HYBA1_BIFL2
ID HYBA1_BIFL2 Reviewed; 658 AA.
AC E8MGH8; G1UHC6;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 05-APR-2011, sequence version 1.
DT 03-AUG-2022, entry version 52.
DE RecName: Full=Non-reducing end beta-L-arabinofuranosidase {ECO:0000305};
DE EC=3.2.1.185 {ECO:0000269|PubMed:24385433};
DE AltName: Full=Beta-L-arabinofuranosidase {ECO:0000303|PubMed:24385433};
DE Short=Beta-AFase {ECO:0000303|PubMed:24680821};
GN Name=hypBA1 {ECO:0000303|PubMed:24385433}; OrderedLocusNames=BLLJ_0211;
OS Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM
OS 1217 / NCTC 11818 / E194b).
OC Bacteria; Actinobacteria; Bifidobacteriales; Bifidobacteriaceae;
OC Bifidobacterium.
OX NCBI_TaxID=565042;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF GLU-322; GLU-338 AND
RP GLU-366.
RC STRAIN=ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b;
RX PubMed=24385433; DOI=10.1074/jbc.m113.528711;
RA Fujita K., Takashi Y., Obuchi E., Kitahara K., Suganuma T.;
RT "Characterization of a novel beta-L-arabinofuranosidase in Bifidobacterium
RT longum: functional elucidation of a DUF1680 protein family member.";
RL J. Biol. Chem. 289:5240-5249(2014).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b;
RX PubMed=21270894; DOI=10.1038/nature09646;
RA Fukuda S., Toh H., Hase K., Oshima K., Nakanishi Y., Yoshimura K., Tobe T.,
RA Clarke J.M., Topping D.L., Suzuki T., Taylor T.D., Itoh K., Kikuchi J.,
RA Morita H., Hattori M., Ohno H.;
RT "Bifidobacteria can protect from enteropathogenic infection through
RT production of acetate.";
RL Nature 469:543-547(2011).
RN [3]
RP RETRACTED PAPER.
RC STRAIN=ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b;
RX PubMed=21914802; DOI=10.1074/jbc.m111.248690;
RA Fujita K., Takashi Y., Obuchi E., Kitahara K., Suganuma T.;
RT "Characterization of a novel beta-L-Arabinofuranosidase in Bifidobacterium
RT longum: functional elucidation of A DUF1680 family member.";
RL J. Biol. Chem. 286:38079-38085(2011).
RN [4]
RP RETRACTION NOTICE OF PUBMED:21914802.
RX PubMed=24143008; DOI=10.1074/jbc.a111.248690;
RA Fujita K., Takashi Y., Obuchi E., Kitahara K., Suganuma T.;
RL J. Biol. Chem. 288:30502-30502(2013).
RN [5]
RP CRYSTALLIZATION.
RC STRAIN=ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b;
RX PubMed=24817727; DOI=10.1107/s2053230x14001812;
RA Zhu Z., He M., Huang C.H., Ko T.P., Zeng Y.F., Huang Y.N., Jia S., Lu F.,
RA Liu J.R., Guo R.T.;
RT "Crystallization and preliminary X-ray diffraction analysis of a novel
RT beta-L-arabinofuranosidase (HypBA1) from Bifidobacterium longum.";
RL Acta Crystallogr. F Struct. Biol. Commun. 70:636-638(2014).
RN [6] {ECO:0007744|PDB:3WKW, ECO:0007744|PDB:3WKX}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP ZINC AND BETA-L-ARABINOFURANOSE, REACTION MECHANISM, COFACTOR, ACTIVITY
RP REGULATION, SUBUNIT, ACTIVE SITE, AND MUTAGENESIS OF GLU-322; GLU-338;
RP CYS-340; CYS-415; CYS-417 AND CYS-418.
RC STRAIN=ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b;
RX PubMed=24680821; DOI=10.1016/j.bbrc.2014.03.096;
RA Ito T., Saikawa K., Kim S., Fujita K., Ishiwata A., Kaeothip S.,
RA Arakawa T., Wakagi T., Beckham G.T., Ito Y., Fushinobu S.;
RT "Crystal structure of glycoside hydrolase family 127 beta-l-
RT arabinofuranosidase from Bifidobacterium longum.";
RL Biochem. Biophys. Res. Commun. 447:32-37(2014).
RN [7] {ECO:0007744|PDB:3WRE, ECO:0007744|PDB:3WRF, ECO:0007744|PDB:3WRG}
RP X-RAY CRYSTALLOGRAPHY (2.23 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP ZINC AND BETA-L-ARABINOFURANOSE, REACTION MECHANISM, COFACTOR, SUBUNIT, AND
RP ACTIVE SITE.
RC STRAIN=ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b;
RX DOI=10.4172/2155-9821.1000171;
RA Huang C.H., Zhu Z., Cheng Y.S., Chan H.C., Ko T.P., Chen C.C., Wang I.,
RA Ho M.R., Hsu S.T., Zeng Y.F., Huang Y.N., Liu J.R., Guo R.T.;
RT "Structure and catalytic mechanism of a glycoside hydrolase family-127
RT beta-L-arabinofuranosidase (HypBA1).";
RL J. Bioprocess. Biotech. 4:1000171-1000171(2014).
CC -!- FUNCTION: Beta-L-arabinofuranosidase that removes the beta-L-
CC arabinofuranose residue from the non-reducing end of various
CC substrates, including beta-L-arabinofuranosyl-hydroxyproline (Ara-Hyp),
CC Ara-beta-1,2-Ara-beta-Hyp (Ara(2)-Hyp), Ara-beta-1,2-Ara-beta-1,2-Ara-
CC beta-Hyp (Ara(3)-Hyp), and beta-L-arabinofuranosyl-(1->2)-1-O-methyl-
CC beta-L-arabinofuranose. In the presence of 1-alkanols, shows
CC transglycosylation activity, retaining the anomeric configuration of
CC the arabinofuranose residue. {ECO:0000269|PubMed:24385433}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose + H2O =
CC 2 beta-L-arabinofuranose; Xref=Rhea:RHEA:36051, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:28272, ChEBI:CHEBI:73180; EC=3.2.1.185;
CC Evidence={ECO:0000269|PubMed:24385433};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:24680821, ECO:0000269|Ref.7};
CC Note=Zn(2+) ion is involved in the catalytic reaction through
CC maintaining the proper configuration of active site.
CC {ECO:0000269|Ref.7};
CC -!- ACTIVITY REGULATION: Strongly inhibited in the presence of thiol
CC modifiers, suggesting a crucial role for cysteine residues in
CC catalysis. Slightly inhibited by EDTA. {ECO:0000269|PubMed:24680821}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.85 mM for L-arabinofuranose-beta-1,2-L-arabinofuranose
CC disaccharide (beta-Ara2) {ECO:0000269|PubMed:24385433};
CC KM=0.43 mM for Ara-Hyp {ECO:0000269|PubMed:24385433};
CC KM=0.31 mM for Ara(2)-Hyp {ECO:0000269|PubMed:24385433};
CC Note=kcat is 2.0 sec(-1) with beta-Ara2. kcat is 0.013 sec(-1) with
CC Ara-Hyp. kcat is 6.3 sec(-1) with Ara(2)-Hyp.
CC {ECO:0000269|PubMed:24385433};
CC -!- SUBUNIT: Homodimer in solution. {ECO:0000269|PubMed:24680821,
CC ECO:0000269|Ref.7}.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 127 family.
CC {ECO:0000305}.
CC -!- CAUTION: The original article describing the function has been
CC retracted because the results of E338A and E366A mutants were reversed.
CC The authors later submitted a corrected manuscript.
CC {ECO:0000305|PubMed:21914802, ECO:0000305|PubMed:24143008}.
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DR EMBL; AB619598; BAK79118.1; -; Genomic_DNA.
DR EMBL; AP010888; BAJ65881.1; -; Genomic_DNA.
DR RefSeq; WP_013582351.1; NC_015067.1.
DR PDB; 3WKW; X-ray; 2.20 A; A=1-658.
DR PDB; 3WKX; X-ray; 2.00 A; A=1-658.
DR PDB; 3WRE; X-ray; 2.78 A; A=1-658.
DR PDB; 3WRF; X-ray; 2.25 A; A=1-658.
DR PDB; 3WRG; X-ray; 2.23 A; A=1-658.
DR PDB; 7BZL; X-ray; 2.30 A; A=1-658.
DR PDB; 7DIF; X-ray; 1.75 A; A=1-658.
DR PDB; 7EXU; X-ray; 2.30 A; A=1-658.
DR PDB; 7EXV; X-ray; 2.60 A; A=1-658.
DR PDB; 7EXW; X-ray; 2.20 A; A=1-658.
DR PDBsum; 3WKW; -.
DR PDBsum; 3WKX; -.
DR PDBsum; 3WRE; -.
DR PDBsum; 3WRF; -.
DR PDBsum; 3WRG; -.
DR PDBsum; 7BZL; -.
DR PDBsum; 7DIF; -.
DR PDBsum; 7EXU; -.
DR PDBsum; 7EXV; -.
DR PDBsum; 7EXW; -.
DR AlphaFoldDB; E8MGH8; -.
DR SMR; E8MGH8; -.
DR CAZy; GH127; Glycoside Hydrolase Family 127.
DR KEGG; blm:BLLJ_0211; -.
DR HOGENOM; CLU_013148_3_1_11; -.
DR OMA; LYSGMAD; -.
DR BRENDA; 3.2.1.185; 851.
DR GO; GO:0102478; F:beta-L-arabinofuranosidase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000272; P:polysaccharide catabolic process; IEA:UniProtKB-KW.
DR Gene3D; 1.50.10.10; -; 1.
DR InterPro; IPR008928; 6-hairpin_glycosidase_sf.
DR InterPro; IPR012341; 6hp_glycosidase-like_sf.
DR InterPro; IPR012878; Glyco_hydro_127.
DR Pfam; PF07944; Glyco_hydro_127; 1.
DR SUPFAM; SSF48208; SSF48208; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Glycosidase; Hydrolase;
KW Metal-binding; Polysaccharide degradation; Zinc.
FT CHAIN 1..658
FT /note="Non-reducing end beta-L-arabinofuranosidase"
FT /id="PRO_0000423555"
FT ACT_SITE 322
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:24680821, ECO:0000305|Ref.7"
FT ACT_SITE 417
FT /note="Nucleophile; S-glycosyl-cysteine intermediate"
FT /evidence="ECO:0000305|PubMed:24680821, ECO:0000305|Ref.7"
FT BINDING 142
FT /ligand="beta-L-arabinofuranose"
FT /ligand_id="ChEBI:CHEBI:28272"
FT /evidence="ECO:0000269|PubMed:24680821, ECO:0000269|Ref.7,
FT ECO:0007744|PDB:3WKX, ECO:0007744|PDB:3WRG"
FT BINDING 192..194
FT /ligand="beta-L-arabinofuranose"
FT /ligand_id="ChEBI:CHEBI:28272"
FT /evidence="ECO:0000269|PubMed:24680821, ECO:0000269|Ref.7,
FT ECO:0007744|PDB:3WKX, ECO:0007744|PDB:3WRG"
FT BINDING 270
FT /ligand="beta-L-arabinofuranose"
FT /ligand_id="ChEBI:CHEBI:28272"
FT /evidence="ECO:0000269|PubMed:24680821, ECO:0000269|Ref.7,
FT ECO:0007744|PDB:3WKX, ECO:0007744|PDB:3WRG"
FT BINDING 322
FT /ligand="beta-L-arabinofuranose"
FT /ligand_id="ChEBI:CHEBI:28272"
FT /evidence="ECO:0000269|PubMed:24680821, ECO:0000269|Ref.7,
FT ECO:0007744|PDB:3WKX, ECO:0007744|PDB:3WRG"
FT BINDING 338
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:24680821, ECO:0000269|Ref.7,
FT ECO:0007744|PDB:3WKX, ECO:0007744|PDB:3WRE,
FT ECO:0007744|PDB:3WRG"
FT BINDING 340
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:24680821, ECO:0000269|Ref.7,
FT ECO:0007744|PDB:3WKX, ECO:0007744|PDB:3WRE,
FT ECO:0007744|PDB:3WRG"
FT BINDING 417
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:24680821, ECO:0000269|Ref.7,
FT ECO:0007744|PDB:3WKX, ECO:0007744|PDB:3WRE,
FT ECO:0007744|PDB:3WRG"
FT BINDING 418
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:24680821, ECO:0000269|Ref.7,
FT ECO:0007744|PDB:3WKX, ECO:0007744|PDB:3WRE,
FT ECO:0007744|PDB:3WRG"
FT MUTAGEN 322
FT /note="E->A: Almost abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:24385433,
FT ECO:0000269|PubMed:24680821"
FT MUTAGEN 322
FT /note="E->Q: Shows very weak activity."
FT /evidence="ECO:0000269|PubMed:24680821"
FT MUTAGEN 338
FT /note="E->A,Q: Decreases Zn(2+) content. Shows very weak
FT activity."
FT /evidence="ECO:0000269|PubMed:24680821"
FT MUTAGEN 338
FT /note="E->A: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:24385433"
FT MUTAGEN 340
FT /note="C->A,S: Decreases Zn(2+) content. Shows very weak
FT activity."
FT /evidence="ECO:0000269|PubMed:24680821"
FT MUTAGEN 366
FT /note="E->A: Insoluble protein with remaining enzyme
FT activity."
FT /evidence="ECO:0000269|PubMed:24385433"
FT MUTAGEN 415
FT /note="C->A,S: Retains weak activity."
FT /evidence="ECO:0000269|PubMed:24680821"
FT MUTAGEN 417
FT /note="C->A,S: Decreases Zn(2+) content. Lack of activity."
FT /evidence="ECO:0000269|PubMed:24680821"
FT MUTAGEN 418
FT /note="C->A,S: Decreases Zn(2+) content. Shows very weak
FT activity."
FT /evidence="ECO:0000269|PubMed:24680821"
FT STRAND 2..5
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 8..19
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 21..29
FT /evidence="ECO:0007829|PDB:7DIF"
FT TURN 30..32
FT /evidence="ECO:0007829|PDB:3WRG"
FT STRAND 41..45
FT /evidence="ECO:0007829|PDB:3WRG"
FT HELIX 53..60
FT /evidence="ECO:0007829|PDB:7DIF"
FT TURN 72..74
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 75..91
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 95..111
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 121..124
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 127..131
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 138..141
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 143..161
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 164..180
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 181..184
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 197..208
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 211..223
FT /evidence="ECO:0007829|PDB:7DIF"
FT TURN 224..226
FT /evidence="ECO:0007829|PDB:7EXW"
FT HELIX 230..237
FT /evidence="ECO:0007829|PDB:7DIF"
FT TURN 238..240
FT /evidence="ECO:0007829|PDB:7DIF"
FT TURN 252..255
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 261..263
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 271..288
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 291..307
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 320..322
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 332..334
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 339..355
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 359..370
FT /evidence="ECO:0007829|PDB:7DIF"
FT TURN 371..373
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 374..376
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 390..392
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 394..398
FT /evidence="ECO:0007829|PDB:7DIF"
FT TURN 400..404
FT /evidence="ECO:0007829|PDB:7DIF"
FT TURN 414..416
FT /evidence="ECO:0007829|PDB:3WRE"
FT HELIX 419..427
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 429..432
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 433..437
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 438..440
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 442..445
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 451..454
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 460..464
FT /evidence="ECO:0007829|PDB:7DIF"
FT TURN 467..469
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 472..478
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 484..493
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 496..498
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 503..506
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 519..525
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 529..535
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 540..543
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 550..552
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 555..560
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 563..568
FT /evidence="ECO:0007829|PDB:7DIF"
FT TURN 569..571
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 572..574
FT /evidence="ECO:0007829|PDB:3WRF"
FT HELIX 576..578
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 579..581
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 587..589
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 591..595
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 601..612
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 631..640
FT /evidence="ECO:0007829|PDB:7DIF"
FT HELIX 641..643
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 646..648
FT /evidence="ECO:0007829|PDB:7DIF"
FT STRAND 652..657
FT /evidence="ECO:0007829|PDB:7DIF"
SQ SEQUENCE 658 AA; 73098 MW; 525D5452021EECB1 CRC64;
MNVTITSPFW KRRRDQIVES VIPYQWGVMN DEIDTTVPDD PAGNQLADSK SHAVANLKVA
AGELDDEFHG MVFQDSDVYK WLEEAAYALA YHPDPELKAL CDRTVDLIAR AQQSDGYLDT
PYQIKSGVWA DRPRFSLIQQ SHEMYVMGHY IEAAVAYHQV TGNEQALEVA KKMADCLDAN
FGPEEGKIHG ADGHPEIELA LAKLYEETGE KRYLTLSQYL IDVRGQDPQF YAKQLKAMNG
DNIFHDLGFY KPTYFQAAEP VRDQQTADGH AVRVGYLCTG VAHVGRLLGD QGLIDTAKRF
WKNIVTRRMY VTGAIGSTHV GESFTYDYDL PNDTMYGETC ASVAMSMFAQ QMLDLEPKGE
YADVLEKELF NGSIAGISLD GKQYYYVNAL ETTPDGLDNP DRHHVLSHRV DWFGCACCPA
NIARLIASVD RYIYTERDGG KTVLSHQFIA NTAEFASGLT VEQRSNFPWD GHVEYTVSLP
ASATDSSVRF GLRIPGWSRG SYTLTVNGKP AVGSLEDGFV YLVVNAGDTL EIALELDMSV
KFVRANSRVR SDAGQVAVMR GPLVYCAEQV DNPGDLWNYR LADGVTGADA AVAFQADLLG
GVDTVDLPAV REHADEDDAP LYVDADEPRA GEPATLRLVP YYSWANREIG EMRVFQRR
