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D5MP61 (3XYN1_VIBSX) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 14. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Beta-1,3-xylanase XYL4
EC=3.2.1.32
Alternative name(s):
Beta-1,3-xylanase
Gene names
Name:xyl4
OrganismVibrio sp.
Taxonomic identifier678 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

Protein attributes

Sequence length576 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1

Catalytic activity

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

Enzyme regulation

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

Domain

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. Ref.2

Sequence similarities

Belongs to the glycosyl hydrolase 26 family. Ref.1

Biophysicochemical properties

Kinetic parameters:

KM=7.4 mM for beta-1,3-xylotetraose Ref.1

KM=7.5 mM for beta-1,3-xylopentaose Ref.1

pH dependence:

Optimum pH is 7.0-7.5. Ref.1

Temperature dependence:

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2222 Potential
Chain23 – 576554Beta-1,3-xylanase XYL4
PRO_0000403220

Regions

Region363 – 45391Carbohydrate binding module (CBM) 1
Region487 – 57488Carbohydrate binding module (CBM) 2
Compositional bias453 – 48432Gly-rich

Amino acid modifications

Disulfide bond368 ↔ 452 By similarity UniProtKB Q8RS40
Disulfide bond399 ↔ 404 By similarity UniProtKB Q8RS40
Disulfide bond490 ↔ 574 By similarity UniProtKB Q8RS40
Disulfide bond521 ↔ 526 By similarity UniProtKB Q8RS40

Experimental info

Mutagenesis1381E → D: Very low catalytic activity. Ref.1
Mutagenesis1381E → Q: Complete loss of catalytic activity. Ref.1
Mutagenesis2341E → D: Very low catalytic activity. Ref.1
Mutagenesis2341E → Q: Complete loss of catalytic activity. Ref.1
Mutagenesis2681E → Q: Catalytic activity reduced by 30%. Ref.1

Secondary structure

1 ............................................................... 576
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
D5MP61 [UniParc].

Last modified July 13, 2010. Version 1.
Checksum: E04449C5F703884D

FASTA57662,591
        10         20         30         40         50         60 
MKRTYLSLIA AGVMSLSVSA WSLDGVLVPE SGILVSVGQD VDSVNDYASA LGTIPAGVTN 

        70         80         90        100        110        120 
YVGIVNLDGL NSDADAGAGR NNIAELANAY PTSALVVGVS MNGEVDAVAS GRYNANIDTL 

       130        140        150        160        170        180 
LNTLAGYDRP VYLRWAYEVD GPWNGHSPSG IVTSFQYVHD RIIALGHQAK ISLVWQVASY 

       190        200        210        220        230        240 
CPTPGGQLDQ WWPGSEYVDW VGLSYFAPQD CNWDRVNEAA QFARSKGKPL FLNESTPQRY 

       250        260        270        280        290        300 
QVADLTYSAD PAKGTNRQSK TSQQLWDEWF APYFQFMSDN SDIVKGFTYI NADWDSQWRW 

       310        320        330        340        350        360 
AAPYNEGYWG DSRVQANALI KSNWQQEIAK GQYINHSETL FETLGYGSTG GGDNGGGDNG 

       370        380        390        400        410        420 
GTNPPEPCNE EFGYRYVSDS TIEVFHKNNG WSAEWNYVCL NGLCLQGEIK NGEYVKQFDA 

       430        440        450        460        470        480 
QLGSTYGIEF KVADGESQFI TDKSVTFENK QCGSTGTPGG GDNGSGGDNG GDNGSGGDNG 

       490        500        510        520        530        540 
SGGGTDPSQC SADFGYNYRS DTEIEVFHKD LGWSASWNYI CLDDYCVPGD KSGDSYNRSF 

       550        560        570 
NATLGSDYKI TFKVEDSASQ FITEKNITFV NTSCAQ

« Hide

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AB121027 Genomic DNA. Translation: BAD51934.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2DDXX-ray0.86A23-349[»]
3VPLX-ray1.20A23-349[»]
ProteinModelPortalD5MP61.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D3.20.20.80. 1 hit.
InterProIPR021016. Beta-xylanase.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PfamPF11606. AlcCBM31. 2 hits.
[Graphical view]
SUPFAMSSF51445. Glyco_hydro_cat. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceD5MP61.

Entry information

Entry name3XYN1_VIBSX
AccessionPrimary (citable) accession number: D5MP61
Entry history
Integrated into UniProtKB/Swiss-Prot: January 11, 2011
Last sequence update: July 13, 2010
Last modified: May 1, 2013
This is version 14 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Glycosyl hydrolases

Classification of glycosyl hydrolase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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