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P45796

- XYND_PAEPO

UniProt

P45796 - XYND_PAEPO

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Protein

Arabinoxylan arabinofuranohydrolase

Gene

xynD

Organism
Paenibacillus polymyxa (Bacillus polymyxa)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Cleaves arabinose units from O-2- or O-3-monosubstituted xylose residues, thereby assisting in arabinoxylan (AX) and short-chain arabinoxylo-oligosaccharide (AXOS) degradation By similarity. Preferres wheat flour xylan over oat spelt xylan as substrate. Does not display endoxylanase activity.By similarity1 Publication

Catalytic activityi

Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.

Enzyme regulationi

Activated by calcium and magnesium. Inhibited by copper.1 Publication

pH dependencei

Optimum pH is 6.5.1 Publication

Temperature dependencei

Optimum temperature is 55 degrees Celsius.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei49 – 491Proton acceptorBy similarity
Sitei188 – 1881Important for catalytic activityBy similarity
Active sitei248 – 2481Proton donorBy similarity
Binding sitei311 – 3111SubstrateBy similarity
Metal bindingi382 – 3821Calcium 1; structuralBy similarity
Metal bindingi384 – 3841Calcium 1; structuralBy similarity
Metal bindingi406 – 4061Calcium 1; structuralBy similarity
Metal bindingi407 – 4071Calcium 1; via carbonyl oxygen; structuralBy similarity
Metal bindingi503 – 5031Calcium 1; structuralBy similarity
Metal bindingi503 – 5031Calcium 1; via carbonyl oxygen; structuralBy similarity
Metal bindingi520 – 5201Calcium 2; structural
Metal bindingi522 – 5221Calcium 2; structural
Metal bindingi539 – 5391Calcium 2; via carbonyl oxygen; structural
Metal bindingi544 – 5441Calcium 3; via carbonyl oxygen; structural
Metal bindingi620 – 6201Calcium 3
Metal bindingi624 – 6241Calcium 3; via carbonyl oxygen; structural
Metal bindingi625 – 6251Calcium 3
Metal bindingi629 – 6291Calcium 2; structural
Metal bindingi629 – 6291Calcium 2; via carbonyl oxygen; structural

GO - Molecular functioni

  1. alpha-L-arabinofuranosidase activity Source: UniProtKB-EC
  2. carbohydrate binding Source: InterPro
  3. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. xylan catabolic process Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Carbohydrate metabolism, Polysaccharide degradation, Xylan degradation

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BRENDAi3.2.1.8. 7322.
UniPathwayiUPA00114.

Protein family/group databases

CAZyiCBM36. Carbohydrate-Binding Module Family 36.
CBM6. Carbohydrate-Binding Module Family 6.
GH43. Glycoside Hydrolase Family 43.

Names & Taxonomyi

Protein namesi
Recommended name:
Arabinoxylan arabinofuranohydrolase (EC:3.2.1.55)
Short name:
AXH
Alternative name(s):
AXH-m2,3
Short name:
AXH-m23
Alpha-L-arabinofuranosidase
Short name:
AF
Gene namesi
Name:xynD
OrganismiPaenibacillus polymyxa (Bacillus polymyxa)
Taxonomic identifieri1406 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesPaenibacillaceaePaenibacillus

Subcellular locationi

GO - Cellular componenti

  1. extracellular region Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 26261 PublicationAdd
BLAST
Chaini27 – 635609Arabinoxylan arabinofuranohydrolasePRO_0000012202Add
BLAST

Structurei

Secondary structure

1
635
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi517 – 5204Combined sources
Helixi521 – 5233Combined sources
Beta strandi524 – 5307Combined sources
Beta strandi532 – 5343Combined sources
Beta strandi536 – 5438Combined sources
Beta strandi549 – 58133Combined sources
Beta strandi584 – 59512Combined sources
Beta strandi597 – 6059Combined sources
Beta strandi609 – 61810Combined sources
Beta strandi620 – 6234Combined sources
Beta strandi626 – 6349Combined sources

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1UX7X-ray1.50A516-635[»]
1W0NX-ray0.80A505-635[»]
ProteinModelPortaliP45796.
SMRiP45796. Positions 516-635.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP45796.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini379 – 508130CBM6 1PROSITE-ProRule annotationAdd
BLAST
Domaini517 – 634118CBM6 2PROSITE-ProRule annotationAdd
BLAST

Domaini

The C-terminal CBM6 domain shows calcium-dependent xylo-oligosaccharide and xylan binding. It binds, next to the structural calcium ion, a second calcium ion that, in addition to its coordination sites on the protein, completes its heptacoordination through coordination to the bound xylose moiety.

Sequence similaritiesi

Belongs to the glycosyl hydrolase 43 family.Curated
Contains 2 CBM6 (carbohydrate binding type-6) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal

Family and domain databases

Gene3Di2.115.10.20. 1 hit.
2.60.120.260. 2 hits.
InterProiIPR006584. Cellulose-bd_IV.
IPR005084. CMB_fam6.
IPR008979. Galactose-bd-like.
IPR006710. Glyco_hydro_43.
IPR023296. Glyco_hydro_beta-prop.
[Graphical view]
PANTHERiPTHR22925. PTHR22925. 1 hit.
PfamiPF03422. CBM_6. 2 hits.
PF04616. Glyco_hydro_43. 1 hit.
[Graphical view]
SMARTiSM00606. CBD_IV. 1 hit.
[Graphical view]
SUPFAMiSSF49785. SSF49785. 2 hits.
SSF75005. SSF75005. 1 hit.
PROSITEiPS51175. CBM6. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P45796-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MIRKCLVLFL SFALLLSVFP MLNVDAANRP LAKIPGNSNP LMDHKLGADP
60 70 80 90 100
YSLVYDGRVY IFMSSDTYVY NKDGSIKEND FSALDRIQVI SSTDMVNWTD
110 120 130 140 150
HGTIPVAGAN NKNSGRGIAK WASNSWAPAV AHKKINGRDK FFLYFANGGA
160 170 180 190 200
GIGVLTADTP IGPWTDPLGK ALVTHSTPGM AGVTWLFDPA VLVDDDGTGY
210 220 230 240 250
LYSGGGIPNE SDPASIANPK TARVIKLGAD MTSVIGSATT IDAPYLFEDS
260 270 280 290 300
GIHKYNGKYY YSYCINFAGT HPQQYPAGEI GYMVSDNPMG PFTYKGHFLK
310 320 330 340 350
NPYTFFGVGG NNHHAVFNFK NEWYVVYHAQ TVSKAQIGAG KGYRSPHINK
360 370 380 390 400
LVHKEDGSIS EVQGNMTGIA QLSNMNPYTR VEAETIAWQA GVTTEPTQAS
410 420 430 440 450
GGPISNLNVT NIHNGDWIAV GKADFGSAGA KTFKANVATN VGGNIEVRLD
460 470 480 490 500
SETGPLVGSL KVPSTGGMQT WREVETTINN ATGVHNIYLV FTGSGSGNLL
510 520 530 540 550
NLDAWQFTPN TGGNTITKVE AENMKIGGTY AGKISAPFDG VALYANADYV
560 570 580 590 600
SYSQYFANST HNISVRGASS NAGTAKVDLV IGGVTVGSFN FTGKTPTVQT
610 620 630
LSNITHATGD QEIKLALTSD DGTWDAYVDF IEFSL
Length:635
Mass (Da):67,914
Last modified:November 1, 1995 - v1
Checksum:iF9DEC69967323316
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X57094 Genomic DNA. Translation: CAA40378.1.
PIRiS19011.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X57094 Genomic DNA. Translation: CAA40378.1 .
PIRi S19011.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1UX7 X-ray 1.50 A 516-635 [» ]
1W0N X-ray 0.80 A 505-635 [» ]
ProteinModelPortali P45796.
SMRi P45796. Positions 516-635.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

CAZyi CBM36. Carbohydrate-Binding Module Family 36.
CBM6. Carbohydrate-Binding Module Family 6.
GH43. Glycoside Hydrolase Family 43.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

UniPathwayi UPA00114 .
BRENDAi 3.2.1.8. 7322.

Miscellaneous databases

EvolutionaryTracei P45796.

Family and domain databases

Gene3Di 2.115.10.20. 1 hit.
2.60.120.260. 2 hits.
InterProi IPR006584. Cellulose-bd_IV.
IPR005084. CMB_fam6.
IPR008979. Galactose-bd-like.
IPR006710. Glyco_hydro_43.
IPR023296. Glyco_hydro_beta-prop.
[Graphical view ]
PANTHERi PTHR22925. PTHR22925. 1 hit.
Pfami PF03422. CBM_6. 2 hits.
PF04616. Glyco_hydro_43. 1 hit.
[Graphical view ]
SMARTi SM00606. CBD_IV. 1 hit.
[Graphical view ]
SUPFAMi SSF49785. SSF49785. 2 hits.
SSF75005. SSF75005. 1 hit.
PROSITEi PS51175. CBM6. 2 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Two beta-glycanase genes are clustered in Bacillus polymyxa: molecular cloning, expression, and sequence analysis of genes encoding a xylanase and an endo-beta-(1,3)-(1,4)-glucanase."
    Gosalbes M.J., Perez-Gonzalez J.A., Gonzalez R., Navarro A.
    J. Bacteriol. 173:7705-7710(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 842 / DSM 36 / JCM 2507 / NBRC 15309 / NCIMB 8158 / NCTC 10343 / NRRL B-4317 / VKM B-514.
  2. "Purification and characterization of an arabinofuranosidase from Bacillus polymyxa expressed in Bacillus subtilis."
    Morales P., Sendra J.M., Perez-Gonzalez J.A.
    Appl. Microbiol. Biotechnol. 44:112-117(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 27-46, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
    Strain: CECT 153 / NCTC 4747 / NRRL NRS-1237.
  3. "Ab initio structure determination and functional characterization of CBM36; a new family of calcium-dependent carbohydrate binding modules."
    Jamal-Talabani S., Boraston A.B., Turkenburg J.P., Tarbouriech N., Ducros V.M.-A., Davies G.J.
    Structure 12:1177-1187(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (0.8 ANGSTROMS) OF 505-635 IN COMPLEX WITH XYLOTRIOSE.
    Strain: ATCC 842 / DSM 36 / JCM 2507 / NBRC 15309 / NCIMB 8158 / NCTC 10343 / NRRL B-4317 / VKM B-514.

Entry informationi

Entry nameiXYND_PAEPO
AccessioniPrimary (citable) accession number: P45796
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: October 29, 2014
This is version 86 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, Direct protein sequencing

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

External Data

Dasty 3