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Q9XBQ3

- IABF_GEOSE

UniProt

Q9XBQ3 - IABF_GEOSE

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Protein

Intracellular exo-alpha-(1->5)-L-arabinofuranosidase

Gene

abfA

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed - 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 cleavage of terminal alpha-(1->5)-arabinofuranosyl bonds in different hemicellulosic homopolysaccharides (branched and debranched arabinans). It acts preferentially on aryl-alpha-L-arabinofuranosides, and is much less effective on aryl-beta-D-xylopyranosides.4 Publications

Catalytic activityi

Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.2 Publications

Enzyme regulationi

Strongly inhibited by Hg2+.1 Publication

Kineticsi

Apparently, AbfA can accommodate xylopyranose in the active site, but without the necessary distortion required for the efficient catalysis of six-membered rings. This explains in part its lower specificity towards the xylopyranosidic substrates (PubMes:14517232).

  1. KM=0.35 mM for 2,5-dinitro-arabinofuranosyl4 Publications
  2. KM=0.42 mM for p-nitrophenyl alpha-L-arabinofuranoside (pNP-Araf) (at 60 degrees Celsius and at pH 6)4 Publications
  3. KM=0.53 mM for 3,4-dinitro-arabinofuranosyl4 Publications
  4. KM=0.65 mM for 4-nitro-arabinofuranosyl4 Publications
  5. KM=4.4 mM for 3,4-dinitro-xylopyranosyl4 Publications
  6. KM=8 mM for 2,5-dinitro-xylopyranosyl4 Publications
  7. KM=15.3 mM for 2-nitro-xylopyranosyl4 Publications

Vmax=749 µmol/min/mg enzyme (at 60 degrees Celsius and at pH 6)4 Publications

pH dependencei

Optimum pH is 5.5-6.0.4 Publications

Temperature dependencei

Optimum temperature is 70 degrees Celsius.4 Publications

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei29 – 291Substrate
Binding sitei74 – 741Substrate; via amide nitrogen
Active sitei175 – 1751Proton donor/acceptor
Binding sitei246 – 2461Substrate
Active sitei294 – 2941Nucleophile
Binding sitei294 – 2941Substrate
Sitei298 – 2981Important for substrate recognitionCurated
Binding sitei351 – 3511SubstrateBy similarity
Sitei351 – 3511Important for substrate recognitionCurated

GO - Molecular functioni

  1. alpha-L-arabinofuranosidase activity Source: UniProtKB-EC

GO - Biological processi

  1. arabinan catabolic process Source: UniProtKB-UniPathway
  2. L-arabinose metabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Carbohydrate metabolism

Enzyme and pathway databases

UniPathwayiUPA00667.

Protein family/group databases

CAZyiGH51. Glycoside Hydrolase Family 51.

Names & Taxonomyi

Protein namesi
Recommended name:
Intracellular exo-alpha-(1->5)-L-arabinofuranosidase (EC:3.2.1.55)
Short name:
ABF
Alternative name(s):
Intracellular arabinan exo-alpha-(1->5)-L-arabinosidase
Short name:
Arabinosidase
Gene namesi
Name:abfA
OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
Taxonomic identifieri1422 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

Subcellular locationi

Cytoplasm By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi175 – 1751E → A: Strongly reduced catalytic activity. Increases affinity for substrates. The mutant has an effect on the glycosylation step. The removal of the acid-base catalyst seems to have affected the ionization state of the nucleophile, elevating its pKa, reducing its acidity, and shifting the optimal pH to higher values. 3 Publications
Mutagenesisi294 – 2941E → A: Abolishes catalytic activity, but the binding affinity shows only a small change. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 502501Intracellular exo-alpha-(1->5)-L-arabinofuranosidasePRO_0000057700Add
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 (Probable).1 Publication

Interactioni

Subunit structurei

Homohexamer; trimer of dimers.3 Publications

Structurei

Secondary structure

1
502
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 94Combined sources
Beta strandi14 – 185Combined sources
Helixi21 – 244Combined sources
Beta strandi25 – 273Combined sources
Turni37 – 393Combined sources
Beta strandi51 – 533Combined sources
Helixi54 – 629Combined sources
Beta strandi67 – 715Combined sources
Helixi74 – 785Combined sources
Helixi81 – 844Combined sources
Helixi88 – 903Combined sources
Beta strandi94 – 963Combined sources
Turni97 – 1004Combined sources
Beta strandi101 – 1033Combined sources
Helixi109 – 11911Combined sources
Beta strandi122 – 1276Combined sources
Helixi134 – 14512Combined sources
Beta strandi148 – 1503Combined sources
Helixi151 – 1588Combined sources
Beta strandi169 – 1746Combined sources
Helixi187 – 20418Combined sources
Beta strandi209 – 2124Combined sources
Turni221 – 2244Combined sources
Helixi225 – 23410Combined sources
Helixi235 – 2373Combined sources
Beta strandi239 – 2479Combined sources
Helixi254 – 2585Combined sources
Helixi261 – 28222Combined sources
Beta strandi289 – 2979Combined sources
Helixi302 – 3054Combined sources
Beta strandi312 – 3143Combined sources
Helixi324 – 33916Combined sources
Turni340 – 3434Combined sources
Beta strandi344 – 3507Combined sources
Beta strandi352 – 3565Combined sources
Beta strandi358 – 3614Combined sources
Beta strandi367 – 3693Combined sources
Helixi373 – 38210Combined sources
Beta strandi385 – 3884Combined sources
Beta strandi391 – 3933Combined sources
Beta strandi403 – 41513Combined sources
Turni416 – 4194Combined sources
Beta strandi420 – 4278Combined sources
Beta strandi430 – 4323Combined sources
Beta strandi434 – 4396Combined sources
Beta strandi447 – 4548Combined sources
Beta strandi473 – 4753Combined sources
Beta strandi479 – 4813Combined sources
Beta strandi484 – 4896Combined sources
Beta strandi491 – 50010Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PZ2X-ray2.00A/B1-502[»]
1PZ3X-ray1.75A/B1-502[»]
1QW8X-ray1.80A/B1-502[»]
1QW9X-ray1.20A/B1-502[»]
ProteinModelPortaliQ9XBQ3.
SMRiQ9XBQ3. Positions 5-501.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9XBQ3.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni174 – 1752Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the glycosyl hydrolase 51 family.Curated

Family and domain databases

Gene3Di3.20.20.80. 1 hit.
InterProiIPR010720. Alpha-L-AF_C.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PfamiPF06964. Alpha-L-AF_C. 1 hit.
[Graphical view]
SMARTiSM00813. Alpha-L-AF_C. 1 hit.
[Graphical view]
SUPFAMiSSF51445. SSF51445. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q9XBQ3-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MATKKATMII EKDFKIAEID KRIYGSFIEH LGRAVYGGIY EPGHPQADEN
60 70 80 90 100
GFRQDVIELV KELQVPIIRY PGGNFVSGYN WEDGVGPKEQ RPRRLDLAWK
110 120 130 140 150
SVETNEIGLN EFMDWAKMVG AEVNMAVNLG TRGIDAARNL VEYCNHPSGS
160 170 180 190 200
YYSDLRIAHG YKEPHKIKTW CLGNEMDGPW QIGHKTAVEY GRIACEAAKV
210 220 230 240 250
MKWVDPTIEL VVCGSSNRNM PTFAEWEATV LDHTYDHVDY ISLHQYYGNR
260 270 280 290 300
DNDTANYLAL SLEMDDFIRS VVAIADYVKA KKRSKKTIHL SFDEWNVWYH
310 320 330 340 350
SNEADKLIEP WTVAPPLLED IYNFEDALLV GCMLITLMKH ADRVKIACLA
360 370 380 390 400
QLVNVIAPIM TEKNGPAWKQ TIYYPFMHAS VYGRGVALHP VISSPKYDSK
410 420 430 440 450
DFTDVPYLES IAVYNEEKEE VTIFAVNRDM EDALLLECDV RSFEDYRVIE
460 470 480 490 500
HIVLEHDNVK QTNSAQSSPV VPHRNGDAQL SDRKVSATLP KLSWNVIRLG

KR
Length:502
Mass (Da):57,212
Last modified:January 23, 2007 - v4
Checksum:i37C048AE29DBB230
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF159625 Genomic DNA. Translation: AAD45520.2.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF159625 Genomic DNA. Translation: AAD45520.2 .

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1PZ2 X-ray 2.00 A/B 1-502 [» ]
1PZ3 X-ray 1.75 A/B 1-502 [» ]
1QW8 X-ray 1.80 A/B 1-502 [» ]
1QW9 X-ray 1.20 A/B 1-502 [» ]
ProteinModelPortali Q9XBQ3.
SMRi Q9XBQ3. Positions 5-501.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

CAZyi GH51. Glycoside Hydrolase Family 51.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

UniPathwayi UPA00667 .

Miscellaneous databases

EvolutionaryTracei Q9XBQ3.

Family and domain databases

Gene3Di 3.20.20.80. 1 hit.
InterProi IPR010720. Alpha-L-AF_C.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view ]
Pfami PF06964. Alpha-L-AF_C. 1 hit.
[Graphical view ]
SMARTi SM00813. Alpha-L-AF_C. 1 hit.
[Graphical view ]
SUPFAMi SSF51445. SSF51445. 1 hit.
ProtoNeti Search...

Publicationsi

  1. Gilead-Gropper S., Gat O., Alchanati I., Yaron S., Bren A., Shoham Y.
    Submitted (NOV-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: T-6 / NCIMB 40222.
  2. "Purification and characterization of alpha-L-arabinofuranosidase from Bacillus stearothermophilus T-6."
    Gilead S., Shoham Y.
    Appl. Environ. Microbiol. 61:170-174(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-51, FUNCTION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, INDUCTION, SUBUNIT.
    Strain: T-6 / NCIMB 40222.
  3. "The identification of the acid-base catalyst of alpha-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase."
    Shallom D., Belakhov V., Solomon D., Gilead-Gropper S., Baasov T., Shoham G., Shoham Y.
    FEBS Lett. 514:163-167(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF GLU-175, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM.
  4. "Detailed kinetic analysis and identification of the nucleophile in alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase."
    Shallom D., Belakhov V., Solomon D., Shoham G., Baasov T., Shoham Y.
    J. Biol. Chem. 277:43667-43673(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-175 AND GLU-294, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM.
  5. "Crystallization and preliminary X-ray analysis of a family 51 glycoside hydrolase, the alpha-l-arabinofuranosidase from Geobacillus stearothermophilus T-6."
    Hovel K., Shallom D., Niefind K., Baasov T., Shoham G., Shoham Y., Schomburg D.
    Acta Crystallogr. D 59:913-915(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  6. "Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase."
    Hovel K., Shallom D., Niefind K., Belakhov V., Shoham G., Baasov T., Shoham Y., Schomburg D.
    EMBO J. 22:4922-4932(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANT ALA-175 IN COMPLEX WITH SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-175, REACTION MECHANISM, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, SUBUNIT.

Entry informationi

Entry nameiIABF_GEOSE
AccessioniPrimary (citable) accession number: Q9XBQ3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 26, 2002
Last sequence update: January 23, 2007
Last modified: November 26, 2014
This is version 63 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

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

External Data

Dasty 3