XYND_PAEPO
ID XYND_PAEPO Reviewed; 635 AA.
AC P45796;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=Arabinoxylan arabinofuranohydrolase;
DE Short=AXH;
DE EC=3.2.1.55;
DE AltName: Full=AXH-m2,3;
DE Short=AXH-m23;
DE AltName: Full=Alpha-L-arabinofuranosidase;
DE Short=AF;
DE Flags: Precursor;
GN Name=xynD;
OS Paenibacillus polymyxa (Bacillus polymyxa).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus.
OX NCBI_TaxID=1406;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 842 / DSM 36 / JCM 2507 / NBRC 15309 / NCIMB 8158 / NCTC 10343
RC / NRRL B-4317 / VKM B-514;
RX PubMed=1938968; DOI=10.1128/jb.173.23.7705-7710.1991;
RA Gosalbes M.J., Perez-Gonzalez J.A., Gonzalez R., Navarro A.;
RT "Two beta-glycanase genes are clustered in Bacillus polymyxa: molecular
RT cloning, expression, and sequence analysis of genes encoding a xylanase and
RT an endo-beta-(1,3)-(1,4)-glucanase.";
RL J. Bacteriol. 173:7705-7710(1991).
RN [2]
RP PROTEIN SEQUENCE OF 27-46, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP ACTIVITY REGULATION.
RC STRAIN=CECT 153 / NCTC 4747 / NRRL NRS-1237;
RX PubMed=8579824; DOI=10.1007/bf00164489;
RA Morales P., Sendra J.M., Perez-Gonzalez J.A.;
RT "Purification and characterization of an arabinofuranosidase from Bacillus
RT polymyxa expressed in Bacillus subtilis.";
RL Appl. Microbiol. Biotechnol. 44:112-117(1995).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (0.8 ANGSTROMS) OF 505-635 IN COMPLEX WITH
RP XYLOTRIOSE.
RC STRAIN=ATCC 842 / DSM 36 / JCM 2507 / NBRC 15309 / NCIMB 8158 / NCTC 10343
RC / NRRL B-4317 / VKM B-514;
RX PubMed=15242594; DOI=10.1016/j.str.2004.04.022;
RA Jamal-Talabani S., Boraston A.B., Turkenburg J.P., Tarbouriech N.,
RA Ducros V.M.-A., Davies G.J.;
RT "Ab initio structure determination and functional characterization of
RT CBM36; a new family of calcium-dependent carbohydrate binding modules.";
RL Structure 12:1177-1187(2004).
CC -!- FUNCTION: Cleaves arabinose units from O-2- or O-3-monosubstituted
CC xylose residues, thereby assisting in arabinoxylan (AX) and short-chain
CC arabinoxylo-oligosaccharide (AXOS) degradation (By similarity).
CC Preferres wheat flour xylan over oat spelt xylan as substrate. Does not
CC display endoxylanase activity. {ECO:0000250,
CC ECO:0000269|PubMed:8579824}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside
CC residues in alpha-L-arabinosides.; EC=3.2.1.55;
CC -!- ACTIVITY REGULATION: Activated by calcium and magnesium. Inhibited by
CC copper. {ECO:0000269|PubMed:8579824}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6.5. {ECO:0000269|PubMed:8579824};
CC Temperature dependence:
CC Optimum temperature is 55 degrees Celsius.
CC {ECO:0000269|PubMed:8579824};
CC -!- PATHWAY: Glycan degradation; xylan degradation.
CC -!- SUBCELLULAR LOCATION: Secreted.
CC -!- DOMAIN: The C-terminal CBM6 domain shows calcium-dependent xylo-
CC oligosaccharide and xylan binding. It binds, next to the structural
CC calcium ion, a second calcium ion that, in addition to its coordination
CC sites on the protein, completes its heptacoordination through
CC coordination to the bound xylose moiety.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 43 family. {ECO:0000305}.
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DR EMBL; X57094; CAA40378.1; -; Genomic_DNA.
DR PIR; S19011; S19011.
DR RefSeq; WP_019687278.1; NZ_UGSC01000001.1.
DR PDB; 1UX7; X-ray; 1.50 A; A=516-635.
DR PDB; 1W0N; X-ray; 0.80 A; A=505-635.
DR PDBsum; 1UX7; -.
DR PDBsum; 1W0N; -.
DR AlphaFoldDB; P45796; -.
DR SMR; P45796; -.
DR STRING; 1052684.PPM_2373; -.
DR CAZy; CBM36; Carbohydrate-Binding Module Family 36.
DR CAZy; CBM6; Carbohydrate-Binding Module Family 6.
DR CAZy; GH43; Glycoside Hydrolase Family 43.
DR GeneID; 66577481; -.
DR eggNOG; COG3507; Bacteria.
DR BRENDA; 3.2.1.8; 683.
DR UniPathway; UPA00114; -.
DR EvolutionaryTrace; P45796; -.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0046556; F:alpha-L-arabinofuranosidase activity; IEA:UniProtKB-EC.
DR GO; GO:0030246; F:carbohydrate binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0045493; P:xylan catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 2.115.10.20; -; 1.
DR InterPro; IPR006584; Cellulose-bd_IV.
DR InterPro; IPR005084; CMB_fam6.
DR InterPro; IPR008979; Galactose-bd-like_sf.
DR InterPro; IPR006710; Glyco_hydro_43.
DR InterPro; IPR023296; Glyco_hydro_beta-prop_sf.
DR Pfam; PF03422; CBM_6; 2.
DR Pfam; PF04616; Glyco_hydro_43; 1.
DR SMART; SM00606; CBD_IV; 1.
DR SUPFAM; SSF49785; SSF49785; 2.
DR SUPFAM; SSF75005; SSF75005; 1.
DR PROSITE; PS51175; CBM6; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Calcium; Carbohydrate metabolism; Direct protein sequencing;
KW Glycosidase; Hydrolase; Metal-binding; Polysaccharide degradation; Repeat;
KW Secreted; Signal; Xylan degradation.
FT SIGNAL 1..26
FT /evidence="ECO:0000269|PubMed:8579824"
FT CHAIN 27..635
FT /note="Arabinoxylan arabinofuranohydrolase"
FT /id="PRO_0000012202"
FT DOMAIN 379..508
FT /note="CBM6 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00523"
FT DOMAIN 517..634
FT /note="CBM6 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00523"
FT ACT_SITE 49
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q45071"
FT ACT_SITE 248
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:Q45071"
FT BINDING 311
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 382
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /ligand_note="structural"
FT /evidence="ECO:0000250"
FT BINDING 384
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /ligand_note="structural"
FT /evidence="ECO:0000250"
FT BINDING 406
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /ligand_note="structural"
FT /evidence="ECO:0000250"
FT BINDING 407
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /ligand_note="structural"
FT /evidence="ECO:0000250"
FT BINDING 503
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /ligand_note="structural"
FT /evidence="ECO:0000250"
FT BINDING 520
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /ligand_note="structural"
FT BINDING 522
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /ligand_note="structural"
FT BINDING 539
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /ligand_note="structural"
FT BINDING 544
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /ligand_note="structural"
FT BINDING 620
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /ligand_note="structural"
FT BINDING 624
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /ligand_note="structural"
FT BINDING 625
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /ligand_note="structural"
FT BINDING 629
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /ligand_note="structural"
FT SITE 188
FT /note="Important for catalytic activity, responsible for
FT pKa modulation of the active site Glu and correct
FT orientation of both the proton donor and substrate"
FT /evidence="ECO:0000250|UniProtKB:Q45071"
FT STRAND 517..520
FT /evidence="ECO:0007829|PDB:1W0N"
FT HELIX 521..523
FT /evidence="ECO:0007829|PDB:1W0N"
FT STRAND 524..530
FT /evidence="ECO:0007829|PDB:1W0N"
FT STRAND 532..534
FT /evidence="ECO:0007829|PDB:1W0N"
FT STRAND 536..543
FT /evidence="ECO:0007829|PDB:1W0N"
FT STRAND 549..581
FT /evidence="ECO:0007829|PDB:1W0N"
FT STRAND 584..595
FT /evidence="ECO:0007829|PDB:1W0N"
FT STRAND 597..605
FT /evidence="ECO:0007829|PDB:1W0N"
FT STRAND 609..618
FT /evidence="ECO:0007829|PDB:1W0N"
FT STRAND 620..623
FT /evidence="ECO:0007829|PDB:1W0N"
FT STRAND 626..634
FT /evidence="ECO:0007829|PDB:1W0N"
SQ SEQUENCE 635 AA; 67914 MW; F9DEC69967323316 CRC64;
MIRKCLVLFL SFALLLSVFP MLNVDAANRP LAKIPGNSNP LMDHKLGADP YSLVYDGRVY
IFMSSDTYVY NKDGSIKEND FSALDRIQVI SSTDMVNWTD HGTIPVAGAN NKNSGRGIAK
WASNSWAPAV AHKKINGRDK FFLYFANGGA GIGVLTADTP IGPWTDPLGK ALVTHSTPGM
AGVTWLFDPA VLVDDDGTGY LYSGGGIPNE SDPASIANPK TARVIKLGAD MTSVIGSATT
IDAPYLFEDS GIHKYNGKYY YSYCINFAGT HPQQYPAGEI GYMVSDNPMG PFTYKGHFLK
NPYTFFGVGG NNHHAVFNFK NEWYVVYHAQ TVSKAQIGAG KGYRSPHINK LVHKEDGSIS
EVQGNMTGIA QLSNMNPYTR VEAETIAWQA GVTTEPTQAS GGPISNLNVT NIHNGDWIAV
GKADFGSAGA KTFKANVATN VGGNIEVRLD SETGPLVGSL KVPSTGGMQT WREVETTINN
ATGVHNIYLV FTGSGSGNLL NLDAWQFTPN TGGNTITKVE AENMKIGGTY AGKISAPFDG
VALYANADYV SYSQYFANST HNISVRGASS NAGTAKVDLV IGGVTVGSFN FTGKTPTVQT
LSNITHATGD QEIKLALTSD DGTWDAYVDF IEFSL
