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PDBsum entry 1wd4

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Hydrolase PDB id
1wd4
Jmol
Contents
Protein chain
482 a.a. *
Ligands
NAG-NAG
AHR ×3
Waters ×230
* Residue conservation analysis
PDB id:
1wd4
Name: Hydrolase
Title: Crystal structure of arabinofuranosidase complexed with arab
Structure: Alpha-l-arabinofuranosidase b. Chain: a. Synonym: arabinofuranosidase. Engineered: yes
Source: Aspergillus kawachii. Organism_taxid: 40384. Expressed in: pichia pastoris. Expression_system_taxid: 4922.
Resolution:
2.07Å     R-factor:   0.188     R-free:   0.221
Authors: A.Miyanaga,T.Koseki,H.Matsuzawa,T.Wakagi,H.Shoun,S.Fushinobu
Key ref:
A.Miyanaga et al. (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. PubMed id: 15292273 DOI: 10.1074/jbc.M405390200
Date:
11-May-04     Release date:   14-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8NK89  (ABFB_ASPKW) -  Alpha-L-arabinofuranosidase B
Seq:
Struc:
499 a.a.
482 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.3.2.1.55  - 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     extracellular region   1 term 
  Biological process     metabolic process   8 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
DOI no: 10.1074/jbc.M405390200 J Biol Chem 279:44907-44914 (2004)
PubMed id: 15292273  
 
 
Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose.
A.Miyanaga, T.Koseki, H.Matsuzawa, T.Wakagi, H.Shoun, S.Fushinobu.
 
  ABSTRACT  
 
As the first known structures of a glycoside hydrolase family 54 (GH54) enzyme, we determined the crystal structures of free and arabinose-complex forms of Aspergillus kawachii IFO4308 alpha-l-arabinofuranosidase (AkAbfB). AkAbfB comprises two domains: a catalytic domain and an arabinose-binding domain (ABD). The catalytic domain has a beta-sandwich fold similar to those of clan-B glycoside hydrolases. ABD has a beta-trefoil fold similar to that of carbohydrate-binding module (CBM) family 13. However, ABD shows a number of characteristics distinctive from those of CBM family 13, suggesting that it could be classified into a new CBM family. In the arabinose-complex structure, one of three arabinofuranose molecules is bound to the catalytic domain through many interactions. Interestingly, a disulfide bond formed between two adjacent cysteine residues recognized the arabinofuranose molecule in the active site. From the location of this arabinofuranose and the results of a mutational study, the nucleophile and acid/base residues were determined to be Glu(221) and Asp(297), respectively. The other two arabinofuranose molecules are bound to ABD. The O-1 atoms of the two arabinofuranose molecules bound at ABD are both pointed toward the solvent, indicating that these sites can both accommodate an arabinofuranose side-chain moiety linked to decorated arabinoxylans.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Folds of AkAbfB and structurally similar enzymes. Ribbon drawing diagrams of AkAbfB (A), TrSA (B), and -carrageenase (C). Catalytic domains are enclosed in blue dotted lines. The catalytic domain of AkAbfB and structurally similar domains are shown in green. Catalytic residues are shown as ball-and-stick models. A, ABD of AkAbfB is shown in yellow-green. Three arabinofuranose molecules are shown as blue Corey-Pauling-Koltun models. Asn202 and the glycoside chain are shown as Corey-Pauling-Koltun colored ball-and-stick and gray wireframe models, respectively. B, 2-deoxy-2,3-dehydro-N-acetylneuraminic acid molecules are shown as blue Corey-Pauling-Koltun models. D, a topological diagram of the catalytic domain of AkAbfB. The locations of the catalytic residues are indicated by asterisks.
Figure 5.
FIG. 5. The active sites of AkAbfB and GH51 GsAbfA. The O-1 atom of the arabinofuranose molecule in AkAbfB is omitted because its electron density was not observed. A, stereoview of the catalytic center of AkAbfB in a complex with arabinofuranose. Hydrogen bonds and disulfide bond are shown as gray and green dotted lines, respectively. B, stereoview of superimpositioning of AkAbfB in a complex with arabinofuranose and GsAbfA with Ara- (1, 3)-Xyl. AkAbfB and GsAbfA are shown in yellow and cyan, respectively. Only the catalytic residues and important residues for substrate binding are shown. GH51 GsAbfA in a complex with Ara- (1, 3)-Xyl was constructed by combining the structures of the native enzyme (1PZ3 [PDB] ) and Ara- (1, 3)-Xyl complex (1QW8 [PDB] ).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 44907-44914) copyright 2004.  
  Figures were selected by the author.  
 
 
    Author's comment    
 
  ABD of AkAbfB (appeared on Fig. 1A) and homologous sequences have been assigned as Carbohydrate Binding Module family 42 (CBM42) in the CAZy database.
S. Fushinobu.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20525292 C.Kim, J.Basner, and B.Lee (2010).
Detecting internally symmetric protein structures.
  BMC Bioinformatics, 11, 303.  
20333513 O.Guais, O.Tourrasse, M.Dourdoigne, J.L.Parrou, and J.M.Francois (2010).
Characterization of the family GH54 alpha-L-arabinofuranosidases in Penicillium funiculosum, including a novel protein bearing a cellulose-binding domain.
  Appl Microbiol Biotechnol, 87, 1007-1021.  
19756576 T.Koseki, K.Mochizuki, H.Kisara, A.Miyanaga, S.Fushinobu, T.Murayama, and Y.Shiono (2010).
Characterization of a chimeric enzyme comprising feruloyl esterase and family 42 carbohydrate-binding module.
  Appl Microbiol Biotechnol, 86, 155-161.  
19505290 A.Alhassid, A.Ben-David, O.Tabachnikov, D.Libster, E.Naveh, G.Zolotnitsky, Y.Shoham, and G.Shoham (2009).
Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate.
  Biochem J, 422, 73-82.
PDB codes: 3cu9 3d5y 3d5z 3d60 3d61
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
17955189 B.J.de Wet, M.K.Matthew, K.H.Storbeck, W.H.van Zyl, and B.A.Prior (2008).
Characterization of a family 54 alpha-L: -arabinofuranosidase from Aureobasidium pullulans.
  Appl Microbiol Biotechnol, 77, 975-983.  
18566914 B.Nocek, L.Bigelow, J.Abdullah, and A.Joachimiak (2008).
Structure of SO2946 orphan from Shewanella oneidensis shows "jelly-roll" fold with carbohydrate-binding module.
  J Struct Funct Genomics, 9, 1-6.
PDB code: 2a5z
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.  
  18997327 Z.Fujimoto, H.Ichinose, and S.Kaneko (2008).
Crystallization and preliminary crystallographic analysis of exo-alpha-1,5-L-arabinofuranosidase from Streptomyces avermitilis NBRC14893.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1007-1009.  
16385399 M.T.Numan, and N.B.Bhosle (2006).
Alpha-L-arabinofuranosidases: the potential applications in biotechnology.
  J Ind Microbiol Biotechnol, 33, 247-260.  
16760304 O.Shoseyov, Z.Shani, and I.Levy (2006).
Carbohydrate binding modules: biochemical properties and novel applications.
  Microbiol Mol Biol Rev, 70, 283-295.  
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.  
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.