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{
"metadata": {
"accession": "cd18830",
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"type": "domain",
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"name": {
"name": "Glycosyl hydrolase family 43 protein such as Cellvibrio japonicus Ueda107 endo-alpha-1,5-L-arabinanase / exo-alpha-1,5-L-arabinanase 43A (ArbA;CJA_0805) (Arb43A)",
"short": "GH43_CjArb43A-like"
},
"description": [
{
"text": "<p>This glycosyl hydrolase family 43 (GH43) subgroup includes mostly enzymes annotated with alpha-L-arabinofuranosidase (ABF; EC 3.2.1.55) and endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities, and includes the bifunctional Cellvibrio japonicus Ueda107 endo-alpha-1,5-L-arabinanase / exo-alpha-1,5-L-arabinanase 43A (ArbA;CJA_0805) (Arb43A). It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43 ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside linkages while the ABF enzymes cleave arabinose side chains so that the combined actions of these two enzymes reduce arabinan to L-arabinose and/or arabinooligosaccharides. Many of these enzymes such as the Bacillus subtilis arabinanase Abn2, that hydrolyzes sugar beet arabinan (branched), linear alpha-1,5-L-arabinan and pectin, are different from other arabinases; they are organized into two different domains with a divalent metal cluster close to the catalytic residues to guarantee the correct protonation state of the catalytic residues and consequently the enzyme activity. These arabinan-degrading enzymes are important in the food industry for efficient production of L-arabinose from agricultural waste; L-arabinose is often used as a bioactive sweetener. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. [[cite:PUB00019624], [cite:PUB00116991], [cite:PUB00116990], [cite:PUB00031910], [cite:PUB00038099], [cite:PUB00116785], [cite:PUB00008353], [cite:PUB00116992], [cite:PUB00116989], [cite:PUB00116996], [cite:PUB00116997]]</p>",
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"title": "Structural basis for thermostability of endo-1,5-alpha-L-arabinanase from Bacillus thermodenitrificans TS-3.",
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"medline_journal": "J Biochem",
"ISO_journal": "J. Biochem.",
"authors": [
"Yamaguchi A",
"Tada T",
"Wada K",
"Nakaniwa T",
"Kitatani T",
"Sogabe Y",
"Takao M",
"Sakai T",
"Nishimura K."
],
"DOI_URL": "http://dx.doi.org/10.1093/jb/mvi078"
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"title": "Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus.",
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"medline_journal": "J Bacteriol",
"ISO_journal": "J Bacteriol",
"authors": [
"DeBoy RT",
"Mongodin EF",
"Fouts DE",
"Tailford LE",
"Khouri H",
"Emerson JB",
"Mohamoud Y",
"Watkins K",
"Henrissat B",
"Gilbert HJ",
"Nelson KE."
],
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},
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"title": "Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization.",
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"raw_pages": "1686-1692",
"medline_journal": "Appl Environ Microbiol",
"ISO_journal": "Appl Environ Microbiol",
"authors": [
"Mewis K",
"Lenfant N",
"Lombard V",
"Henrissat B."
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"volume": "9",
"issue": "9",
"year": 2002,
"title": "Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold.",
"URL": null,
"raw_pages": "665-8",
"medline_journal": "Nat Struct Biol",
"ISO_journal": "Nat. Struct. Biol.",
"authors": [
"Nurizzo D",
"Turkenburg JP",
"Charnock SJ",
"Roberts SM",
"Dodson EJ",
"McKie VA",
"Taylor EJ",
"Gilbert HJ",
"Davies GJ."
],
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"volume": "102",
"issue": "8",
"year": 2005,
"title": "Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A.",
"URL": null,
"raw_pages": "2697-702",
"medline_journal": "Proc Natl Acad Sci U S A",
"ISO_journal": "Proc. Natl. Acad. Sci. U.S.A.",
"authors": [
"Proctor MR",
"Taylor EJ",
"Nurizzo D",
"Turkenburg JP",
"Lloyd RM",
"Vardakou M",
"Davies GJ",
"Gilbert HJ."
],
"DOI_URL": "http://dx.doi.org/10.1073/pnas.0500051102"
},
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"volume": "268",
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"year": 2001,
"title": "Biochemical characterization and identification of catalytic residues in alpha-glucuronidase from Bacillus stearothermophilus T-6.",
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"raw_pages": "3006-16",
"medline_journal": "Eur J Biochem",
"ISO_journal": "Eur. J. Biochem.",
"authors": [
"Zaide G",
"Shallom D",
"Shulami S",
"Zolotnitsky G",
"Golan G",
"Baasov T",
"Shoham G",
"Shoham Y."
],
"DOI_URL": "http://dx.doi.org/10.1046/j.1432-1327.2001.02193.x"
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"issue": "Database issue",
"year": 2014,
"title": "The carbohydrate-active enzymes database (CAZy) in 2013.",
"URL": null,
"raw_pages": "D490-5",
"medline_journal": "Nucleic Acids Res",
"ISO_journal": "Nucleic Acids Res",
"authors": [
"Lombard V",
"Golaconda Ramulu H",
"Drula E",
"Coutinho PM",
"Henrissat B."
],
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},
"PUB00116989": {
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"issue": "7",
"year": 2008,
"title": "Factors affecting xylanase functionality in the degradation of arabinoxylans.",
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"raw_pages": "1139-50",
"medline_journal": "Biotechnol Lett",
"ISO_journal": "Biotechnol Lett",
"authors": [
"Berrin JG",
"Juge N."
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"issue": "4-5",
"year": 2014,
"title": "The importance of the Abn2 calcium cluster in the endo-1,5-arabinanase activity from Bacillus subtilis.",
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"medline_journal": "J Biol Inorg Chem",
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"authors": [
"McVey CE",
"Ferreira MJ",
"Correia B",
"Lahiri S",
"de Sanctis D",
"Carrondo MA",
"Lindley PF",
"de Sa Nogueira I",
"Soares CM",
"Bento I."
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"issue": "2-3",
"year": 1993,
"title": "Molecular cloning, expression and structure of the endo-1,5-alpha-L-arabinase gene of Aspergillus niger.",
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"medline_journal": "Appl Microbiol Biotechnol",
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"authors": [
"Flipphi MJ",
"Panneman H",
"van der Veen P",
"Visser J",
"de Graaff LH."
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"title": "Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases.",
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"raw_pages": "7362-73",
"medline_journal": "J Biol Chem",
"ISO_journal": "J Biol Chem",
"authors": [
"Santos CR",
"Polo CC",
"Costa MC",
"Nascimento AF",
"Meza AN",
"Cota J",
"Hoffmam ZB",
"Honorato RV",
"Oliveira PS",
"Goldman GH",
"Gilbert HJ",
"Prade RA",
"Ruller R",
"Squina FM",
"Wong DW",
"Murakami MT."
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},
"set_info": {
"accession": "cl14647",
"name": "GH43_62_32_68_117_130"
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"counters": {
"subfamilies": 0,
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"matches": 527,
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"is_llm": false,
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"representative_structure": {
"accession": "1gyh",
"name": "Structure of D158A Cellvibrio cellulosa alpha-L-arabinanase mutant"
}
}
}
