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PDBsum entry 1o4z
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1o4z

 

 

 

 

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Contents
Protein chains
295 a.a. *
Ligands
EPE ×4
Metals
_NA ×7
_MG ×2
Waters ×888
* Residue conservation analysis
PDB id:
1o4z
Name: Hydrolase
Title: The three-dimensional structure of beta-agarase b from zobellia galactanivorans
Structure: Beta-agarase b. Chain: a, b, c, d. Engineered: yes
Source: Zobellia galactanivorans. Organism_taxid: 63186. Strain: dsij. Gene: agab. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.169     R-free:   0.224
Authors: J.Allouch,M.Jam,W.Helbert,T.Barbeyron,B.Kloareg,B.Henrissat,M.Czjzek
Key ref:
J.Allouch et al. (2003). The three-dimensional structures of two beta-agarases. J Biol Chem, 278, 47171-47180. PubMed id: 12970344 DOI: 10.1074/jbc.M308313200
Date:
29-Jul-03     Release date:   09-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Q9RGX8  (AGAB_ZOBGA) -  Beta-agarase B from Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij)
Seq:
Struc: 		353 a.a.
295 a.a.
Key:    Secondary structure  CATH domain

 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.

 

 
DOI no: 10.1074/jbc.M308313200 J Biol Chem 278:47171-47180 (2003)
PubMed id: 12970344  
 
 
The three-dimensional structures of two beta-agarases.
J.Allouch, M.Jam, W.Helbert, T.Barbeyron, B.Kloareg, B.Henrissat, M.Czjzek.
 
  ABSTRACT  
 
Agars are important gelifying agents for biochemical use and the food industry. To cleave the beta-1,4-linkages between beta-d-galactose and alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called beta-agarases. Beta-agarases A and B from Zobellia galactanivorans Dsij have recently been biochemically characterized. Here we report the first crystal structure of these two beta-agarases. The two proteins were overproduced in Escherichia coli and crystallized, and the crystal structures were determined at 1.48 and 2.3 A for beta-agarases A and B, respectively. The structure of beta-agarase A was solved by the multiple anomalous diffraction method, whereas beta-agarase B was solved with molecular replacement using beta-agarase A as model. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic machinery, namely the nucleophilic residues Glu-147 and Glu-184 and the acid/base residues Glu-152 and Glu-189 for beta-agarases A and B, respectively. The structures of the agarases were compared with those of two lichenases and of a kappa-carrageenase, which all belong to family 16 of the glycoside hydrolases in order to pinpoint the residues responsible for their widely differing substrate specificity. The relationship between structure and enzymatic activity of the two beta-agarases from Z. galactanivorans Dsij was studied by analysis of the degradation products starting with different oligosaccharides. The combination of the structural and biochemical results allowed the determination of the number of subsites present in the catalytic cleft of the beta-agarases.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. a, schematic diagram showing a disaccharide unit of agarose. The (1, 4) bond cleaved during catalysis is labeled. b, organization of the modules of -agarases A and B, respectively. 		Figure 3.
FIG. 3. a, stereo view of -AgaA_CM (top) and -AgaB (bottom) ribbon models. The calcium ion is displayed in purple, located on the convex side of the protein. The figure was produced with Molscript (44). b, electrostatic surface potential of -AgaA_CM (left) and -AgaB (right). Blue patches represent positive potential, red represent negative potential, and white surface is neutral. The number of subsites and their location within the molecule are represented by numbers (-4 to +4). The aromatic residues supposed to interact with the substrate are labeled at their location on the protein. The figure was produced with GRASP (45).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 47171-47180) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21332624 E.Rebuffet, A.Groisillier, A.Thompson, A.Jeudy, T.Barbeyron, M.Czjzek, and G.Michel (2011).
Discovery and structural characterization of a novel glycosidase family of marine origin.
  Environ Microbiol, 13, 1253-1270.
PDB code: 3p2n
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.  
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.  
19802606 H.T.Kim, S.Lee, D.Lee, H.S.Kim, W.G.Bang, K.H.Kim, and I.G.Choi (2010).
Overexpression and molecular characterization of Aga50D from Saccharophagus degradans 2-40: an exo-type beta-agarase producing neoagarobiose.
  Appl Microbiol Biotechnol, 86, 227-234.  
20376150 J.H.Hehemann, G.Correc, T.Barbeyron, W.Helbert, M.Czjzek, and G.Michel (2010).
Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota.
  Nature, 464, 908-912.
PDB codes: 3ilf 3juu
20213521 M.K.Jang, S.W.Lee, D.G.Lee, N.Y.Kim, K.H.Yu, H.J.Jang, S.Kim, A.Kim, and S.H.Lee (2010).
Enhancement of the thermostability of a recombinant beta-agarase, AgaB, from Zobellia galactanivorans by random mutagenesis.
  Biotechnol Lett, 32, 943-949.  
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.  
19292880 B.Yang, G.Yu, X.Zhao, G.Jiao, S.Ren, and W.Chai (2009).
Mechanism of mild acid hydrolysis of galactan polysaccharides with highly ordered disaccharide repeats leading to a complete series of exclusively odd-numbered oligosaccharides.
  FEBS J, 276, 2125-2137.  
19504047 X.Lu, Y.Chu, Q.Wu, Y.Gu, F.Han, and W.Yu (2009).
Cloning, expression and characterization of a new agarase-encoding gene from marine Pseudoalteromonas sp.
  Biotechnol Lett, 31, 1565-1570.  
18785021 C.Shi, X.Lu, C.Ma, Y.Ma, X.Fu, and W.Yu (2008).
Enhancing the thermostability of a novel beta-agarase AgaB through directed evolution.
  Appl Biochem Biotechnol, 151, 51-59.  
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.  
17340109 J.Dong, Y.Tamaru, and T.Araki (2007).
A unique beta-agarase, AgaA, from a marine bacterium, Vibrio sp. strain PO-303.
  Appl Microbiol Biotechnol, 74, 1248-1255.  
17213669 J.Dong, Y.Tamaru, and T.Araki (2007).
Molecular cloning, expression, and characterization of a beta-agarase gene, agaD, from a marine bacterium, Vibrio sp. strain PO-303.
  Biosci Biotechnol Biochem, 71, 38-46.  
17999688 R.Chiaraluce, R.Florio, S.Angelaccio, G.Gianese, J.F.van Lieshout, J.van der Oost, and V.Consalvi (2007).
Tertiary structure in 7.9 M guanidinium chloride--the role of Glu53 and Asp287 in Pyrococcus furiosus endo-beta-1,3-glucanase.
  FEBS J, 274, 6167-6179.  
17337564 W.W.Zhang, and L.Sun (2007).
Cloning, characterization, and molecular application of a beta-agarase gene from Vibrio sp. strain V134.
  Appl Environ Microbiol, 73, 2825-2831.  
16892287 A.Giordano, G.Andreotti, A.Tramice, and A.Trincone (2006).
Marine glycosyl hydrolases in the hydrolysis and synthesis of oligosaccharides.
  Biotechnol J, 1, 511-530.  
17028783 D.G.Lee, G.T.Park, N.Y.Kim, E.J.Lee, M.K.Jang, Y.G.Shin, G.S.Park, T.M.Kim, J.H.Lee, J.H.Lee, S.J.Kim, and S.H.Lee (2006).
Cloning, expression, and characterization of a glycoside hydrolase family 50 beta-agarase from a marine Agarivorans isolate.
  Biotechnol Lett, 28, 1925-1932.  
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.  
17057348 J.Vasur, R.Kawai, A.M.Larsson, K.Igarashi, M.Sandgren, M.Samejima, and J.Ståhlberg (2006).
X-ray crystallographic native sulfur SAD structure determination of laminarinase Lam16A from Phanerochaete chrysosporium.
  Acta Crystallogr D Biol Crystallogr, 62, 1422-1429.
PDB code: 2cl2
17006642 K.N.Neustroev, A.M.Golubev, M.L.Sinnott, R.Borriss, M.Krah, H.Brumer, E.V.Eneyskaya, S.Shishlyannikov, K.A.Shabalin, V.T.Peshechonov, V.G.Korolev, and A.A.Kulminskaya (2006).
Transferase and hydrolytic activities of the laminarinase from Rhodothermus marinus and its M133A, M133C, and M133W mutants.
  Glycoconj J, 23, 501-511.  
16672483 N.A.Ekborg, L.E.Taylor, A.G.Longmire, B.Henrissat, R.M.Weiner, and S.W.Hutcheson (2006).
Genomic and proteomic analyses of the agarolytic system expressed by Saccharophagus degradans 2-40.
  Appl Environ Microbiol, 72, 3396-3405.  
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
15902469 Y.Ohta, Y.Hatada, M.Miyazaki, Y.Nogi, S.Ito, and K.Horikoshi (2005).
Purification and characterization of a novel alpha-agarase from a Thalassomonas sp.
  Curr Microbiol, 50, 212-216.  
15614968 A.Ilari, S.Angelaccio, A.Fiorillo, R.Florio, V.Consalvi, and R.Chiaraluce (2004).
Crystalization and preliminary X-ray crystallographic analysis of the laminarinase endo-beta-1,3-glucanase from Pyrococcus furiosus.
  Acta Crystallogr D Biol Crystallogr, 60, 2394-2395.  
15062085 J.Allouch, W.Helbert, B.Henrissat, and M.Czjzek (2004).
Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.
  Structure, 12, 623-632.
PDB code: 1urx
15490156 Y.Ohta, Y.Hatada, Y.Nogi, Z.Li, S.Ito, and K.Horikoshi (2004).
Cloning, expression, and characterization of a glycoside hydrolase family 86 beta-agarase from a deep-sea Microbulbifer-like isolate.
  Appl Microbiol Biotechnol, 66, 266-275.  
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 code is shown on the right.

 

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