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Protein

Endo-beta-1,4-xylanase Xyn10C

Gene

xyn10C

Organism
Cellvibrio japonicus (Pseudomonas fluorescens subsp. cellulosa)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Endo-acting xylanase which specifically cleaves internal linkages on the xylan backbone, releasing xylooligosaccharides. Is able to hydrolyze oat spelt xylan, the arabinoxylans from wheat and rye, and glucuronoxylan. Also displays very low activity against xylooligosaccharides. During the xylan degradation process, Xyn10C may act on the soluble xylans and long xylooligosaccharides products released by the secreted xylanases Xyn11A, Xyn11B and Xyn10A.2 Publications

Catalytic activityi

Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.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
Binding sitei106 – 1061Carbohydrate
Binding sitei171 – 1711Carbohydrate
Binding sitei217 – 2171Carbohydrate
Binding sitei332 – 3321Substrate
Binding sitei384 – 3841Substrate
Active sitei385 – 3851Proton donorBy similarity
Active sitei497 – 4971Nucleophile1 Publication
Binding sitei552 – 5521Substrate

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Carbohydrate metabolism, Polysaccharide degradation, Xylan degradation

Enzyme and pathway databases

BRENDAi3.2.1.8. 5103.
UniPathwayiUPA00114.

Protein family/group databases

CAZyiCBM15. Carbohydrate-Binding Module Family 15.
GH10. Glycoside Hydrolase Family 10.

Names & Taxonomyi

Protein namesi
Recommended name:
Endo-beta-1,4-xylanase Xyn10C (EC:3.2.1.8)
Short name:
Xylanase 10C
Alternative name(s):
XYLF
Gene namesi
Name:xyn10C
Synonyms:xynF
OrganismiCellvibrio japonicus (Pseudomonas fluorescens subsp. cellulosa)
Taxonomic identifieri155077 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaCellvibrionalesCellvibrionaceaeCellvibrio

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell outer membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi340 – 3401Y → A: Significantly reduces the catalytic activity against xylotetraose and xylan. Also modifies the cleavage pattern of xylotetraose. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1919PROSITE-ProRule annotationAdd
BLAST
Chaini20 – 606587Endo-beta-1,4-xylanase Xyn10CPRO_5000147609Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi20 – 201N-palmitoyl cysteinePROSITE-ProRule annotation
Lipidationi20 – 201S-diacylglycerol cysteinePROSITE-ProRule annotation
Disulfide bondi183 ↔ 200PROSITE-ProRule annotation1 Publication

Keywords - PTMi

Disulfide bond, Lipoprotein, Palmitate

Expressioni

Inductioni

Induced when the bacterium is cultured on xylan or beta-glucan but not on medium containing mannan. Is repressed by glucose.1 Publication

Interactioni

Protein-protein interaction databases

STRINGi498211.CJA_3066.

Structurei

Secondary structure

1
606
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi92 – 965Combined sources
Beta strandi99 – 1024Combined sources
Beta strandi104 – 1074Combined sources
Beta strandi109 – 1113Combined sources
Beta strandi117 – 1193Combined sources
Beta strandi122 – 1265Combined sources
Beta strandi132 – 1387Combined sources
Beta strandi140 – 1434Combined sources
Beta strandi148 – 1558Combined sources
Helixi157 – 1626Combined sources
Beta strandi165 – 1728Combined sources
Beta strandi175 – 1806Combined sources
Helixi187 – 1893Combined sources
Beta strandi192 – 1943Combined sources
Beta strandi196 – 2016Combined sources
Beta strandi210 – 2134Combined sources
Beta strandi216 – 22510Combined sources
Beta strandi228 – 24215Combined sources
Helixi251 – 2544Combined sources
Beta strandi256 – 2583Combined sources
Beta strandi261 – 2666Combined sources
Turni271 – 2733Combined sources
Turni275 – 2773Combined sources
Helixi279 – 28810Combined sources
Beta strandi290 – 2967Combined sources
Helixi300 – 3034Combined sources
Helixi313 – 32412Combined sources
Beta strandi328 – 3358Combined sources
Helixi339 – 3413Combined sources
Helixi344 – 3474Combined sources
Helixi353 – 37422Combined sources
Beta strandi379 – 3857Combined sources
Beta strandi389 – 3924Combined sources
Helixi401 – 4055Combined sources
Helixi412 – 42312Combined sources
Beta strandi427 – 4359Combined sources
Helixi441 – 45515Combined sources
Beta strandi462 – 4654Combined sources
Beta strandi468 – 4725Combined sources
Helixi476 – 48712Combined sources
Turni488 – 4903Combined sources
Beta strandi492 – 50312Combined sources
Turni508 – 5136Combined sources
Helixi520 – 54021Combined sources
Helixi543 – 5453Combined sources
Beta strandi546 – 5527Combined sources
Helixi556 – 5583Combined sources
Helixi560 – 5645Combined sources
Turni565 – 5717Combined sources
Beta strandi578 – 5803Combined sources
Helixi588 – 59811Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GNYX-ray1.63A91-243[»]
1US2X-ray1.85A86-606[»]
1US3X-ray1.85A86-606[»]
ProteinModelPortaliQ59675.
SMRiQ59675. Positions 95-606.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ59675.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini91 – 242152CBM15PROSITE-ProRule annotationAdd
BLAST
Domaini245 – 596352GH10PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni296 – 2994Substrate binding

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi33 – 8957Ser-richAdd
BLAST

Domaini

The N-terminal CBM15 domain binds xylan, including decorated xylans and xylooligosaccharides, but the physiological role of this domain is unclear. It may act as a product capture system: large xylooligosaccharides generated by Xyn10C would bind to CBM15 and this would restrict the diffusion of these polymers into the environment and therefore increase the selective utilization of these molecules by C.japonicus. Xylanase activity resides in the C-terminal domain.3 Publications

Sequence similaritiesi

Contains 1 CBM15 (carbohydrate binding type-15) domain.PROSITE-ProRule annotationCurated
Contains 1 GH10 (glycosyl hydrolase family 10) domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105D9F. Bacteria.
COG3693. LUCA.

Family and domain databases

Gene3Di2.60.120.260. 1 hit.
3.20.20.80. 1 hit.
InterProiIPR005088. CBM_fam15.
IPR008979. Galactose-bd-like.
IPR001000. GH10.
IPR031158. GH10_AS.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PfamiPF03426. CBM_15. 1 hit.
PF00331. Glyco_hydro_10. 1 hit.
[Graphical view]
PRINTSiPR00134. GLHYDRLASE10.
SMARTiSM00633. Glyco_10. 1 hit.
[Graphical view]
SUPFAMiSSF49785. SSF49785. 1 hit.
SSF51445. SSF51445. 1 hit.
PROSITEiPS51759. CBM15. 1 hit.
PS00591. GH10_1. 1 hit.
PS51760. GH10_2. 1 hit.
PS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q59675-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKIQQLLML SLISSTLIAC GGGGGGGSTP TTSSSPQSSS PASTPSSASS
60 70 80 90 100
SSIISSSSLS SSLSSSSLSS SSLSSSSASS VSSSSVAASE GNVVIEVDMA
110 120 130 140 150
NGWRGNASGS TSHSGITYSA DGVTFAALGD GVGAVFDIAR PTTLEDAVIA
160 170 180 190 200
MVVNVSAEFK ASEANLQIFA QLKEDWSKGE WDCLAASSEL TADTDLTLTC
210 220 230 240 250
TIDEDDDKFN QTARDVQVGI QAKGTPAGTI TIKSVTITLA QEAYSANVDH
260 270 280 290 300
LRDLAPSDFP IGVAVSNTDS ATYNLLTNSR EQAVVKKHFN HLTAGNIMKM
310 320 330 340 350
SYMQPTEGNF NFTNADAFVD WATENNMTVH GHALVWHSDY QVPNFMKNWA
360 370 380 390 400
GSAEDFLAAL DTHITTIVDH YEAKGNLVSW DVVNEAIDDN SPANFRTTDS
410 420 430 440 450
AFYVKSGNSS VYIERAFQTA RAADPAVILY YNDYNIEQNN AKTTKMVDMV
460 470 480 490 500
KDFQARSIPI DGVGFQMHVC MNYPSIANIS AAMKKVVDLG LLVKITELDV
510 520 530 540 550
AVNQPHCDAY PANKINPLTE AAQLAQKKRY CDVVKAYLDT VPVNQRGGIS
560 570 580 590 600
VWGTTDANTW LDGLYREQFE DEKISWPLLF DNNYNDKPAL RGFADALIGT

QCTNTH
Length:606
Mass (Da):64,884
Last modified:March 1, 2004 - v2
Checksum:i56E149954CE6BFEE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48928 Genomic DNA. Translation: CAA88764.2.
PIRiS59634.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48928 Genomic DNA. Translation: CAA88764.2.
PIRiS59634.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GNYX-ray1.63A91-243[»]
1US2X-ray1.85A86-606[»]
1US3X-ray1.85A86-606[»]
ProteinModelPortaliQ59675.
SMRiQ59675. Positions 95-606.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi498211.CJA_3066.

Protein family/group databases

CAZyiCBM15. Carbohydrate-Binding Module Family 15.
GH10. Glycoside Hydrolase Family 10.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105D9F. Bacteria.
COG3693. LUCA.

Enzyme and pathway databases

UniPathwayiUPA00114.
BRENDAi3.2.1.8. 5103.

Miscellaneous databases

EvolutionaryTraceiQ59675.

Family and domain databases

Gene3Di2.60.120.260. 1 hit.
3.20.20.80. 1 hit.
InterProiIPR005088. CBM_fam15.
IPR008979. Galactose-bd-like.
IPR001000. GH10.
IPR031158. GH10_AS.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PfamiPF03426. CBM_15. 1 hit.
PF00331. Glyco_hydro_10. 1 hit.
[Graphical view]
PRINTSiPR00134. GLHYDRLASE10.
SMARTiSM00633. Glyco_10. 1 hit.
[Graphical view]
SUPFAMiSSF49785. SSF49785. 1 hit.
SSF51445. SSF51445. 1 hit.
PROSITEiPS51759. CBM15. 1 hit.
PS00591. GH10_1. 1 hit.
PS51760. GH10_2. 1 hit.
PS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Novel cellulose-binding domains, NodB homologues and conserved modular architecture in xylanases from the aerobic soil bacteria Pseudomonas fluorescens subsp. cellulosa and Cellvibrio mixtus."
    Millward-Sadler S.J., Davidson K., Hazlewood G.P., Black G.W., Gilbert H.J., Clarke J.H.
    Biochem. J. 312:39-48(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, DOMAIN.
    Strain: NCIMB 10462.
  2. Gilbert H.J.
    Submitted (NOV-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION.
  3. "Evidence for temporal regulation of the two Pseudomonas cellulosa xylanases belonging to glycoside hydrolase family 11."
    Emami K., Nagy T., Fontes C.M., Ferreira L.M., Gilbert H.J.
    J. Bacteriol. 184:4124-4133(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, INDUCTION.
  4. "Structure of a family 15 carbohydrate-binding module in complex with xylopentaose. Evidence that xylan binds in an approximate 3-fold helical conformation."
    Szabo L., Jamal S., Xie H., Charnock S.J., Bolam D.N., Gilbert H.J., Davies G.J.
    J. Biol. Chem. 276:49061-49065(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.63 ANGSTROMS) OF 91-243 IN COMPLEX WITH XYLOPENTAOSE, DISULFIDE BOND, DOMAIN.
  5. "Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases."
    Pell G., Szabo L., Charnock S.J., Xie H., Gloster T.M., Davies G.J., Gilbert H.J.
    J. Biol. Chem. 279:11777-11788(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 86-606 OF WILD-TYPE AND MUTANT ALA-385 IN COMPLEX WITH XYLOTETRAOSE, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, ACTIVE SITE, DOMAIN, MUTAGENESIS OF TYR-340.

Entry informationi

Entry nameiXY10C_CELJA
AccessioniPrimary (citable) accession number: Q59675
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 11, 2013
Last sequence update: March 1, 2004
Last modified: March 16, 2016
This is version 88 of the entry and version 2 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. 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.