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D5MP61

- 3XYN1_VIBSX

UniProt

D5MP61 - 3XYN1_VIBSX

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Protein
Beta-1,3-xylanase XYL4
Gene
xyl4
Organism
Vibrio sp.
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalyzes the hydrolysis of beta-1,3-xylan into oligosaccharides, mainly xylobiose, xylotriose and xylotetraose. Converts beta-1,3-xylotriose into xylose and xylobiose, converts beta-1,3-xylotetraose mainly into xylotriose and xylose, converts beta-1,3-xylopentaose into xylobiose and xylotriose. Does not hydrolyze beta-1,4-xylan, beta-1,4-mannan, beta-1,4-glucan, beta-1,3-xylobiose or p-nitrophenyl-beta-xyloside.1 Publication

Catalytic activityi

Random hydrolysis of (1->3)-beta-D-glycosidic linkages in (1->3)-beta-D-xylans.1 Publication

Enzyme regulationi

Completely inhibited by Hg2+, partially inhibited by Mn2+, Cu2+ and Pb2+. Unaffected by Ca2+, Mg2+ and EDTA.1 Publication

Kineticsi

  1. KM=7.4 mM for beta-1,3-xylotetraose1 Publication
  2. KM=7.5 mM for beta-1,3-xylopentaose1 Publication

pH dependencei

Optimum pH is 7.0-7.5.1 Publication

Temperature dependencei

Optimum temperature is 37 degrees Celsius. Inactive above 60 degrees Celsius.1 Publication

GO - Molecular functioni

  1. polysaccharide binding Source: UniProtKB
  2. xylan endo-1,3-beta-xylosidase activity Source: UniProtKB

GO - Biological processi

  1. cellulose catabolic process Source: UniProtKB-KW
  2. xylan catabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Carbohydrate metabolism, Cellulose degradation, Polysaccharide degradation, Xylan degradation

Names & Taxonomyi

Protein namesi
Recommended name:
Beta-1,3-xylanase XYL4 (EC:3.2.1.32)
Alternative name(s):
Beta-1,3-xylanase
Gene namesi
Name:xyl4
OrganismiVibrio sp.
Taxonomic identifieri678 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi138 – 1381E → D: Very low catalytic activity. 1 Publication
Mutagenesisi138 – 1381E → Q: Complete loss of catalytic activity. 1 Publication
Mutagenesisi234 – 2341E → D: Very low catalytic activity. 1 Publication
Mutagenesisi234 – 2341E → Q: Complete loss of catalytic activity. 1 Publication
Mutagenesisi268 – 2681E → Q: Catalytic activity reduced by 30%. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2222 Reviewed prediction
Add
BLAST
Chaini23 – 576554Beta-1,3-xylanase XYL4
PRO_0000403220Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi368 ↔ 452 By similarityBy similarity
Disulfide bondi399 ↔ 404 By similarityBy similarity
Disulfide bondi490 ↔ 574 By similarityBy similarity
Disulfide bondi521 ↔ 526 By similarityBy similarity

Keywords - PTMi

Disulfide bond

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni24 – 274
Beta strandi30 – 4011
Helixi41 – 5111
Beta strandi56 – 638
Turni64 – 663
Beta strandi70 – 723
Beta strandi74 – 785
Helixi83 – 897
Beta strandi93 – 1008
Helixi105 – 1095
Turni110 – 1134
Helixi114 – 12512
Beta strandi131 – 1355
Helixi142 – 1443
Helixi148 – 16518
Turni168 – 1703
Beta strandi171 – 1766
Helixi189 – 1913
Helixi195 – 1973
Beta strandi199 – 2079
Helixi208 – 2114
Helixi214 – 22613
Beta strandi230 – 2356
Turni242 – 2454
Turni251 – 2533
Helixi262 – 2687
Helixi270 – 27910
Turni280 – 2834
Beta strandi284 – 2907
Helixi294 – 2963
Helixi298 – 3003
Turni302 – 3065
Helixi314 – 3163
Helixi318 – 32811
Helixi340 – 3434

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DDXX-ray0.86A23-349[»]
3VPLX-ray1.20A23-349[»]
ProteinModelPortaliD5MP61.

Miscellaneous databases

EvolutionaryTraceiD5MP61.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni363 – 45391Carbohydrate binding module (CBM) 1
Add
BLAST
Regioni487 – 57488Carbohydrate binding module (CBM) 2
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi453 – 48432Gly-rich
Add
BLAST

Domaini

The carbohydrate binding modules (CBM) bind to insoluble beta-1,3-xylan, but not to insoluble beta-1,4-xylan, beta-1,4-glucan, beta-1,4-mannan, curdlan, chitin, or soluble polysaccharides.1 Publication

Sequence similaritiesi

Belongs to the glycosyl hydrolase 26 family.1 Publication

Keywords - Domaini

Repeat, Signal

Family and domain databases

Gene3Di3.20.20.80. 1 hit.
InterProiIPR021016. Beta-xylanase.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PfamiPF11606. AlcCBM31. 2 hits.
[Graphical view]
SUPFAMiSSF51445. SSF51445. 1 hit.

Sequencei

Sequence statusi: Complete.

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

D5MP61-1 [UniParc]FASTAAdd to Basket

« Hide

MKRTYLSLIA AGVMSLSVSA WSLDGVLVPE SGILVSVGQD VDSVNDYASA    50
LGTIPAGVTN YVGIVNLDGL NSDADAGAGR NNIAELANAY PTSALVVGVS 100
MNGEVDAVAS GRYNANIDTL LNTLAGYDRP VYLRWAYEVD GPWNGHSPSG 150
IVTSFQYVHD RIIALGHQAK ISLVWQVASY CPTPGGQLDQ WWPGSEYVDW 200
VGLSYFAPQD CNWDRVNEAA QFARSKGKPL FLNESTPQRY QVADLTYSAD 250
PAKGTNRQSK TSQQLWDEWF APYFQFMSDN SDIVKGFTYI NADWDSQWRW 300
AAPYNEGYWG DSRVQANALI KSNWQQEIAK GQYINHSETL FETLGYGSTG 350
GGDNGGGDNG GTNPPEPCNE EFGYRYVSDS TIEVFHKNNG WSAEWNYVCL 400
NGLCLQGEIK NGEYVKQFDA QLGSTYGIEF KVADGESQFI TDKSVTFENK 450
QCGSTGTPGG GDNGSGGDNG GDNGSGGDNG SGGGTDPSQC SADFGYNYRS 500
DTEIEVFHKD LGWSASWNYI CLDDYCVPGD KSGDSYNRSF NATLGSDYKI 550
TFKVEDSASQ FITEKNITFV NTSCAQ 576
Length:576
Mass (Da):62,591
Last modified:July 13, 2010 - v1
Checksum:iE04449C5F703884D
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB121027 Genomic DNA. Translation: BAD51934.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB121027 Genomic DNA. Translation: BAD51934.1 .

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2DDX X-ray 0.86 A 23-349 [» ]
3VPL X-ray 1.20 A 23-349 [» ]
ProteinModelPortali D5MP61.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei D5MP61.

Family and domain databases

Gene3Di 3.20.20.80. 1 hit.
InterProi IPR021016. Beta-xylanase.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view ]
Pfami PF11606. AlcCBM31. 2 hits.
[Graphical view ]
SUPFAMi SSF51445. SSF51445. 1 hit.
ProtoNeti Search...

Publicationsi

  1. "Molecular cloning and characterization of a novel beta-1,3-xylanase possessing two putative carbohydrate-binding modules from a marine bacterium Vibrio sp. strain AX-4."
    Kiyohara M., Sakaguchi K., Yamaguchi K., Araki T., Nakamura T., Ito M.
    Biochem. J. 388:949-957(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF GLU-138; GLU-234 AND GLU-268.
    Strain: AX-4.
  2. "Characterization and application of carbohydrate-binding modules of beta-1,3-xylanase XYL4."
    Kiyohara M., Sakaguchi K., Yamaguchi K., Araki T., Ito M.
    J. Biochem. 146:633-641(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: CBM31 DOMAIN.
    Strain: AX-4.
  3. "Atomic resolution analysis of beta-1,3-xylanase catalytic module from Vibrio sp. AX-4."
    Sakaguchi K., Kawamura T., Watanabe N., Kiyohara M., Yamaguchi K., Ito M., Tanaka I.
    Submitted (FEB-2006) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (0.86 ANGSTROMS) OF 23-349 IN COMPLEX WITH MAGNESIUM.
    Strain: AX-4.

Entry informationi

Entry namei3XYN1_VIBSX
AccessioniPrimary (citable) accession number: D5MP61
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2011
Last sequence update: July 13, 2010
Last modified: October 16, 2013
This is version 15 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

Documents

  1. Glycosyl hydrolases
    Classification of glycosyl hydrolase families and list of entries
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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