Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

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

Gene

abfA

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 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 (PubMed: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
  1. 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: 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)DescriptionActionsGraphical viewLength
Binding sitei29Substrate1
Binding sitei74Substrate; via amide nitrogen1
Active sitei175Proton donor/acceptor1
Binding sitei246Substrate1
Active sitei294Nucleophile1
Binding sitei294Substrate1
Sitei298Important for substrate recognitionCurated1
Binding sitei351SubstrateBy similarity1
Sitei351Important for substrate recognitionCurated1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Carbohydrate metabolism

Enzyme and pathway databases

BRENDAi3.2.1.55. 623.
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

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi175E → 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 Publications1
Mutagenesisi294E → A: Abolishes catalytic activity, but the binding affinity shows only a small change. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000577002 – 502Intracellular exo-alpha-(1->5)-L-arabinofuranosidaseAdd BLAST501

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

1502
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 9Combined sources4
Beta strandi14 – 18Combined sources5
Helixi21 – 24Combined sources4
Beta strandi25 – 27Combined sources3
Turni37 – 39Combined sources3
Beta strandi51 – 53Combined sources3
Helixi54 – 62Combined sources9
Beta strandi67 – 71Combined sources5
Helixi74 – 78Combined sources5
Helixi81 – 84Combined sources4
Helixi88 – 90Combined sources3
Beta strandi94 – 96Combined sources3
Turni97 – 100Combined sources4
Beta strandi101 – 103Combined sources3
Helixi109 – 119Combined sources11
Beta strandi122 – 127Combined sources6
Helixi134 – 145Combined sources12
Beta strandi148 – 150Combined sources3
Helixi151 – 158Combined sources8
Beta strandi169 – 174Combined sources6
Helixi187 – 204Combined sources18
Beta strandi209 – 212Combined sources4
Turni221 – 224Combined sources4
Helixi225 – 234Combined sources10
Helixi235 – 237Combined sources3
Beta strandi239 – 247Combined sources9
Helixi254 – 258Combined sources5
Helixi261 – 282Combined sources22
Beta strandi289 – 297Combined sources9
Helixi302 – 305Combined sources4
Beta strandi312 – 314Combined sources3
Helixi324 – 339Combined sources16
Turni340 – 343Combined sources4
Beta strandi344 – 350Combined sources7
Beta strandi352 – 356Combined sources5
Beta strandi358 – 361Combined sources4
Beta strandi367 – 369Combined sources3
Helixi373 – 382Combined sources10
Beta strandi385 – 388Combined sources4
Beta strandi391 – 393Combined sources3
Beta strandi403 – 415Combined sources13
Turni416 – 419Combined sources4
Beta strandi420 – 427Combined sources8
Beta strandi430 – 432Combined sources3
Beta strandi434 – 439Combined sources6
Beta strandi447 – 454Combined sources8
Beta strandi473 – 475Combined sources3
Beta strandi479 – 481Combined sources3
Beta strandi484 – 489Combined sources6
Beta strandi491 – 500Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9XBQ3.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni174 – 175Substrate bindingBy similarity2

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

CAZyiGH51. Glycoside Hydrolase Family 51.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00667.
BRENDAi3.2.1.55. 623.

Miscellaneous databases

EvolutionaryTraceiQ9XBQ3.

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.
ProtoNetiSearch...

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 2, 2016
This is version 70 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

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.