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Protein

Extracellular endo-alpha-(1->5)-L-arabinanase 2

Gene

abn2

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues of the alpha-1,5-L-arabinan to produce arabino-oligosaccharides and L-arabinose. It is also active toward linear branched sugar beet arabinan, and pectin from apple.2 Publications

Catalytic activityi

Endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5)-arabinans.1 Publication

Cofactori

Ca2+CuratedNote: Binds 1 Ca2+ ion per subunit.Curated

Kineticsi

  1. KM=0.11 mM for linear-alpha-1,5-L-arabinan2 Publications
  2. KM=2 mM for linear-alpha-1,5-L-arabinan (at pH 7.0 and 50 degrees Celsius)2 Publications
  1. Vmax=0.25 mmol/min/mg enzyme for linear-alpha-1,5-L-arabinan (at pH 7.0 and 50 degrees Celsius)2 Publications

pH dependencei

Optimum pH is 7.2 Publications

Temperature dependencei

Optimum temperature is 50 degrees Celsius. It remains fully active after 30 minutes of preincubation at 50 degrees Celsius, however, after preincubation at 60 degrees Celsius, the residual activity is only 15%.2 Publications

Pathwayi: L-arabinan degradation

This protein is involved in the pathway L-arabinan degradation, which is part of Glycan metabolism.
View all proteins of this organism that are known to be involved in the pathway L-arabinan degradation and in Glycan metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei38 – 381Proton acceptor1 Publication
Binding sitei38 – 381SubstrateBy similarity
Binding sitei122 – 1221Substrate; via amide nitrogenBy similarity
Sitei171 – 1711Important for catalytic activity
Active sitei224 – 2241Proton donor1 Publication
Metal bindingi318 – 3181CalciumSequence analysis
Sitei318 – 3181Important for substrate recognition

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Carbohydrate metabolism

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BioCyciBSUB:BSU39330-MONOMER.
BRENDAi3.2.1.99. 658.
UniPathwayiUPA00667.

Protein family/group databases

CAZyiGH43. Glycoside Hydrolase Family 43.

Names & Taxonomyi

Protein namesi
Recommended name:
Extracellular endo-alpha-(1->5)-L-arabinanase 2 (EC:3.2.1.99)
Short name:
ABN
Alternative name(s):
Endo-1,5-alpha-L-arabinanase
Gene namesi
Name:abn2
Synonyms:J3A, yxiA
Ordered Locus Names:BSU39330
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Disruption phenotypei

No visible phenotype. Double mutant abn2/abnA induce an almost complete loss of this activity.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi38 – 381D → A: Loss of arabinanase activity. 1 Publication
Mutagenesisi171 – 1711D → A: Loss of arabinanase activity. 1 Publication
Mutagenesisi224 – 2241E → A: Loss of arabinanase activity. 1 Publication
Mutagenesisi318 – 3181H → A: Drastic decrease in arabinanase activity. Does not unduly disrupt the calcium cluster. Mutation does not disrupt the calcium cluster, but it relaxes the geometry of the cluster, resulting in a more planar arrangement of the calcium ion with five of the water molecules. 1 Publication
Mutagenesisi318 – 3181H → Q: Loss of arabinanase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2626Sequence analysisAdd
BLAST
Chaini27 – 469443Extracellular endo-alpha-(1->5)-L-arabinanase 2PRO_0000012205Add
BLAST

Proteomic databases

PaxDbiP42293.

Expressioni

Inductioni

Repressed by glucose, and induced by pectin and arabinan.1 Publication

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100021221.

Structurei

Secondary structure

1
469
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi40 – 445Combined sources
Beta strandi47 – 515Combined sources
Helixi53 – 553Combined sources
Beta strandi57 – 659Combined sources
Beta strandi67 – 704Combined sources
Helixi83 – 864Combined sources
Helixi88 – 947Combined sources
Beta strandi103 – 1064Combined sources
Beta strandi112 – 1198Combined sources
Beta strandi121 – 1233Combined sources
Beta strandi126 – 13510Combined sources
Beta strandi141 – 1499Combined sources
Beta strandi152 – 1543Combined sources
Beta strandi158 – 1603Combined sources
Turni163 – 1653Combined sources
Beta strandi173 – 1764Combined sources
Beta strandi182 – 1865Combined sources
Beta strandi193 – 1986Combined sources
Turni200 – 2023Combined sources
Beta strandi203 – 2053Combined sources
Beta strandi213 – 2164Combined sources
Beta strandi222 – 23110Combined sources
Turni232 – 2354Combined sources
Beta strandi236 – 24712Combined sources
Beta strandi253 – 2619Combined sources
Helixi274 – 2763Combined sources
Helixi287 – 2904Combined sources
Beta strandi293 – 2986Combined sources
Beta strandi300 – 3023Combined sources
Beta strandi306 – 3083Combined sources
Beta strandi312 – 32312Combined sources
Turni325 – 3273Combined sources
Beta strandi330 – 3378Combined sources
Beta strandi346 – 3549Combined sources
Beta strandi360 – 3623Combined sources
Helixi377 – 3804Combined sources
Beta strandi382 – 3887Combined sources
Beta strandi401 – 4055Combined sources
Beta strandi409 – 4157Combined sources
Beta strandi417 – 4226Combined sources
Turni423 – 4253Combined sources
Beta strandi426 – 4316Combined sources
Beta strandi434 – 44512Combined sources
Turni446 – 4494Combined sources
Beta strandi450 – 4589Combined sources
Beta strandi464 – 4696Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2X8FX-ray1.90A/B1-469[»]
2X8SX-ray1.50A/B1-469[»]
2X8TX-ray1.79A/B1-469[»]
4COTX-ray1.90A1-469[»]
ProteinModelPortaliP42293.
SMRiP42293. Positions 28-469.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni168 – 1714Substrate bindingBy similarity
Regioni188 – 1903Substrate binding
Regioni220 – 2245Substrate binding

Sequence similaritiesi

Belongs to the glycosyl hydrolase 43 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4106Z5D. Bacteria.
COG3507. LUCA.
HOGENOMiHOG000292084.
InParanoidiP42293.
KOiK06113.
OMAiYYMYYNA.
OrthoDBiEOG66TG2T.
PhylomeDBiP42293.

Family and domain databases

Gene3Di2.115.10.20. 1 hit.
InterProiIPR032291. Abn2_C.
IPR006710. Glyco_hydro_43.
IPR023296. Glyco_hydro_beta-prop.
[Graphical view]
PANTHERiPTHR22925. PTHR22925. 3 hits.
PfamiPF16369. GH43_C. 1 hit.
PF04616. Glyco_hydro_43. 1 hit.
[Graphical view]
SUPFAMiSSF75005. SSF75005. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P42293-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFNRLFRVCF LAALIMAFTL PNSVYAQKPI FKEVSVHDPS IIETNGTFYV
60 70 80 90 100
FGSHLASAKS NDLMQWQQLT TSVSNDNPLI PNVYEELKET FEWAQSDTLW
110 120 130 140 150
AADVTQLADG KYYMYYNACR GDSPRSAMGV AVADNIEGPY KNKGIFLKSG
160 170 180 190 200
MEGTSSDGTP YDATKHPNVV DPHTFFDKDG KLWMVYGSYS GGIFILEMNP
210 220 230 240 250
KTGFPLPGQG YGKKLLGGNH SRIEGPYVLY NPDTQYYYLY LSYGGLDATG
260 270 280 290 300
GYNIRVARSK KPDGPYYDAE GNPMLDVRGK GGTFFDDRSI EPYGVKLMGS
310 320 330 340 350
YTFETENEKG TGYVSPGHNS AYYDEKTGRS YLIFHTRFPG RGEEHEVRVH
360 370 380 390 400
QLFMNKDGWP VAAPYRYAGE TLKEVKQKDI TGTYKLIQHG KDISADIKQT
410 420 430 440 450
INIQLNKNHT ISGEMTGTWR KTGKNTADIT LAGKKYNGVF LRQWDSVREK
460
NVMTFSVLNT SGEAVWGSK
Length:469
Mass (Da):52,607
Last modified:July 28, 2009 - v2
Checksum:i1AB8F3D8EF2B3E2E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti175 – 1751F → S in BAA06646 (PubMed:7704263).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D31856 Genomic DNA. Translation: BAA06646.1.
EU373814 Genomic DNA. Translation: ACB06752.1.
AL009126 Genomic DNA. Translation: CAB15969.2.
M20659 Genomic DNA. No translation available.
PIRiE70076.
RefSeqiNP_391812.2. NC_000964.3.

Genome annotation databases

EnsemblBacteriaiCAB15969; CAB15969; BSU39330.
GeneIDi937533.
KEGGibsu:BSU39330.
PATRICi18979926. VBIBacSub10457_4125.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D31856 Genomic DNA. Translation: BAA06646.1.
EU373814 Genomic DNA. Translation: ACB06752.1.
AL009126 Genomic DNA. Translation: CAB15969.2.
M20659 Genomic DNA. No translation available.
PIRiE70076.
RefSeqiNP_391812.2. NC_000964.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2X8FX-ray1.90A/B1-469[»]
2X8SX-ray1.50A/B1-469[»]
2X8TX-ray1.79A/B1-469[»]
4COTX-ray1.90A1-469[»]
ProteinModelPortaliP42293.
SMRiP42293. Positions 28-469.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100021221.

Protein family/group databases

CAZyiGH43. Glycoside Hydrolase Family 43.

Proteomic databases

PaxDbiP42293.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB15969; CAB15969; BSU39330.
GeneIDi937533.
KEGGibsu:BSU39330.
PATRICi18979926. VBIBacSub10457_4125.

Phylogenomic databases

eggNOGiENOG4106Z5D. Bacteria.
COG3507. LUCA.
HOGENOMiHOG000292084.
InParanoidiP42293.
KOiK06113.
OMAiYYMYYNA.
OrthoDBiEOG66TG2T.
PhylomeDBiP42293.

Enzyme and pathway databases

UniPathwayiUPA00667.
BioCyciBSUB:BSU39330-MONOMER.
BRENDAi3.2.1.99. 658.

Family and domain databases

Gene3Di2.115.10.20. 1 hit.
InterProiIPR032291. Abn2_C.
IPR006710. Glyco_hydro_43.
IPR023296. Glyco_hydro_beta-prop.
[Graphical view]
PANTHERiPTHR22925. PTHR22925. 3 hits.
PfamiPF16369. GH43_C. 1 hit.
PF04616. Glyco_hydro_43. 1 hit.
[Graphical view]
SUPFAMiSSF75005. SSF75005. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and sequencing of a 29 kb region of the Bacillus subtilis genome containing the hut and wapA loci."
    Yoshida K., Sano H., Seki S., Oda M., Fujimura M., Fujita Y.
    Microbiology 141:337-343(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / BGSC1A1.
  2. "Characterization of abn2 (yxiA), encoding a Bacillus subtilis GH43 arabinanase, Abn2, and its role in arabino-polysaccharide degradation."
    Inacio J.M., de Sa-Nogueira I.
    J. Bacteriol. 190:4272-4280(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 27-31, FUNCTION, DISRUPTION PHENOTYPE, BIOPHYSICOCHEMICAL PROPERTIES, INDUCTION, SUBCELLULAR LOCATION, SUBSTRATE SPECIFICITY, NOMENCLATURE.
    Strain: 168.
  3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  4. "From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later."
    Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A., Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.
    Microbiology 155:1758-1775(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: SEQUENCE REVISION TO 175.
  5. "Cloning and nucleotide sequences of histidase and regulatory genes in the Bacillus subtilis hut operon and positive regulation of the operon."
    Oda M., Sugishita A., Furukawa K.
    J. Bacteriol. 170:3199-3205(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-171.
  6. "Overproduction, crystallization and preliminary X-ray characterization of Abn2, an endo-1,5-alpha-arabinanase from Bacillus subtilis."
    de Sanctis D., Bento I., Inacio J.M., Custodio S., de Sa-Nogueira I., Carrondo M.A.
    Acta Crystallogr. F 64:636-638(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  7. "New evidence for the role of calcium in the glycosidase reaction of GH43 arabinanases."
    de Sanctis D., Inacio J.M., Lindley P.F., de Sa-Nogueira I., Bento I.
    FEBS J. 277:4562-4574(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF MUTANTS ALA-171 AND HIS-318 IN COMPLEX WITH ALPHA-L-ARABINOFURANOSE AND CALCIUM IONS, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, MUTAGENESIS OF ASP-38; ASP-171; GLU-224 AND HIS-318, SUBCELLULAR LOCATION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBUNIT.

Entry informationi

Entry nameiEABN2_BACSU
AccessioniPrimary (citable) accession number: P42293
Secondary accession number(s): B3FRL6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: July 28, 2009
Last modified: February 17, 2016
This is version 103 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. Glycosyl hydrolases
    Classification of glycosyl hydrolase families and list of entries
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.