XYND_BACSU
ID XYND_BACSU Reviewed; 513 AA.
AC Q45071;
DT 20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 2.
DT 03-AUG-2022, entry version 124.
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; OrderedLocusNames=BSU18160;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [2]
RP PROTEIN SEQUENCE OF 27-37, AND SUBCELLULAR LOCATION.
RC STRAIN=168;
RX PubMed=10658653; DOI=10.1099/00221287-146-1-65;
RA Hirose I., Sano K., Shioda I., Kumano M., Nakamura K., Yamane K.;
RT "Proteome analysis of Bacillus subtilis extracellular proteins: a two-
RT dimensional protein electrophoretic study.";
RL Microbiology 146:65-75(2000).
RN [3]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND MASS SPECTROMETRY.
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=17426966; DOI=10.1007/s00253-007-0956-2;
RA Bourgois T.M., Van Craeyveld V., Van Campenhout S., Courtin C.M.,
RA Delcour J.A., Robben J., Volckaert G.;
RT "Recombinant expression and characterization of XynD from Bacillus subtilis
RT subsp. subtilis ATCC 6051: a GH 43 arabinoxylan arabinofuranohydrolase.";
RL Appl. Microbiol. Biotechnol. 75:1309-1317(2007).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF 27-513 IN COMPLEXES WITH
RP XYLOTRIOSE; XYLOTETRAOSE; ARABINOXYLO-OLIGOSACCHARIDES AND CELLOTETRAOSE,
RP AND ACTIVE SITE.
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=18980579; DOI=10.1042/bj20081256;
RA Vandermarliere E., Bourgois T.M., Winn M.D., van Campenhout S.,
RA Volckaert G., Delcour J.A., Strelkov S.V., Rabijns A., Courtin C.M.;
RT "Structural analysis of a glycoside hydrolase family 43 arabinoxylan
RT arabinofuranohydrolase in complex with xylotetraose reveals a different
RT binding mechanism compared with other members of the same family.";
RL Biochem. J. 418:39-47(2009).
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. Is more active on wheat
CC bran AXOS than on wheat water-extractable AX and rye water-extractable
CC AX. Does not display endoxylanase, xylosidase or arabinanase activity.
CC {ECO:0000269|PubMed:17426966}.
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 -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 5.6. Stable from pH 4.4 to 7.6.
CC {ECO:0000269|PubMed:17426966};
CC Temperature dependence:
CC Optimum temperature is 45 degrees Celsius. Thermostable for 40 min
CC from 4 to 45 degrees Celsius. {ECO:0000269|PubMed:17426966};
CC -!- PATHWAY: Glycan degradation; xylan degradation.
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000269|PubMed:10658653}.
CC -!- DOMAIN: The CBM6 domain lost its carbohydrate binding capacity.
CC -!- MASS SPECTROMETRY: Mass=52080; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:17426966};
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 43 family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AL009126; CAB13699.1; -; Genomic_DNA.
DR PIR; H69735; H69735.
DR RefSeq; NP_389698.1; NC_000964.3.
DR RefSeq; WP_003245027.1; NZ_JNCM01000035.1.
DR PDB; 3C7E; X-ray; 2.00 A; A=27-513.
DR PDB; 3C7F; X-ray; 1.55 A; A=27-513.
DR PDB; 3C7G; X-ray; 2.02 A; A=27-513.
DR PDB; 3C7H; X-ray; 2.00 A; A=27-513.
DR PDB; 3C7O; X-ray; 1.80 A; A=27-513.
DR PDBsum; 3C7E; -.
DR PDBsum; 3C7F; -.
DR PDBsum; 3C7G; -.
DR PDBsum; 3C7H; -.
DR PDBsum; 3C7O; -.
DR AlphaFoldDB; Q45071; -.
DR SMR; Q45071; -.
DR STRING; 224308.BSU18160; -.
DR CAZy; CBM6; Carbohydrate-Binding Module Family 6.
DR CAZy; GH43; Glycoside Hydrolase Family 43.
DR PaxDb; Q45071; -.
DR PRIDE; Q45071; -.
DR EnsemblBacteria; CAB13699; CAB13699; BSU_18160.
DR GeneID; 936433; -.
DR KEGG; bsu:BSU18160; -.
DR PATRIC; fig|224308.179.peg.1980; -.
DR eggNOG; COG3507; Bacteria.
DR InParanoid; Q45071; -.
DR OMA; FNFNWWQ; -.
DR PhylomeDB; Q45071; -.
DR BioCyc; BSUB:BSU18160-MON; -.
DR BioCyc; MetaCyc:BSU18160-MON; -.
DR BRENDA; 3.2.1.55; 658.
DR UniPathway; UPA00114; -.
DR EvolutionaryTrace; Q45071; -.
DR Proteomes; UP000001570; Chromosome.
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; 1.
DR Pfam; PF04616; Glyco_hydro_43; 1.
DR SMART; SM00606; CBD_IV; 1.
DR SUPFAM; SSF49785; SSF49785; 1.
DR SUPFAM; SSF75005; SSF75005; 1.
DR PROSITE; PS51175; CBM6; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Calcium; Carbohydrate metabolism; Direct protein sequencing;
KW Glycosidase; Hydrolase; Metal-binding; Polysaccharide degradation;
KW Reference proteome; Secreted; Signal; Xylan degradation.
FT SIGNAL 1..26
FT /evidence="ECO:0000269|PubMed:10658653"
FT CHAIN 27..513
FT /note="Arabinoxylan arabinofuranohydrolase"
FT /id="PRO_0000360828"
FT DOMAIN 382..511
FT /note="CBM6"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00523"
FT ACT_SITE 50
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:18980579"
FT ACT_SITE 251
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:18980579"
FT BINDING 314
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18980579"
FT BINDING 385
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:18980579"
FT BINDING 387
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:18980579"
FT BINDING 409
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:18980579"
FT BINDING 410
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:18980579"
FT BINDING 506
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:18980579"
FT SITE 189
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:0000305|PubMed:18980579"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 49..56
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 59..65
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 87..105
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 110..112
FT /evidence="ECO:0007829|PDB:3C7G"
FT HELIX 113..116
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 127..136
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 139..148
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 153..160
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 168..171
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 185..187
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 191..194
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 200..205
FT /evidence="ECO:0007829|PDB:3C7F"
FT HELIX 216..220
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 225..230
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 234..244
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 249..258
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 261..268
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 270..272
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 282..290
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 296..302
FT /evidence="ECO:0007829|PDB:3C7F"
FT HELIX 305..309
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 317..322
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 325..333
FT /evidence="ECO:0007829|PDB:3C7F"
FT HELIX 334..340
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 348..353
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 388..394
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 396..399
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 410..413
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 420..427
FT /evidence="ECO:0007829|PDB:3C7F"
FT TURN 429..431
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 433..441
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 446..454
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 459..465
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 475..480
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 486..495
FT /evidence="ECO:0007829|PDB:3C7F"
FT STRAND 497..500
FT /evidence="ECO:0007829|PDB:3C7O"
FT STRAND 504..512
FT /evidence="ECO:0007829|PDB:3C7F"
SQ SEQUENCE 513 AA; 54498 MW; 1EBC94AB6CE1490F CRC64;
MRKKCSVCLW ILVLLLSCLS GKSAYAATST TIAKHIGNSN PLIDHHLGAD PVALTYNGRV
YIYMSSDDYE YNSNGTIKDN SFANLNRVFV ISSADMVNWT DHGAIPVAGA NGANGGRGIA
KWAGASWAPS IAVKKINGKD KFFLYFANSG GGIGVLTADS PIGPWTDPIG KPLVTPSTPG
MSGVVWLFDP AVFVDDDGTG YLYAGGGVPG VSNPTQGQWA NPKTARVIKL GPDMTSVVGS
ASTIDAPFMF EDSGLHKYNG TYYYSYCINF GGTHPADKPP GEIGYMTSSS PMGPFTYRGH
FLKNPGAFFG GGGNNHHAVF NFKNEWYVVY HAQTVSSALF GAGKGYRSPH INKLVHNADG
SIQEVAANYA GVTQISNLNP YNRVEAETFA WNGRILTEKS TAPGGPVNNQ HVTSIQNGDW
IAVGNADFGA GGARSFKANV ASTLGGKIEV RLDSADGKLV GTLNVPSTGG AQTWREIETA
VSGATGVHKV FFVFTGTGTG NLFNFDYWQF TQR
