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Protein

Endo-1,4-beta-xylanase B

Gene

xynB

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

Functioni

Plays a role in plant xylan biodegradation, probably via the hydrolysis of short xylooligosaccharides resulting from extracellular xylan hydrolysis, once they have been transported inside cells. Shows similar activity on xylans of different rate of arabinose or methylglucuronic substitution. Also displays high activity on aryl-xylosides. Is active on xylotetraose and xylotriose, but does not hydrolyze xylobiose, indicating that XynB is a xylanase and not a beta-xylosidase.2 Publications

Catalytic activityi

Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.2 Publications

Enzyme regulationi

Completely inhibited by Ag2+, Cu2+, Hg2+, Mn2+, Pb2+ and Sn2+. Strongly inhibited by Fe2+ and Zn2+. Co2+ and Ni2+ cause little inhibition while Ca2+ and Mg2+ do not affect enzyme activity, and Ba2+ produces a small stimulating effect. Irreversibly inactivated by SDS in vitro.1 Publication

pH dependencei

Optimum pH is 5.5. Shows more than 75% of maximum activity from pH 5 to 10. Is still active at pH 12.1 Publication

Temperature dependencei

Optimum temperature is 50 degrees Celsius. Loses 100% activity after incubation for 15 minutes at 50 degrees Celsius.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei134 – 1341Proton donorBy similarity
Active sitei241 – 2411NucleophileBy similarity

GO - Molecular functioni

  1. endo-1,4-beta-xylanase activity Source: UniProtKB-EC

GO - Biological processi

  1. xylan catabolic process Source: UniProtKB-UniPathway
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

CAZyiGH10. Glycoside Hydrolase Family 10.

Names & Taxonomyi

Protein namesi
Recommended name:
Endo-1,4-beta-xylanase B (EC:3.2.1.8)
Short name:
Xylanase B
Alternative name(s):
1,4-beta-D-xylan xylanohydrolase B
Gene namesi
Name:xynB
OrganismiPaenibacillus barcinonensis
Taxonomic identifieri198119 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesPaenibacillaceaePaenibacillus

Subcellular locationi

Cytoplasm 1 Publication
Note: Is not secreted to the medium but instead remains cell-associated, in the soluble fraction, even in late stationary-phase cultures.

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 332331Endo-1,4-beta-xylanase BPRO_0000366196Add
BLAST

Structurei

Secondary structure

1
332
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi10 – 123Combined sources
Turni13 – 153Combined sources
Beta strandi17 – 226Combined sources
Helixi24 – 3714Combined sources
Beta strandi39 – 457Combined sources
Helixi49 – 524Combined sources
Beta strandi54 – 574Combined sources
Helixi62 – 7211Combined sources
Turni73 – 753Combined sources
Beta strandi77 – 804Combined sources
Beta strandi86 – 883Combined sources
Helixi91 – 944Combined sources
Beta strandi99 – 1013Combined sources
Helixi104 – 12118Combined sources
Turni122 – 1254Combined sources
Beta strandi127 – 1337Combined sources
Helixi148 – 1525Combined sources
Helixi157 – 16812Combined sources
Beta strandi172 – 1809Combined sources
Helixi184 – 19916Combined sources
Beta strandi206 – 2094Combined sources
Beta strandi212 – 2143Combined sources
Helixi220 – 23112Combined sources
Turni232 – 2343Combined sources
Beta strandi236 – 24712Combined sources
Helixi261 – 28020Combined sources
Turni281 – 2844Combined sources
Beta strandi285 – 29410Combined sources
Helixi299 – 3013Combined sources
Beta strandi302 – 3054Combined sources
Beta strandi313 – 3153Combined sources
Helixi323 – 3286Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EMCX-ray2.10A2-332[»]
3EMQX-ray2.73A2-332[»]
3EMZX-ray2.08A2-332[»]
ProteinModelPortaliO69231.
SMRiO69231. Positions 2-330.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO69231.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di3.20.20.80. 1 hit.
InterProiIPR001000. Glyco_hydro_10.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PfamiPF00331. Glyco_hydro_10. 1 hit.
[Graphical view]
PRINTSiPR00134. GLHYDRLASE10.
SMARTiSM00633. Glyco_10. 1 hit.
[Graphical view]
SUPFAMiSSF51445. SSF51445. 1 hit.

Sequencei

Sequence statusi: Complete.

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

O69231-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTEIPSLSA SYANSFKIGA AVHTRMLQTE GEFIAKHYNS VTAENQMKFE
60 70 80 90 100
EVHPREHEYT FEAADEIVDF AVARGIGVRG HTLVWHNQTP AWMFEDASGG
110 120 130 140 150
TASREMMLSR LKQHIDTVVG RYKDQIYAWD VVNEAIEDKT DLIMRDTKWL
160 170 180 190 200
RLLGEDYLVQ AFNMAHEADP NALLFYNDYN ETDPVKREKI YNLVRSLLDQ
210 220 230 240 250
GAPVHGIGMQ GHWNIHGPSM DEIRQAIERY ASLDVQLHVT ELDLSVFRHE
260 270 280 290 300
DQRTDLTEPT AEMAELQQKR YEDIFGLFRE YRSNITSVTF WGVADNYTWL
310 320 330
DNFPVRGRKN WPFVFDTELQ PKDSFWRIIG QD
Length:332
Mass (Da):38,561
Last modified:July 31, 1998 - v1
Checksum:iDDEF7BCF17C8A72E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ006646 Genomic DNA. Translation: CAA07174.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ006646 Genomic DNA. Translation: CAA07174.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EMCX-ray2.10A2-332[»]
3EMQX-ray2.73A2-332[»]
3EMZX-ray2.08A2-332[»]
ProteinModelPortaliO69231.
SMRiO69231. Positions 2-330.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

CAZyiGH10. Glycoside Hydrolase Family 10.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00114.

Miscellaneous databases

EvolutionaryTraceiO69231.

Family and domain databases

Gene3Di3.20.20.80. 1 hit.
InterProiIPR001000. Glyco_hydro_10.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PfamiPF00331. Glyco_hydro_10. 1 hit.
[Graphical view]
PRINTSiPR00134. GLHYDRLASE10.
SMARTiSM00633. Glyco_10. 1 hit.
[Graphical view]
SUPFAMiSSF51445. SSF51445. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Characterization of a Paenibacillus cell-associated xylanase with high activity on aryl-xylosides: a new subclass of family 10 xylanases."
    Gallardo O., Diaz P., Pastor F.I.J.
    Appl. Microbiol. Biotechnol. 61:226-233(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-11, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, SUBCELLULAR LOCATION.
    Strain: DSM 15478 / CECT 7022 / BP-23.
  2. "Cloning of a Bacillus sp. BP-23 gene encoding a xylanase with high activity against aryl xylosides."
    Blanco A., Diaz P., Martinez J., Lopez O., Soler C., Pastor F.I.J.
    FEMS Microbiol. Lett. 137:285-290(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: DSM 15478 / CECT 7022 / BP-23.

Entry informationi

Entry nameiXYNB_PAEBA
AccessioniPrimary (citable) accession number: O69231
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 2, 2009
Last sequence update: July 31, 1998
Last modified: January 6, 2015
This is version 59 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, Direct protein sequencing

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

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.