PDBsum entry 1xsj

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Hydrolase PDB id
Protein chains
(+ 0 more) 773 a.a. *
TRS ×12
Waters ×1438
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of a family 31 alpha glycosidase
Structure: Putative family 31 glucosidase yici. Chain: a, b, c, d, e, f. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: yici. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PQS)
2.10Å     R-factor:   0.180     R-free:   0.220
Authors: A.L.Lovering,S.S.Lee,Y.W.Kim,S.G.Withers,N.C.Strynadka
Key ref:
A.L.Lovering et al. (2005). Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate. J Biol Chem, 280, 2105-2115. PubMed id: 15501829 DOI: 10.1074/jbc.M410468200
19-Oct-04     Release date:   26-Oct-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P31434  (XYLS_ECOLI) -  Alpha-xylosidase
772 a.a.
773 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Alpha-D-xyloside xylohydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     8 terms  


DOI no: 10.1074/jbc.M410468200 J Biol Chem 280:2105-2115 (2005)
PubMed id: 15501829  
Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate.
A.L.Lovering, S.S.Lee, Y.W.Kim, S.G.Withers, N.C.Strynadka.
We have determined the first structure of a family 31 alpha-glycosidase, that of YicI from Escherichia coli, both free and trapped as a 5-fluoroxylopyranosyl-enzyme intermediate via reaction with 5-fluoro-alpha-D-xylopyranosyl fluoride. Our 2.2-A resolution structure shows an intimately associated hexamer with structural elements from several monomers converging at each of the six active sites. Our kinetic and mass spectrometry analyses verified several of the features observed in our structural data, including a covalent linkage from the carboxylate side chain of the identified nucleophile Asp(416) to C-1 of the sugar ring. Structure-based sequence comparison of YicI with the mammalian alpha-glucosidases lysosomal alpha-glucosidase and sucrase-isomaltase predicts a high level of structural similarity and provides a foundation for understanding the various mutations of these enzymes that elicit human disease.
  Selected figure(s)  
Figure 3.
FIG. 3. Chemical structures and values of inhibitors (A) and mechanism-based inactivators (B).
Figure 6.
FIG. 6. Domain structure of a YicI monomer. The individual domains are colored as indicated: N-terminal domain (domain N), yellow; catalytic [8] [8]-domain, red; insert in the catalytic domain, purple; proximal C-terminal domain, blue; and distal C-terminal domain, green. The active-site nucleophile Asp416 is shown in ball-and-stick form, colored according to atom type (carbon, yellow; and oxygen, red). The figure was prepared using Molscript (70) and Raster3D (71).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 2105-2115) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21477255 M.Répérant, G.Porcheron, G.Rouquet, and P.Gilot (2011).
The yicJI metabolic operon of Escherichia coli is involved in bacterial fitness.
  FEMS Microbiol Lett, 319, 180-186.  
19940122 A.I.Guce, N.E.Clark, E.N.Salgado, D.R.Ivanen, A.A.Kulminskaya, H.Brumer, and S.C.Garman (2010).
Catalytic mechanism of human alpha-galactosidase.
  J Biol Chem, 285, 3625-3632.
PDB codes: 3hg2 3hg3 3hg4 3hg5
20352422 D.B.Jordan, and K.Wagschal (2010).
Properties and applications of microbial beta-D-xylosidases featuring the catalytically efficient enzyme from Selenomonas ruminantium.
  Appl Microbiol Biotechnol, 86, 1647-1658.  
19907056 G.E.Whitworth, W.F.Zandberg, T.Clark, and D.J.Vocadlo (2010).
Mammalian Notch is modified by D-Xyl-alpha1-3-D-Xyl-alpha1-3-D-Glc-beta1-O-Ser: implementation of a method to study O-glucosylation.
  Glycobiology, 20, 287-299.  
20349118 J.Sikora, J.Urinovská, F.Majer, H.Poupetová, J.Hlavatá, M.Kostrouchová, J.Ledvinová, and M.Hrebícek (2010).
Bioinformatic and biochemical studies point to AAGR-1 as the ortholog of human acid alpha-glucosidase in Caenorhabditis elegans.
  Mol Cell Biochem, 341, 51-63.  
19862843 J.J.Flanagan, B.Rossi, K.Tang, X.Wu, K.Mascioli, F.Donaudy, M.R.Tuzzi, F.Fontana, M.V.Cubellis, C.Porto, E.Benjamin, D.J.Lockhart, K.J.Valenzano, G.Andria, G.Parenti, and H.V.Do (2009).
The pharmacological chaperone 1-deoxynojirimycin increases the activity and lysosomal trafficking of multiple mutant forms of acid alpha-glucosidase.
  Hum Mutat, 30, 1683-1692.  
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
18458862 L.Wan, C.C.Lee, C.M.Hsu, W.L.Hwu, C.C.Yang, C.H.Tsai, and F.J.Tsai (2008).
Identification of eight novel mutations of the acid alpha-glucosidase gene causing the infantile or juvenile form of glycogen storage disease type II.
  J Neurol, 255, 831-838.  
18981178 M.Kitamura, M.Okuyama, F.Tanzawa, H.Mori, Y.Kitago, N.Watanabe, A.Kimura, I.Tanaka, and M.Yao (2008).
Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron.
  J Biol Chem, 283, 36328-36337.
PDB codes: 2d73 2zq0
18076078 N.S.Kumar, D.A.Kuntz, X.Wen, B.M.Pinto, and D.R.Rose (2008).
Binding of sulfonium-ion analogues of di-epi-swainsonine and 8-epi-lentiginosine to Drosophila Golgi alpha-mannosidase II: the role of water in inhibitor binding.
  Proteins, 71, 1484-1496.
PDB codes: 2ow6 2ow7
18785261 S.Yu (2008).
The anhydrofructose pathway of glycogen catabolism.
  IUBMB Life, 60, 798-809.  
17970751 M.S.Kang, M.Okuyama, K.Yaoi, Y.Mitsuishi, Y.M.Kim, H.Mori, D.Kim, and A.Kimura (2007).
Aglycone specificity of Escherichia coli alpha-xylosidase investigated by transxylosylation.
  FEBS J, 274, 6074-6084.  
17112388 M.D.Lozyk, S.Papp, X.Zhang, K.Nakamura, M.Michalak, and M.Opas (2006).
Ultrastructural analysis of development of myocardium in calreticulin-deficient mice.
  BMC Dev Biol, 6, 54.  
16495121 V.L.Yip, and S.G.Withers (2006).
Breakdown of oligosaccharides by the process of elimination.
  Curr Opin Chem Biol, 10, 147-155.  
16131397 D.G.Naumoff (2005).
GH97 is a new family of glycoside hydrolases, which is related to the alpha-galactosidase superfamily.
  BMC Genomics, 6, 112.  
16262690 M.Machovic, B.Svensson, E.A.MacGregor, and S.Janecek (2005).
A new clan of CBM families based on bioinformatics of starch-binding domains from families CBM20 and CBM21.
  FEBS J, 272, 5497-5513.  
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.