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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 XYL41 Publication (EC:3.2.1.32)
Alternative name(s):
Beta-1,3-xylanaseImported
Gene namesi
Name:xyl4Imported
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 – 2222Sequence AnalysisAdd
BLAST
Chaini23 – 576554Beta-1,3-xylanase XYL4Sequence AnalysisPRO_0000403220Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Disulfide bond

Structurei

Secondary structure

1
576
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni24 – 274Combined sources
Beta strandi30 – 4011Combined sources
Helixi41 – 5111Combined sources
Beta strandi56 – 638Combined sources
Turni64 – 663Combined sources
Beta strandi70 – 723Combined sources
Beta strandi74 – 785Combined sources
Helixi83 – 897Combined sources
Beta strandi93 – 1008Combined sources
Helixi105 – 1095Combined sources
Turni110 – 1134Combined sources
Helixi114 – 12512Combined sources
Beta strandi131 – 1355Combined sources
Helixi142 – 1443Combined sources
Helixi148 – 16518Combined sources
Turni168 – 1703Combined sources
Beta strandi171 – 1766Combined sources
Helixi189 – 1913Combined sources
Helixi195 – 1973Combined sources
Beta strandi199 – 2079Combined sources
Helixi208 – 2114Combined sources
Helixi214 – 22613Combined sources
Beta strandi230 – 2356Combined sources
Turni242 – 2454Combined sources
Turni251 – 2533Combined sources
Helixi262 – 2687Combined sources
Helixi270 – 27910Combined sources
Turni280 – 2834Combined sources
Beta strandi284 – 2907Combined sources
Helixi294 – 2963Combined sources
Helixi298 – 3003Combined sources
Turni302 – 3065Combined sources
Helixi314 – 3163Combined sources
Helixi318 – 32811Combined sources
Helixi340 – 3434Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DDXX-ray0.86A23-349[»]
3VPLX-ray1.20A23-349[»]
ProteinModelPortaliD5MP61.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiD5MP61.

Family & Domainsi

Region

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

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi453 – 48432Gly-richSequence AnalysisAdd
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.

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

        10         20         30         40         50
MKRTYLSLIA AGVMSLSVSA WSLDGVLVPE SGILVSVGQD VDSVNDYASA
60 70 80 90 100
LGTIPAGVTN YVGIVNLDGL NSDADAGAGR NNIAELANAY PTSALVVGVS
110 120 130 140 150
MNGEVDAVAS GRYNANIDTL LNTLAGYDRP VYLRWAYEVD GPWNGHSPSG
160 170 180 190 200
IVTSFQYVHD RIIALGHQAK ISLVWQVASY CPTPGGQLDQ WWPGSEYVDW
210 220 230 240 250
VGLSYFAPQD CNWDRVNEAA QFARSKGKPL FLNESTPQRY QVADLTYSAD
260 270 280 290 300
PAKGTNRQSK TSQQLWDEWF APYFQFMSDN SDIVKGFTYI NADWDSQWRW
310 320 330 340 350
AAPYNEGYWG DSRVQANALI KSNWQQEIAK GQYINHSETL FETLGYGSTG
360 370 380 390 400
GGDNGGGDNG GTNPPEPCNE EFGYRYVSDS TIEVFHKNNG WSAEWNYVCL
410 420 430 440 450
NGLCLQGEIK NGEYVKQFDA QLGSTYGIEF KVADGESQFI TDKSVTFENK
460 470 480 490 500
QCGSTGTPGG GDNGSGGDNG GDNGSGGDNG SGGGTDPSQC SADFGYNYRS
510 520 530 540 550
DTEIEVFHKD LGWSASWNYI CLDDYCVPGD KSGDSYNRSF NATLGSDYKI
560 570
TFKVEDSASQ FITEKNITFV NTSCAQ
Length:576
Mass (Da):62,591
Last modified:July 13, 2010 - v1
Checksum:iE04449C5F703884D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB121027 Genomic DNA. Translation: BAD51934.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB121027 Genomic DNA. Translation: BAD51934.1 .

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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-4Imported.
  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-41 Publication.
  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-41 Publication.

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 29, 2014
This is version 17 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