PDBsum entry 2ead

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Hydrolase PDB id
Protein chains
886 a.a. *
_CA ×4
Waters ×1783
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of 1,2-a-l-fucosidase from bifidobacterium bifidum in complex with substrate
Structure: Alpha-fucosidase. Chain: a, b. Fragment: catalytic domain. Synonym: afca 1,2a-l-fucosidase. Engineered: yes. Mutation: yes
Source: Bifidobacterium bifidum. Organism_taxid: 1681. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.89Å     R-factor:   0.162     R-free:   0.210
Authors: M.Nagae,A.Tsuchiya,T.Katayama,K.Yamamoto,S.Wakatsuki,R.Kato
Key ref:
M.Nagae et al. (2007). Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum. J Biol Chem, 282, 18497-18509. PubMed id: 17459873 DOI: 10.1074/jbc.M702246200
31-Jan-07     Release date:   24-Apr-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q6JV24  (Q6JV24_BIFBI) -  Alpha-fucosidase
1959 a.a.
886 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     catalytic activity     2 terms  


DOI no: 10.1074/jbc.M702246200 J Biol Chem 282:18497-18509 (2007)
PubMed id: 17459873  
Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum.
M.Nagae, A.Tsuchiya, T.Katayamka, K.Yamamoto, S.Wakatsuki, R.Kato.
1,2-alpha-L-Fucosidase (AfcA), which hydrolyzes the glycosidic linkage of Fucalpha1-2Gal via an inverting mechanism, was recently isolated from Bifidobacterium bifidum and classified as the first member of the novel glycoside hydrolase family 95 (GH95). To better understand the molecular mechanism of this enzyme, we determined the X-ray crystal structures of the AfcA catalytic (Fuc) domain in unliganded and complexed forms with deoxyfuconojirimycin (inhibitor), 2'-fucosyllactose (substrate), and L-fucose and lactose (products) at 1.12-2.10 A resolution. The AfcA Fuc domain is composed of four regions, an N-terminal beta region, a helical linker, an (alpha/alpha)6 helical barrel domain, and a C-terminal beta region, and this arrangement is similar to bacterial phosphorylases. In the complex structures, the ligands were buried in the central cavity of the helical barrel domain. Structural analyses in combination with mutational experiments revealed that the highly conserved Glu566 likely acts as a general acid catalyst. However, no carboxylic acid residue is found at the appropriate position for a general base catalyst. Instead, a water molecule stabilized by Asn423 in the substrate-bound complex is suitably located to perform a nucleophilic attack on the C1 atom of L-fucose moiety in 2'-fucosyllactose, and its location is nearly identical near the O1 atom of beta-L-fucose in the products-bound complex. Based on these data, we propose and discuss a novel catalytic reaction mechanism of AfcA.
  Selected figure(s)  
Figure 1.
FIGURE 1. Crystal structure of B. bifidum AfcA fucosidase catalytic domain (Fuc domain). a, ribbon model of the Fuc domain is shown. The N-terminal region, helical linker region, central helical barrel domain, and C-terminal region are colored in blue, cyan, yellow, and red, respectively. b, electrostatic surface potential map of the Fuc domain. Positive (blue) and negative (red) potentials are mapped on the van der Waals surfaces in the range -10 K[b]T (red) to +10 K[b]T (blue), where K[b] is Boltzmann's constant and T is the absolute temperature.
Figure 6.
FIGURE 6. Proposed catalytic reaction mechanism of the AfcA fucosidase. Hydrogen bonds are depicted by dotted lines. The directions of nucleophilic attack and proton donation are indicated by blank arrows.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 18497-18509) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20679197 A.M.Zivkovic, J.B.German, C.B.Lebrilla, and D.A.Mills (2011).
Human milk glycobiome and its impact on the infant gastrointestinal microbiota.
  Proc Natl Acad Sci U S A, 108, 4653-4658.  
21036948 M.Kiyohara, K.Tanigawa, T.Chaiwangsri, T.Katayama, H.Ashida, and K.Yamamoto (2011).
An exo-{alpha}-sialidase from bifidobacteria involved in the degradation of sialyloligosaccharides in human milk and intestinal glycoconjugates.
  Glycobiology, 21, 437-447.  
20974960 F.Turroni, F.Bottacini, E.Foroni, I.Mulder, J.H.Kim, A.Zomer, B.Sánchez, A.Bidossi, A.Ferrarini, V.Giubellini, M.Delledonne, B.Henrissat, P.Coutinho, M.Oggioni, G.F.Fitzgerald, D.Mills, A.Margolles, D.Kelly, D.van Sinderen, and M.Ventura (2010).
Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging.
  Proc Natl Acad Sci U S A, 107, 19514-19519.  
19819900 M.Hidaka, S.Fushinobu, Y.Honda, T.Wakagi, H.Shoun, and M.Kitaoka (2010).
Structural explanation for the acquisition of glycosynthase activity.
  J Biochem, 147, 237-244.
PDB codes: 2dro 2drq 2drr 2drs 3a3v
20581010 M.Miwa, T.Horimoto, M.Kiyohara, T.Katayama, M.Kitaoka, H.Ashida, and K.Yamamoto (2010).
Cooperation of β-galactosidase and β-N-acetylhexosaminidase from bifidobacteria in assimilation of human milk oligosaccharides with type 2 structure.
  Glycobiology, 20, 1402-1409.  
21150123 S.Fushinobu (2010).
Unique sugar metabolic pathways of bifidobacteria.
  Biosci Biotechnol Biochem, 74, 2374-2384.  
20552664 T.V.Vuong, and D.B.Wilson (2010).
Glycoside hydrolases: catalytic base/nucleophile diversity.
  Biotechnol Bioeng, 107, 195-205.  
19304844 D.Dodd, S.A.Kocherginskaya, M.A.Spies, K.E.Beery, C.A.Abbas, R.I.Mackie, and I.K.Cann (2009).
Biochemical analysis of a beta-D-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23.
  J Bacteriol, 191, 3328-3338.  
19520709 H.Ashida, A.Miyake, M.Kiyohara, J.Wada, E.Yoshida, H.Kumagai, T.Katayama, and K.Yamamoto (2009).
Two distinct alpha-L-fucosidases from Bifidobacterium bifidum are essential for the utilization of fucosylated milk oligosaccharides and glycoconjugates.
  Glycobiology, 19, 1010-1017.  
19420691 M.Kiyohara, A.Tachizawa, M.Nishimoto, M.Kitaoka, H.Ashida, and K.Yamamoto (2009).
Prebiotic effect of lacto-N-biose I on bifidobacterial growth.
  Biosci Biotechnol Biochem, 73, 1175-1179.  
19491100 M.Nakajima, M.Nishimoto, and M.Kitaoka (2009).
Characterization of three beta-galactoside phosphorylases from Clostridium phytofermentans: discovery of d-galactosyl-beta1->4-l-rhamnose phosphorylase.
  J Biol Chem, 284, 19220-19227.  
19193645 T.Ishida, S.Fushinobu, R.Kawai, M.Kitaoka, K.Igarashi, and M.Samejima (2009).
Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium.
  J Biol Chem, 284, 10100-10109.
PDB codes: 3eqn 3eqo
19523117 T.V.Vuong, and D.B.Wilson (2009).
The absence of an identifiable single catalytic base residue in Thermobifida fusca exocellulase Cel6B.
  FEBS J, 276, 3837-3845.  
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
18469123 J.Wada, T.Ando, M.Kiyohara, H.Ashida, M.Kitaoka, M.Yamaguchi, H.Kumagai, T.Katayama, and K.Yamamoto (2008).
Bifidobacterium bifidum lacto-N-biosidase, a critical enzyme for the degradation of human milk oligosaccharides with a type 1 structure.
  Appl Environ Microbiol, 74, 3996-4004.  
18223105 P.Ruas-Madiedo, M.Gueimonde, M.Fernández-García, los Reyes-Gavilán, and A.Margolles (2008).
Mucin degradation by Bifidobacterium strains isolated from the human intestinal microbiota.
  Appl Environ Microbiol, 74, 1936-1940.  
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.