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Protein

Intracellular endo-alpha-(1->5)-L-arabinanase

Gene

abnB

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
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 debranched arabinan, linear arabinan and short arabino-oligosaccharides (degree of polymerization from 2 to 8). It exhibits marginal activity toward sugar beet arabinan.1 Publication

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

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 sitei27 – 271Proton acceptor1 Publication
Binding sitei27 – 271Substrate
Binding sitei105 – 1051Substrate; via amide nitrogen
Sitei147 – 1471Important for catalytic activity
Active sitei201 – 2011Proton donor1 Publication
Metal bindingi271 – 2711CalciumSequence analysis
Sitei271 – 2711Important for substrate recognitionBy similarity

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

BRENDAi3.2.1.99. 623.
UniPathwayiUPA00667.

Protein family/group databases

CAZyiGH43. Glycoside Hydrolase Family 43.

Names & Taxonomyi

Protein namesi
Recommended name:
Intracellular endo-alpha-(1->5)-L-arabinanase (EC:3.2.1.99)
Short name:
ABN
Alternative name(s):
Endo-1,5-alpha-L-arabinanase
Gene namesi
Name:abnB
OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
Taxonomic identifieri1422 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

Subcellular locationi

  • Cytoplasm 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 315315Intracellular endo-alpha-(1->5)-L-arabinanasePRO_0000422129Add
BLAST

Expressioni

Inductioni

Transcription is repressed by glucose and by the binding of AraR to the operon promoter. L-arabinose acts as an inducer by inhibiting the binding of AraR to the DNA, thus allowing expression of the gene.1 Publication

Interactioni

Subunit structurei

Monomer.1 Publication

Structurei

Secondary structure

1
315
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi12 – 143Combined sources
Beta strandi29 – 335Combined sources
Beta strandi36 – 449Combined sources
Beta strandi46 – 6318Combined sources
Helixi71 – 744Combined sources
Beta strandi82 – 9110Combined sources
Beta strandi94 – 1018Combined sources
Beta strandi109 – 1179Combined sources
Beta strandi129 – 1379Combined sources
Beta strandi141 – 1433Combined sources
Beta strandi149 – 1524Combined sources
Beta strandi158 – 1625Combined sources
Beta strandi169 – 1735Combined sources
Turni176 – 1783Combined sources
Beta strandi188 – 1914Combined sources
Beta strandi194 – 1974Combined sources
Beta strandi200 – 2089Combined sources
Beta strandi211 – 2199Combined sources
Helixi224 – 2263Combined sources
Beta strandi230 – 2389Combined sources
Helixi251 – 2533Combined sources
Beta strandi257 – 2604Combined sources
Beta strandi264 – 27714Combined sources
Beta strandi280 – 28910Combined sources
Turni290 – 2945Combined sources
Beta strandi296 – 30510Combined sources
Beta strandi311 – 3133Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3CU9X-ray1.06A2-315[»]
3D5YX-ray1.22A2-315[»]
3D5ZX-ray1.90A2-315[»]
3D60X-ray1.90A2-315[»]
3D61X-ray1.95A2-315[»]
ProteinModelPortaliB3EYM8.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiB3EYM8.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni144 – 1474Substrate binding
Regioni164 – 1663Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the glycosyl hydrolase 43 family.Curated

Family and domain databases

Gene3Di2.115.10.20. 1 hit.
InterProiIPR006710. Glyco_hydro_43.
IPR016840. Glyco_hydro_43_endo_a_Ara-ase.
IPR023296. Glyco_hydro_beta-prop.
[Graphical view]
PANTHERiPTHR22925. PTHR22925. 1 hit.
PfamiPF04616. Glyco_hydro_43. 1 hit.
[Graphical view]
PIRSFiPIRSF026534. Endo_alpha-L-arabinosidase. 1 hit.
SUPFAMiSSF75005. SSF75005. 1 hit.

Sequencei

Sequence statusi: Complete.

B3EYM8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVHFHPFGNV NFYEMDWSLK GDLWAHDPVI AKEGSRWYVF HTGSGIQIKT
60 70 80 90 100
SEDGVHWENM GWVFPSLPDW YKQYVPEKDE DHLWAPDICF YNGIYYLYYS
110 120 130 140 150
VSTFGKNTSV IGLATNQTLD PRDPDYEWKD MGPVIHSTAS DNYNAIDPNV
160 170 180 190 200
VFDQEGQPWL SFGSFWSGIQ LIQLDTETMK PAAQAELLTI ASRGEEPNAI
210 220 230 240 250
EAPFIVCRNG YYYLFVSFDF CCRGIESTYK IAVGRSKDIT GPYVDKNGVS
260 270 280 290 300
MMQGGGTILD EGNDRWIGPG HCAVYFSGVS AILVNHAYDA LKNGEPTLQI
310
RPLYWDDEGW PYLSV
Length:315
Mass (Da):35,763
Last modified:July 22, 2008 - v1
Checksum:i86861395D823A044
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ868502 Genomic DNA. Translation: ACE73676.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ868502 Genomic DNA. Translation: ACE73676.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3CU9X-ray1.06A2-315[»]
3D5YX-ray1.22A2-315[»]
3D5ZX-ray1.90A2-315[»]
3D60X-ray1.90A2-315[»]
3D61X-ray1.95A2-315[»]
ProteinModelPortaliB3EYM8.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

CAZyiGH43. Glycoside Hydrolase Family 43.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00667.
BRENDAi3.2.1.99. 623.

Miscellaneous databases

EvolutionaryTraceiB3EYM8.

Family and domain databases

Gene3Di2.115.10.20. 1 hit.
InterProiIPR006710. Glyco_hydro_43.
IPR016840. Glyco_hydro_43_endo_a_Ara-ase.
IPR023296. Glyco_hydro_beta-prop.
[Graphical view]
PANTHERiPTHR22925. PTHR22925. 1 hit.
PfamiPF04616. Glyco_hydro_43. 1 hit.
[Graphical view]
PIRSFiPIRSF026534. Endo_alpha-L-arabinosidase. 1 hit.
SUPFAMiSSF75005. SSF75005. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Cloning and DNA sequence of the gene coding for Bacillus stearothermophilus T-6 xylanase."
    Gat O., Lapidot A., Alchanati I., Regueros C., Shoham Y.
    Appl. Environ. Microbiol. 60:1889-1896(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: T-6.
  2. "The glucuronic acid utilization gene cluster from Bacillus stearothermophilus T-6."
    Shulami S., Gat O., Sonenshein A.L., Shoham Y.
    J. Bacteriol. 181:3695-3704(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: T-6.
  3. "Biochemical characterization and identification of catalytic residues in alpha-glucuronidase from Bacillus stearothermophilus T-6."
    Zaide G., Shallom D., Shulami S., Zolotnitsky G., Golan G., Baasov T., Shoham G., Shoham Y.
    Eur. J. Biochem. 268:3006-3016(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: T-6.
  4. "Stereochemistry of family 52 glycosyl hydrolases: a beta-xylosidase from Bacillus stearothermophilus T-6 is a retaining enzyme."
    Bravman T., Zolotnitsky G., Shulami S., Belakhov V., Solomon D., Baasov T., Shoham G., Shoham Y.
    FEBS Lett. 495:39-43(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: T-6.
  5. "A two-component system regulates the expression of an ABC transporter for xylo-oligosaccharides in Geobacillus stearothermophilus."
    Shulami S., Zaide G., Zolotnitsky G., Langut Y., Feld G., Sonenshein A.L., Shoham Y.
    Appl. Environ. Microbiol. 73:874-884(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: T-6.
  6. "Hemicellulose utilization cluster in Geobacillus stearothermophilus strain T-6."
    Shoham Y., Shulami S., Ben-David A., Langut Y.
    Submitted (JUN-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: T-6.
  7. "The L-Arabinan utilization system of Geobacillus stearothermophilus."
    Shulami S., Raz-Pasteur A., Tabachnikov O., Gilead-Gropper S., Shner I., Shoham Y.
    J. Bacteriol. 193:2838-2850(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  8. "Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate."
    Alhassid A., Ben-David A., Tabachnikov O., Libster D., Naveh E., Zolotnitsky G., Shoham Y., Shoham G.
    Biochem. J. 422:73-82(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.06 ANGSTROMS) OF 2-315 OF MUTANTS ALA-27; ALA-201 AND ALA-1747 IN COMPLEX WITH ALPHA-L-ARABINOFURANOSE AND CALCIUM ION, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, COFACTOR, SUBCELLULAR LOCATION, SUBSTRATE SPECIFICITY, SUBUNIT.

Entry informationi

Entry nameiIABN_GEOSE
AccessioniPrimary (citable) accession number: B3EYM8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 2013
Last sequence update: July 22, 2008
Last modified: April 1, 2015
This is version 30 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. Glycosyl hydrolases
    Classification of glycosyl hydrolase families and list of entries
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.