Reviewed, UniProtKB/Swiss-Prot P45796 (XYND_PAEPO)

Names and origin

Protein names

Recommended name:
    Arabinoxylan arabinofuranohydrolase
      Short name=AXH
    EC=3.2.1.55
Alternative name(s):
    AXH-m2,3
      Short name=AXH-m23
    Alpha-L-arabinofuranosidase
      Short name=AF

Gene names

Name:

xynD

Organism

Paenibacillus polymyxa (Bacillus polymyxa)

Taxonomic identifier

1406 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Paenibacillaceae › Paenibacillus

Protein attributes

Sequence length	635 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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.
Catalytic activity	Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.
Enzyme regulation	Activated by calcium and magnesium. Inhibited by copper. Ref.2
Pathway	Glycan degradation; xylan degradation.
Subcellular location	Secreted.
Domain	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 similarities	Belongs to the glycosyl hydrolase 43 family. Contains 2 CBM6 (carbohydrate binding type-6) domains.
biophysicochemical properties	pH dependence: Optimum pH is 6.5. Temperature dependence: Optimum temperature is 55 degrees Celsius.

Ontologies

Keywords
Biological process	Xylan degradation
Cellular component	Secreted
Domain	Repeat Signal
Ligand	Calcium Metal-binding
Molecular function	Glycosidase Hydrolase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	xylan catabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	extracellular region Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	alpha-N-arabinofuranosidase activity Inferred from electronic annotation. Source: EC calcium ion binding Inferred from electronic annotation. Source: UniProtKB-KW carbohydrate binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 26

26

Ref.2

Chain

27 – 635

609

Arabinoxylan arabinofuranohydrolase

PRO_0000012202

Regions

Domain

379 – 508

130

CBM6 1

Domain

517 – 634

118

CBM6 2

Sites

Active site

49

1

Proton acceptor By similarity

Active site

248

1

Proton donor By similarity

Metal binding

382

1

Calcium 1; structural By similarity

Metal binding

384

1

Calcium 1; structural By similarity

Metal binding

406

1

Calcium 1; structural By similarity

Metal binding

407

1

Calcium 1; via carbonyl oxygen; structural By similarity

Metal binding

503

1

Calcium 1; structural By similarity

Metal binding

503

1

Calcium 1; via carbonyl oxygen; structural By similarity

Metal binding

520

1

Calcium 2; structural

Metal binding

522

1

Calcium 2; structural

Metal binding

539

1

Calcium 2; via carbonyl oxygen; structural

Metal binding

544

1

Calcium 3; via carbonyl oxygen; structural

Metal binding

620

1

Calcium 3

Metal binding

624

1

Calcium 3; via carbonyl oxygen; structural

Metal binding

625

1

Calcium 3

Metal binding

629

1

Calcium 2; structural

Metal binding

629

1

Calcium 2; via carbonyl oxygen; structural

Binding site

311

1

Substrate By similarity

Site

188

1

Important for catalytic activity By similarity

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

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.

635

Helix Strand Turn

Details...

Beta strand

517 – 520

4

Helix

521 – 523

3

Beta strand

524 – 530

7

Beta strand

532 – 534

3

Beta strand

536 – 543

8

Beta strand

549 – 581

33

Beta strand

584 – 595

12

Beta strand

597 – 605

9

Beta strand

609 – 618

10

Beta strand

620 – 623

4

Beta strand

626 – 634

9

Sequences

	Sequence		Length	Mass (Da)
	P45796-1 [UniParc]. Last modified November 1, 1995. Version 1. Checksum: F9DEC69967323316	FASTA	635	67,914
	10 20 30 40 50 60 MIRKCLVLFL SFALLLSVFP MLNVDAANRP LAKIPGNSNP LMDHKLGADP YSLVYDGRVY 70 80 90 100 110 120 IFMSSDTYVY NKDGSIKEND FSALDRIQVI SSTDMVNWTD HGTIPVAGAN NKNSGRGIAK 130 140 150 160 170 180 WASNSWAPAV AHKKINGRDK FFLYFANGGA GIGVLTADTP IGPWTDPLGK ALVTHSTPGM 190 200 210 220 230 240 AGVTWLFDPA VLVDDDGTGY LYSGGGIPNE SDPASIANPK TARVIKLGAD MTSVIGSATT 250 260 270 280 290 300 IDAPYLFEDS GIHKYNGKYY YSYCINFAGT HPQQYPAGEI GYMVSDNPMG PFTYKGHFLK 310 320 330 340 350 360 NPYTFFGVGG NNHHAVFNFK NEWYVVYHAQ TVSKAQIGAG KGYRSPHINK LVHKEDGSIS 370 380 390 400 410 420 EVQGNMTGIA QLSNMNPYTR VEAETIAWQA GVTTEPTQAS GGPISNLNVT NIHNGDWIAV 430 440 450 460 470 480 GKADFGSAGA KTFKANVATN VGGNIEVRLD SETGPLVGSL KVPSTGGMQT WREVETTINN 490 500 510 520 530 540 ATGVHNIYLV FTGSGSGNLL NLDAWQFTPN TGGNTITKVE AENMKIGGTY AGKISAPFDG 550 560 570 580 590 600 VALYANADYV SYSQYFANST HNISVRGASS NAGTAKVDLV IGGVTVGSFN FTGKTPTVQT 610 620 630 LSNITHATGD QEIKLALTSD DGTWDAYVDF IEFSL

References

[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: 1938968] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 842 / DSM 36 / IFO 15309 / NCIB 8158 / NCTC 10343.
[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: 8579824] [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: 15242594] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (0.8 ANGSTROMS) OF 505-635 IN COMPLEX WITH XYLOTRIOSE. Strain: ATCC 842 / DSM 36 / IFO 15309 / NCIB 8158 / NCTC 10343.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X57094 Genomic DNA. Translation: CAA40378.1.

PIR

S19011.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1UX7	X-ray	1.50	A	516-635	[»]
1W0N	X-ray	0.80	A	505-635	[»]

ModBase

Search...

Protein family/group databases

CAZy

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

Enzyme and pathway databases

BRENDA

3.2.1.8. 276031.

Family and domain databases

InterPro

IPR005084. CBM_6.
IPR006584. Cellulose_bd_IV.
IPR006710. Glyco_hydro_43.
[Graphical view]

PANTHER

PTHR22925. Glyco_hydro_43. 1 hit.

Pfam

PF03422. CBM_6. 2 hits.
PF04616. Glyco_hydro_43. 1 hit.
[Graphical view]

SMART

SM00606. CBD_IV. 1 hit.
[Graphical view]

PROSITE

PS51175. CBM6. 2 hits.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

XYND_PAEPO

Accession

Primary (citable) accession number: P45796

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	November 1, 1995
Last modified:	June 16, 2009
This is version 60 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)