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Protein

Arabinoxylan arabinofuranohydrolase

Gene

xynD

Organism
Paenibacillus polymyxa (Bacillus polymyxa)
Status
Reviewed-Annotation score: -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.

Activity 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: 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
Active sitei49Proton acceptorBy similarity1
Sitei188Important for catalytic activity, responsible for pKa modulation of the active site Glu and correct orientation of both the proton donor and substrateBy similarity1
Active sitei248Proton donorBy similarity1
Binding sitei311SubstrateBy similarity1
Metal bindingi382Calcium 1; structuralBy similarity1
Metal bindingi384Calcium 1; structuralBy similarity1
Metal bindingi406Calcium 1; structuralBy similarity1
Metal bindingi407Calcium 1; via carbonyl oxygen; structuralBy similarity1
Metal bindingi503Calcium 1; structuralBy similarity1
Metal bindingi503Calcium 1; via carbonyl oxygen; structuralBy similarity1
Metal bindingi520Calcium 2; structural1
Metal bindingi522Calcium 2; structural1
Metal bindingi539Calcium 2; via carbonyl oxygen; structural1
Metal bindingi544Calcium 3; via carbonyl oxygen; structural1
Metal bindingi620Calcium 31
Metal bindingi624Calcium 3; via carbonyl oxygen; structural1
Metal bindingi625Calcium 31
Metal bindingi629Calcium 2; structural1
Metal bindingi629Calcium 2; via carbonyl oxygen; structural1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionGlycosidase, Hydrolase
Biological processCarbohydrate metabolism, Polysaccharide degradation, Xylan degradation
LigandCalcium, Metal-binding

Enzyme and pathway databases

BRENDAi3.2.1.8 683
UniPathwayi
UPA00114

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

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 261 PublicationAdd BLAST26
ChainiPRO_000001220227 – 635Arabinoxylan arabinofuranohydrolaseAdd BLAST609

Proteomic databases

PRIDEiP45796

Structurei

Secondary structure

1635
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP45796
SMRiP45796
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP45796

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini379 – 508CBM6 1PROSITE-ProRule annotationAdd BLAST130
Domaini517 – 634CBM6 2PROSITE-ProRule annotationAdd BLAST118

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

Keywords - Domaini

Repeat, Signal

Family and domain databases

Gene3Di2.115.10.20, 1 hit
2.60.120.260, 2 hits
InterProiView protein in InterPro
IPR006584 Cellulose-bd_IV
IPR005084 CMB_fam6
IPR008979 Galactose-bd-like_sf
IPR006710 Glyco_hydro_43
IPR023296 Glyco_hydro_beta-prop_sf
PfamiView protein in Pfam
PF03422 CBM_6, 2 hits
PF04616 Glyco_hydro_43, 1 hit
SMARTiView protein in SMART
SM00606 CBD_IV, 1 hit
SUPFAMiSSF49785 SSF49785, 2 hits
SSF75005 SSF75005, 1 hit
PROSITEiView protein in PROSITE
PS51175 CBM6, 2 hits

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:
EMBLi
GenBanki
DDBJi
Links Updated
X57094 Genomic DNA Translation: CAA40378.1
PIRiS19011

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X57094 Genomic DNA Translation: CAA40378.1
PIRiS19011

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UX7X-ray1.50A516-635[»]
1W0NX-ray0.80A505-635[»]
ProteinModelPortaliP45796
SMRiP45796
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

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

Proteomic databases

PRIDEiP45796

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayi
UPA00114

BRENDAi3.2.1.8 683

Miscellaneous databases

EvolutionaryTraceiP45796

Family and domain databases

Gene3Di2.115.10.20, 1 hit
2.60.120.260, 2 hits
InterProiView protein in InterPro
IPR006584 Cellulose-bd_IV
IPR005084 CMB_fam6
IPR008979 Galactose-bd-like_sf
IPR006710 Glyco_hydro_43
IPR023296 Glyco_hydro_beta-prop_sf
PfamiView protein in Pfam
PF03422 CBM_6, 2 hits
PF04616 Glyco_hydro_43, 1 hit
SMARTiView protein in SMART
SM00606 CBD_IV, 1 hit
SUPFAMiSSF49785 SSF49785, 2 hits
SSF75005 SSF75005, 1 hit
PROSITEiView protein in PROSITE
PS51175 CBM6, 2 hits
ProtoNetiSearch...

Entry informationi

Entry nameiXYND_PAEPO
AccessioniPrimary (citable) accession number: P45796
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: September 12, 2018
This is version 102 of the entry and version 1 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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