PDBsum entry 1pz2

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Hydrolase PDB id
Protein chains
497 a.a. *
AHR ×2
Waters ×767
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of a transient covalent reaction intermediate of a family 51 alpha-l-arabinofuranosidase
Structure: Alpha-l-arabinofuranosidase. Chain: a, b. Synonym: arabinosidase. Engineered: yes. Mutation: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Strain: t-6. Gene: abfa. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Trimer (from PDB file)
2.00Å     R-factor:   0.169     R-free:   0.215
Authors: K.Hoevel,D.Shallom,K.Niefind,V.Belakhov,G.Shoham,T.Baasov, Y.Shoham,D.Schomburg
Key ref: K.Hövel et al. (2003). Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase. EMBO J, 22, 4922-4932. PubMed id: 14517232
09-Jul-03     Release date:   07-Oct-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9XBQ3  (ABFA_GEOSE) -  Intracellular exo-alpha-(1->5)-L-arabinofuranosidase
502 a.a.
497 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Non-reducing end alpha-L-arabinofuranosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     3 terms  


EMBO J 22:4922-4932 (2003)
PubMed id: 14517232  
Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase.
K.Hövel, D.Shallom, K.Niefind, V.Belakhov, G.Shoham, T.Baasov, Y.Shoham, D.Schomburg.
High-resolution crystal structures of alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycosidase, are described. The enzyme is a hexamer, and each monomer is organized into two domains: a (beta/alpha)8-barrel and a 12-stranded beta sandwich with jelly-roll topology. The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl-enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. The arabinofuranose sugar is tightly bound and distorted by an extensive network of hydrogen bonds. The two catalytic residues are 4.7 A apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion-like transition state via charge delocalization and specific protein-substrate interactions. The enzyme is an anti-protonator, and a 1.7 A electrophilic migration of the anomeric carbon takes place during the hydrolysis.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21445259 G.Agarwal, S.Mahajan, N.Srinivasan, and Brevern (2011).
Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks.
  PLoS One, 6, e17826.  
20376631 C.S.Park, M.H.Yoo, K.H.Noh, and D.K.Oh (2010).
Biotransformation of ginsenosides by hydrolyzing the sugar moieties of ginsenosides using microbial glycosidases.
  Appl Microbiol Biotechnol, 87, 9.  
20560210 S.B.Daly, J.E.Urquhart, E.Hilton, E.A.McKenzie, R.A.Kammerer, M.Lewis, B.Kerr, H.Stuart, D.Donnai, D.A.Long, B.Burgu, O.Aydogdu, M.Derbent, S.Garcia-Minaur, W.Reardon, B.Gener, S.Shalev, R.Smith, A.S.Woolf, G.C.Black, and W.G.Newman (2010).
Mutations in HPSE2 cause urofacial syndrome.
  Am J Hum Genet, 86, 963-969.  
20477891 Y.R.Lim, R.Y.Yoon, E.S.Seo, Y.S.Kim, C.S.Park, and D.K.Oh (2010).
Hydrolytic properties of a thermostable α-L-arabinofuranosidase from Caldicellulosiruptor saccharolyticus.
  J Appl Microbiol, 109, 1188-1197.  
19244131 L.Fux, N.Feibish, V.Cohen-Kaplan, S.Gingis-Velitski, S.Feld, C.Geffen, I.Vlodavsky, and N.Ilan (2009).
Structure-function approach identifies a COOH-terminal domain that mediates heparanase signaling.
  Cancer Res, 69, 1758-1767.  
19269961 R.Carapito, A.Imberty, J.M.Jeltsch, S.C.Byrns, P.H.Tam, T.L.Lowary, A.Varrot, and V.Phalip (2009).
Molecular Basis of Arabinobio-hydrolase Activity in Phytopathogenic Fungi: CRYSTAL STRUCTURE AND CATALYTIC MECHANISM OF FUSARIUM GRAMINEARUM GH93 EXO-{alpha}-L-ARABINANASE.
  J Biol Chem, 284, 12285-12296.
PDB codes: 2w5n 2w5o
19279191 R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, and A.Kuno (2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
  J Biochem, 146, 61-70.
PDB codes: 2d1z 2d20 2d22 2d23 2d24
18665359 H.Ichinose, M.Yoshida, Z.Fujimoto, and S.Kaneko (2008).
Characterization of a modular enzyme of exo-1,5-alpha-L: -arabinofuranosidase and arabinan binding module from Streptomyces avermitilis NBRC14893.
  Appl Microbiol Biotechnol, 80, 399-408.  
18679678 S.Canakci, M.Kacagan, K.Inan, A.O.Belduz, and B.C.Saha (2008).
Cloning, purification, and characterization of a thermostable alpha-L-arabinofuranosidase from Anoxybacillus kestanbolensis AC26Sari.
  Appl Microbiol Biotechnol, 81, 61-68.  
17955483 A.Ben-David, T.Bravman, Y.S.Balazs, M.Czjzek, D.Schomburg, G.Shoham, and Y.Shoham (2007).
Glycosynthase activity of Geobacillus stearothermophilus GH52 beta-xylosidase: efficient synthesis of xylooligosaccharides from alpha-D-xylopyranosyl fluoride through a conjugated reaction.
  Chembiochem, 8, 2145-2151.  
17142383 S.Shulami, G.Zaide, G.Zolotnitsky, Y.Langut, G.Feld, A.L.Sonenshein, and Y.Shoham (2007).
A two-component system regulates the expression of an ABC transporter for xylo-oligosaccharides in Geobacillus stearothermophilus.
  Appl Environ Microbiol, 73, 874-884.  
17905739 Y.Kitago, S.Karita, N.Watanabe, M.Kamiya, T.Aizawa, K.Sakka, and I.Tanaka (2007).
Crystal structure of Cel44A, a glycoside hydrolase family 44 endoglucanase from Clostridium thermocellum.
  J Biol Chem, 282, 35703-35711.
PDB codes: 2e0p 2e4t 2eex 2ej1 2eo7 2eqd
16385399 M.T.Numan, and N.B.Bhosle (2006).
Alpha-L-arabinofuranosidases: the potential applications in biotechnology.
  J Ind Microbiol Biotechnol, 33, 247-260.  
15501829 A.L.Lovering, S.S.Lee, Y.W.Kim, S.G.Withers, and N.C.Strynadka (2005).
Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate.
  J Biol Chem, 280, 2105-2115.
PDB codes: 1xsi 1xsj 1xsk
15965714 K.Miyazaki (2005).
Hyperthermophilic alpha-L: -arabinofuranosidase from Thermotoga maritima MSB8: molecular cloning, gene expression, and characterization of the recombinant protein.
  Extremophiles, 9, 399-406.  
15708971 M.R.Proctor, E.J.Taylor, D.Nurizzo, J.P.Turkenburg, R.M.Lloyd, M.Vardakou, G.J.Davies, and H.J.Gilbert (2005).
Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A.
  Proc Natl Acad Sci U S A, 102, 2697-2702.
PDB code: 1uv4
15213394 A.Miyanaga, T.Koseki, H.Matsuzawa, T.Wakagi, H.Shoun, and S.Fushinobu (2004).
Expression, purification, crystallization and preliminary X-ray analysis of alpha-L-arabinofuranosidase B from Aspergillus kawachii.
  Acta Crystallogr D Biol Crystallogr, 60, 1286-1288.  
15292273 A.Miyanaga, T.Koseki, H.Matsuzawa, T.Wakagi, H.Shoun, and S.Fushinobu (2004).
Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose.
  J Biol Chem, 279, 44907-44914.
PDB codes: 1wd3 1wd4
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.