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Protein

Arabinoxylan arabinofuranohydrolase

Gene

xynD

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

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. 683.
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

Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

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

Interactioni

Protein-protein interaction databases

STRINGi1052684.PPM_2373.

Structurei

Secondary structure

1635
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi517 – 520Combined sources4
Helixi521 – 523Combined sources3
Beta strandi524 – 530Combined sources7
Beta strandi532 – 534Combined sources3
Beta strandi536 – 543Combined sources8
Beta strandi549 – 581Combined sources33
Beta strandi584 – 595Combined sources12
Beta strandi597 – 605Combined sources9
Beta strandi609 – 618Combined sources10
Beta strandi620 – 623Combined sources4
Beta strandi626 – 634Combined sources9

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...

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

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-protein interaction databases

STRINGi1052684.PPM_2373.

Protein family/group databases

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

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00114.
BRENDAi3.2.1.8. 683.

Miscellaneous databases

EvolutionaryTraceiP45796.

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. 2 hits.
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]
ProtoNetiSearch...

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: November 2, 2016
This is version 95 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.