASE10.
    SMARTiSM00633. Glyco_10. 1 hit.
    [Graphical view]
    SUPFAMiSSF49785. SSF49785. 3 hits.
    SSF51445. SSF51445. 1 hit.
    PROSITEiPS00591. GH10_1. 1 hit.
    PS51760. GH10_2. 1 hit.
    PS51272. SLH. 3 hits.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiXYNA1_PAESJ
    AccessioniPrimary (citable) accession number: C6CRV0
    Secondary accession number(s): Q53I45
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 31, 2011
    Last sequence update: September 1, 2009
    Last modified: November 2, 2016
    This is version 51 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, Complete proteome, Reference proteome

    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

    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.