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Hydrolase PDB id
1urx
Jmol
Contents
Protein chain
268 a.a. *
Ligands
AAL-GAL-AAL-GLA
AAL-GAL-AAL-GAL-
AAL-GAL-AAL
Metals
_CA
Waters ×354
* Residue conservation analysis
PDB id:
1urx
Name: Hydrolase
Title: Crystallographic structure of beta-agarase a in complex with oligoagarose
Structure: Beta-agarase a. Chain: a. Fragment: beta-agarase a domain, residues 20-290. Engineered: yes. Mutation: yes. Other_details: two molecules of oligoagarose
Source: Zobellia galactanivorans. Zobellia galactanivora, s. Organism_taxid: 63186. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.7Å     R-factor:   0.156     R-free:   0.182
Authors: J.Allouch,W.Helbert,B.Henrissat,M.Czjzek
Key ref:
J.Allouch et al. (2004). Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose. Structure, 12, 623-632. PubMed id: 15062085 DOI: 10.1016/j.str.2004.02.020
Date:
12-Nov-03     Release date:   04-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam  
Q9RGX9  (Q9RGX9_ZOBGA) -  Beta-agarase A
Seq:
Struc: 		 
Seq:
Struc: 		539 a.a.
268 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.81  - Beta-agarase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of 1,3-beta-D-galactosidic linkages in agarose, giving the tetramer as the predominant product.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  

 

 
DOI no: 10.1016/j.str.2004.02.020 Structure 12:623-632 (2004)
PubMed id: 15062085  
 
 
Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.
J.Allouch, W.Helbert, B.Henrissat, M.Czjzek.
 
  ABSTRACT  
 
Agarose is a gel-forming polysaccharide with an alpha-L(1,4)-3,6-anhydro-galactose, beta-D(1,3)-galactose repeat unit, from the cell walls of marine red algae. beta-agarase A, from the Gram-negative bacterium Zobellia galactanivorans, is secreted to the external medium and degrades agarose with an endo-mechanism. The structure of the inactive mutant beta-agarase A-E147S in complex with agaro-octaose has been solved at 1.7 A resolution. Two oligosaccharide chains are bound to the protein. The first one resides in the active site channel, spanning subsites -4 to -1. A second oligosaccharide binding site, on the opposite side of the protein, was filled with eight sugar units, parallel to the active site. The crystal structure of the beta-agarase A with agaro-octaose provides detailed information on agarose recognition in the catalytic site. The presence of the second, parallel, binding site suggests that the enzyme might be able to unwind the double-helical structure of agarose prior to the catalytic cleavage.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Overall View of the Constructed Model of b-Agarase A in Interaction with an Unwinding Double Helix of Agarose

 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 623-632) copyright 2004.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21426903 L.C.Tsai, C.H.Hsiao, W.Y.Liu, L.M.Yin, and L.F.Shyur (2011).
Structural basis for the inhibition of 1,3-1,4-β-d-glucanase by noncompetitive calcium ion and competitive Tris inhibitors.
  Biochem Biophys Res Commun, 407, 593-598.  
21261814 S.Cuyvers, E.Dornez, M.N.Rezaei, A.Pollet, J.A.Delcour, and C.M.Courtin (2011).
Secondary substrate binding strongly affects activity and binding affinity of Bacillus subtilis and Aspergillus niger GH11 xylanases.
  FEBS J, 278, 1098-1111.  
20213114 C.Oh, C.Nikapitiya, Y.Lee, I.Whang, S.J.Kim, D.H.Kang, and J.Lee (2010).
Cloning, purification and biochemical characterization of beta agarase from the marine bacterium Pseudoalteromonas sp. AG4.
  J Ind Microbiol Biotechnol, 37, 483-494.  
20161978 X.T.Fu, and S.M.Kim (2010).
Agarase: review of major sources, categories, purification method, enzyme characteristics and applications.
  Mar Drugs, 8, 200-218.  
19189377 B.Mertz, X.Gu, and P.J.Reilly (2009).
Analysis of functional divergence within two structurally related glycoside hydrolase families.
  Biopolymers, 91, 478-495.  
19338387 C.Montanier, V.A.Money, V.M.Pires, J.E.Flint, B.A.Pinheiro, A.Goyal, J.A.Prates, A.Izumi, H.Stålbrand, C.Morland, A.Cartmell, K.Kolenova, E.Topakas, E.J.Dodson, D.N.Bolam, G.J.Davies, C.M.Fontes, and H.J.Gilbert (2009).
The active site of a carbohydrate esterase displays divergent catalytic and noncatalytic binding functions.
  PLoS Biol, 7, e71.
PDB codes: 2w9x 2waa 2wab 2wao
19553672 E.C.Martens, N.M.Koropatkin, T.J.Smith, and J.I.Gordon (2009).
Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm.
  J Biol Chem, 284, 24673-24677.  
19018102 L.C.Tsai, H.C.Huang, C.H.Hsiao, Y.N.Chiang, L.F.Shyur, Y.S.Lin, and S.H.Lee (2008).
Mutational and structural studies of the active-site residues in truncated Fibrobacter succinogenes1,3-1,4-beta-D-glucanase.
  Acta Crystallogr D Biol Crystallogr, 64, 1259-1266.  
17513582 D.Flament, T.Barbeyron, M.Jam, P.Potin, M.Czjzek, B.Kloareg, and G.Michel (2007).
Alpha-agarases define a new family of glycoside hydrolases, distinct from beta-agarase families.
  Appl Environ Microbiol, 73, 4691-4694.  
16550377 G.Michel, P.Nyval-Collen, T.Barbeyron, M.Czjzek, and W.Helbert (2006).
Bioconversion of red seaweed galactans: a focus on bacterial agarases and carrageenases.
  Appl Microbiol Biotechnol, 71, 23-33.  
16601125 J.Henshaw, A.Horne-Bitschy, A.L.van Bueren, V.A.Money, D.N.Bolam, M.Czjzek, N.A.Ekborg, R.M.Weiner, S.W.Hutcheson, G.J.Davies, A.B.Boraston, and H.J.Gilbert (2006).
Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains.
  J Biol Chem, 281, 17099-17107.
PDB codes: 2cdo 2cdp
16421930 V.Receveur-Bréchot, M.Czjzek, A.Barre, A.Roussel, W.J.Peumans, E.J.Van Damme, and P.Rougé (2006).
Crystal structure at 1.45-A resolution of the major allergen endo-beta-1,3-glucanase of banana as a molecular basis for the latex-fruit syndrome.
  Proteins, 63, 235-242.
PDB code: 2cyg
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.