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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)DescriptionActionsGraphical viewLength
Binding sitei106Carbohydrate1
Binding sitei171Carbohydrate1
Binding sitei217Carbohydrate1
Binding sitei332Substrate1
Binding sitei384Substrate1
Active sitei385Proton donorBy similarity1
Active sitei497Nucleophile1 Publication1
Binding sitei552Substrate1

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)DescriptionActionsGraphical viewLength
Mutagenesisi340Y → A: Significantly reduces the catalytic activity against xylotetraose and xylan. Also modifies the cleavage pattern of xylotetraose. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 19PROSITE-ProRule annotationAdd BLAST19
ChainiPRO_500014760920 – 606Endo-beta-1,4-xylanase Xyn10CAdd BLAST587

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi20N-palmitoyl cysteinePROSITE-ProRule annotation1
Lipidationi20S-diacylglycerol cysteinePROSITE-ProRule annotation1
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

1606
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi92 – 96Combined sources5
Beta strandi99 – 102Combined sources4
Beta strandi104 – 107Combined sources4
Beta strandi109 – 111Combined sources3
Beta strandi117 – 119Combined sources3
Beta strandi122 – 126Combined sources5
Beta strandi132 – 138Combined sources7
Beta strandi140 – 143Combined sources4
Beta strandi148 – 155Combined sources8
Helixi157 – 162Combined sources6
Beta strandi165 – 172Combined sources8
Beta strandi175 – 180Combined sources6
Helixi187 – 189Combined sources3
Beta strandi192 – 194Combined sources3
Beta strandi196 – 201Combined sources6
Beta strandi210 – 213Combined sources4
Beta strandi216 – 225Combined sources10
Beta strandi228 – 242Combined sources15
Helixi251 – 254Combined sources4
Beta strandi256 – 258Combined sources3
Beta strandi261 – 266Combined sources6
Turni271 – 273Combined sources3
Turni275 – 277Combined sources3
Helixi279 – 288Combined sources10
Beta strandi290 – 296Combined sources7
Helixi300 – 303Combined sources4
Helixi313 – 324Combined sources12
Beta strandi328 – 335Combined sources8
Helixi339 – 341Combined sources3
Helixi344 – 347Combined sources4
Helixi353 – 374Combined sources22
Beta strandi379 – 385Combined sources7
Beta strandi389 – 392Combined sources4
Helixi401 – 405Combined sources5
Helixi412 – 423Combined sources12
Beta strandi427 – 435Combined sources9
Helixi441 – 455Combined sources15
Beta strandi462 – 465Combined sources4
Beta strandi468 – 472Combined sources5
Helixi476 – 487Combined sources12
Turni488 – 490Combined sources3
Beta strandi492 – 503Combined sources12
Turni508 – 513Combined sources6
Helixi520 – 540Combined sources21
Helixi543 – 545Combined sources3
Beta strandi546 – 552Combined sources7
Helixi556 – 558Combined sources3
Helixi560 – 564Combined sources5
Turni565 – 571Combined sources7
Beta strandi578 – 580Combined sources3
Helixi588 – 598Combined sources11

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ59675.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini91 – 242CBM15PROSITE-ProRule annotationAdd BLAST152
Domaini245 – 596GH10PROSITE-ProRule annotationAdd BLAST352

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni296 – 299Substrate binding4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi33 – 89Ser-richAdd BLAST57

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1GNYX-ray1.63A91-243[»]
1US2X-ray1.85A86-606[»]
1US3X-ray1.85A86-606[»]
ProteinModelPortaliQ59675.
SMRiQ59675.
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...

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: November 2, 2016
This is version 91 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.