IABF_GEOSE
ID IABF_GEOSE Reviewed; 502 AA.
AC Q9XBQ3;
DT 26-JUL-2002, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 4.
DT 03-AUG-2022, entry version 86.
DE RecName: Full=Intracellular exo-alpha-(1->5)-L-arabinofuranosidase;
DE Short=ABF;
DE EC=3.2.1.55;
DE AltName: Full=Intracellular arabinan exo-alpha-(1->5)-L-arabinosidase;
DE Short=Arabinosidase;
GN Name=abfA;
OS Geobacillus stearothermophilus (Bacillus stearothermophilus).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX NCBI_TaxID=1422;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=T-6 / NCIMB 40222;
RA Gilead-Gropper S., Gat O., Alchanati I., Yaron S., Bren A., Shoham Y.;
RL Submitted (NOV-2001) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP PROTEIN SEQUENCE OF 2-51, FUNCTION, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL
RP PROPERTIES, INDUCTION, AND SUBUNIT.
RC STRAIN=T-6 / NCIMB 40222;
RX PubMed=7887599; DOI=10.1128/aem.61.1.170-174.1995;
RA Gilead S., Shoham Y.;
RT "Purification and characterization of alpha-L-arabinofuranosidase from
RT Bacillus stearothermophilus T-6.";
RL Appl. Environ. Microbiol. 61:170-174(1995).
RN [3]
RP FUNCTION, MUTAGENESIS OF GLU-175, ACTIVE SITE, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND REACTION MECHANISM.
RX PubMed=11943144; DOI=10.1016/s0014-5793(02)02343-8;
RA Shallom D., Belakhov V., Solomon D., Gilead-Gropper S., Baasov T.,
RA Shoham G., Shoham Y.;
RT "The identification of the acid-base catalyst of alpha-arabinofuranosidase
RT from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase.";
RL FEBS Lett. 514:163-167(2002).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-175 AND GLU-294, ACTIVE
RP SITE, BIOPHYSICOCHEMICAL PROPERTIES, AND REACTION MECHANISM.
RX PubMed=12221104; DOI=10.1074/jbc.m208285200;
RA Shallom D., Belakhov V., Solomon D., Shoham G., Baasov T., Shoham Y.;
RT "Detailed kinetic analysis and identification of the nucleophile in alpha-
RT L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51
RT glycoside hydrolase.";
RL J. Biol. Chem. 277:43667-43673(2002).
RN [5]
RP SUBUNIT.
RX PubMed=12777810; DOI=10.1107/s0907444903004037;
RA Hovel K., Shallom D., Niefind K., Baasov T., Shoham G., Shoham Y.,
RA Schomburg D.;
RT "Crystallization and preliminary X-ray analysis of a family 51 glycoside
RT hydrolase, the alpha-l-arabinofuranosidase from Geobacillus
RT stearothermophilus T-6.";
RL Acta Crystallogr. D 59:913-915(2003).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANT ALA-175 IN COMPLEX WITH
RP SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-175,
RP REACTION MECHANISM, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP SPECIFICITY, AND SUBUNIT.
RX PubMed=14517232; DOI=10.1093/emboj/cdg494;
RA Hovel K., Shallom D., Niefind K., Belakhov V., Shoham G., Baasov T.,
RA Shoham Y., Schomburg D.;
RT "Crystal structure and snapshots along the reaction pathway of a family 51
RT alpha-L-arabinofuranosidase.";
RL EMBO J. 22:4922-4932(2003).
CC -!- FUNCTION: Involved in the degradation of arabinan and is a key enzyme
CC in the complete degradation of the plant cell wall. Catalyzes the
CC cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different
CC hemicellulosic homopolysaccharides (branched and debranched arabinans).
CC It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much
CC less effective on aryl-beta-D-xylopyranosides.
CC {ECO:0000269|PubMed:11943144, ECO:0000269|PubMed:12221104,
CC ECO:0000269|PubMed:14517232, ECO:0000269|PubMed:7887599}.
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 Evidence={ECO:0000269|PubMed:12221104, ECO:0000269|PubMed:14517232};
CC -!- ACTIVITY REGULATION: Strongly inhibited by Hg(2+).
CC {ECO:0000269|PubMed:7887599}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.35 mM for 2,5-dinitro-arabinofuranosyl
CC {ECO:0000269|PubMed:11943144, ECO:0000269|PubMed:12221104,
CC ECO:0000269|PubMed:14517232, ECO:0000269|PubMed:7887599};
CC KM=0.42 mM for p-nitrophenyl alpha-L-arabinofuranoside (pNP-Araf) (at
CC 60 degrees Celsius and at pH 6) {ECO:0000269|PubMed:11943144,
CC ECO:0000269|PubMed:12221104, ECO:0000269|PubMed:14517232,
CC ECO:0000269|PubMed:7887599};
CC KM=0.53 mM for 3,4-dinitro-arabinofuranosyl
CC {ECO:0000269|PubMed:11943144, ECO:0000269|PubMed:12221104,
CC ECO:0000269|PubMed:14517232, ECO:0000269|PubMed:7887599};
CC KM=0.65 mM for 4-nitro-arabinofuranosyl {ECO:0000269|PubMed:11943144,
CC ECO:0000269|PubMed:12221104, ECO:0000269|PubMed:14517232,
CC ECO:0000269|PubMed:7887599};
CC KM=4.4 mM for 3,4-dinitro-xylopyranosyl {ECO:0000269|PubMed:11943144,
CC ECO:0000269|PubMed:12221104, ECO:0000269|PubMed:14517232,
CC ECO:0000269|PubMed:7887599};
CC KM=8 mM for 2,5-dinitro-xylopyranosyl {ECO:0000269|PubMed:11943144,
CC ECO:0000269|PubMed:12221104, ECO:0000269|PubMed:14517232,
CC ECO:0000269|PubMed:7887599};
CC KM=15.3 mM for 2-nitro-xylopyranosyl {ECO:0000269|PubMed:11943144,
CC ECO:0000269|PubMed:12221104, ECO:0000269|PubMed:14517232,
CC ECO:0000269|PubMed:7887599};
CC Vmax=749 umol/min/mg enzyme (at 60 degrees Celsius and at pH 6)
CC {ECO:0000269|PubMed:11943144, ECO:0000269|PubMed:12221104,
CC ECO:0000269|PubMed:14517232, ECO:0000269|PubMed:7887599};
CC Note=Apparently, AbfA can accommodate xylopyranose in the active
CC site, but without the necessary distortion required for the efficient
CC catalysis of six-membered rings. This explains in part its lower
CC specificity towards the xylopyranosidic substrates
CC (PubMed:14517232).;
CC pH dependence:
CC Optimum pH is 5.5-6.0. {ECO:0000269|PubMed:11943144,
CC ECO:0000269|PubMed:12221104, ECO:0000269|PubMed:14517232,
CC ECO:0000269|PubMed:7887599};
CC Temperature dependence:
CC Optimum temperature is 70 degrees Celsius.
CC {ECO:0000269|PubMed:11943144, ECO:0000269|PubMed:12221104,
CC ECO:0000269|PubMed:14517232, ECO:0000269|PubMed:7887599};
CC -!- PATHWAY: Glycan metabolism; L-arabinan degradation.
CC -!- SUBUNIT: Homohexamer; trimer of dimers. {ECO:0000305|PubMed:12777810,
CC ECO:0000305|PubMed:14517232, ECO:0000305|PubMed:7887599}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- INDUCTION: Transcription is repressed by glucose and by the binding of
CC AraR to the operon promoter. L-arabinose acts as an inducer by
CC inhibiting the binding of AraR to the DNA, thus allowing expression of
CC the gene (Probable). {ECO:0000305|PubMed:7887599}.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 51 family. {ECO:0000305}.
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DR EMBL; AF159625; AAD45520.2; -; Genomic_DNA.
DR PDB; 1PZ2; X-ray; 2.00 A; A/B=1-502.
DR PDB; 1PZ3; X-ray; 1.75 A; A/B=1-502.
DR PDB; 1QW8; X-ray; 1.80 A; A/B=1-502.
DR PDB; 1QW9; X-ray; 1.20 A; A/B=1-502.
DR PDB; 6SXU; X-ray; 1.40 A; AAA/BBB=1-502.
DR PDB; 6SXV; X-ray; 1.40 A; A/B=1-502.
DR PDBsum; 1PZ2; -.
DR PDBsum; 1PZ3; -.
DR PDBsum; 1QW8; -.
DR PDBsum; 1QW9; -.
DR PDBsum; 6SXU; -.
DR PDBsum; 6SXV; -.
DR AlphaFoldDB; Q9XBQ3; -.
DR SMR; Q9XBQ3; -.
DR DrugBank; DB03196; 4-Nitrophenyl-Ara.
DR DrugBank; DB03870; Ara-Alpha(1,3)-Xyl.
DR CAZy; GH51; Glycoside Hydrolase Family 51.
DR BRENDA; 3.2.1.55; 623.
DR UniPathway; UPA00667; -.
DR EvolutionaryTrace; Q9XBQ3; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0046556; F:alpha-L-arabinofuranosidase activity; IEA:UniProtKB-EC.
DR GO; GO:0031222; P:arabinan catabolic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0046373; P:L-arabinose metabolic process; IEA:InterPro.
DR Gene3D; 2.60.40.1180; -; 1.
DR InterPro; IPR010720; Alpha-L-AF_C.
DR InterPro; IPR013780; Glyco_hydro_b.
DR InterPro; IPR017853; Glycoside_hydrolase_SF.
DR Pfam; PF06964; Alpha-L-AF_C; 1.
DR SMART; SM00813; Alpha-L-AF_C; 1.
DR SUPFAM; SSF51445; SSF51445; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Cytoplasm;
KW Direct protein sequencing; Glycosidase; Hydrolase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:7887599"
FT CHAIN 2..502
FT /note="Intracellular exo-alpha-(1->5)-L-
FT arabinofuranosidase"
FT /id="PRO_0000057700"
FT ACT_SITE 175
FT /note="Proton donor/acceptor"
FT ACT_SITE 294
FT /note="Nucleophile"
FT BINDING 29
FT /ligand="substrate"
FT BINDING 74
FT /ligand="substrate"
FT BINDING 174..175
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 246
FT /ligand="substrate"
FT BINDING 294
FT /ligand="substrate"
FT BINDING 351
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 298
FT /note="Important for substrate recognition"
FT /evidence="ECO:0000305"
FT SITE 351
FT /note="Important for substrate recognition"
FT /evidence="ECO:0000305"
FT MUTAGEN 175
FT /note="E->A: Strongly reduced catalytic activity. Increases
FT affinity for substrates. The mutant has an effect on the
FT glycosylation step. The removal of the acid-base catalyst
FT seems to have affected the ionization state of the
FT nucleophile, elevating its pKa, reducing its acidity, and
FT shifting the optimal pH to higher values."
FT /evidence="ECO:0000269|PubMed:11943144,
FT ECO:0000269|PubMed:12221104, ECO:0000269|PubMed:14517232"
FT MUTAGEN 294
FT /note="E->A: Abolishes catalytic activity, but the binding
FT affinity shows only a small change."
FT /evidence="ECO:0000269|PubMed:12221104"
FT STRAND 6..9
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 14..18
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 21..24
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 25..27
FT /evidence="ECO:0007829|PDB:1QW9"
FT TURN 37..39
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 54..62
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 67..71
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 74..78
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 81..84
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 88..90
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 94..96
FT /evidence="ECO:0007829|PDB:1QW9"
FT TURN 97..100
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 109..119
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 122..127
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 134..145
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 151..158
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 169..174
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 187..204
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 209..212
FT /evidence="ECO:0007829|PDB:1QW9"
FT TURN 221..224
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 225..234
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 239..247
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 254..258
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 261..282
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 289..297
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 302..305
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 312..314
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 324..339
FT /evidence="ECO:0007829|PDB:1QW9"
FT TURN 340..343
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 344..350
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 352..356
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 358..361
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 367..369
FT /evidence="ECO:0007829|PDB:1QW9"
FT HELIX 373..382
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 385..388
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 391..393
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 403..415
FT /evidence="ECO:0007829|PDB:1QW9"
FT TURN 416..419
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 420..427
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 430..432
FT /evidence="ECO:0007829|PDB:1PZ3"
FT STRAND 434..439
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 447..454
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 473..475
FT /evidence="ECO:0007829|PDB:1PZ3"
FT STRAND 479..481
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 484..489
FT /evidence="ECO:0007829|PDB:1QW9"
FT STRAND 491..500
FT /evidence="ECO:0007829|PDB:1QW9"
SQ SEQUENCE 502 AA; 57212 MW; 37C048AE29DBB230 CRC64;
MATKKATMII EKDFKIAEID KRIYGSFIEH LGRAVYGGIY EPGHPQADEN GFRQDVIELV
KELQVPIIRY PGGNFVSGYN WEDGVGPKEQ RPRRLDLAWK SVETNEIGLN EFMDWAKMVG
AEVNMAVNLG TRGIDAARNL VEYCNHPSGS YYSDLRIAHG YKEPHKIKTW CLGNEMDGPW
QIGHKTAVEY GRIACEAAKV MKWVDPTIEL VVCGSSNRNM PTFAEWEATV LDHTYDHVDY
ISLHQYYGNR DNDTANYLAL SLEMDDFIRS VVAIADYVKA KKRSKKTIHL SFDEWNVWYH
SNEADKLIEP WTVAPPLLED IYNFEDALLV GCMLITLMKH ADRVKIACLA QLVNVIAPIM
TEKNGPAWKQ TIYYPFMHAS VYGRGVALHP VISSPKYDSK DFTDVPYLES IAVYNEEKEE
VTIFAVNRDM EDALLLECDV RSFEDYRVIE HIVLEHDNVK QTNSAQSSPV VPHRNGDAQL
SDRKVSATLP KLSWNVIRLG KR
