PDBsum entry 1j0m

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protein metals links
Lyase PDB id
Protein chain
752 a.a. *
Waters ×247
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of bacillus sp. Gl1 xanthan lyase that act chains of xanthan
Structure: Xanthan lyase. Chain: a. Engineered: yes
Source: Bacillus sp.. Organism_taxid: 84635. Strain: gl1. Gene: xly. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.30Å     R-factor:   0.175     R-free:   0.240
Authors: W.Hashimoto,H.Nankai,B.Mikami,K.Murata
Key ref:
W.Hashimoto et al. (2003). Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan. J Biol Chem, 278, 7663-7673. PubMed id: 12475987 DOI: 10.1074/jbc.M208100200
19-Nov-02     Release date:   01-Apr-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9AQS0  (XANLY_BACGL) -  Xanthan lyase
930 a.a.
752 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.  - Xanthan lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Eliminative cleavage of the terminal beta-D-mannosyl-beta-D-1,4- glucuronosyl linkage of the side-chain of the polysaccharide xanthan, leaving a 4-deoxy-alpha-L-threo-hex-4-enuronosyl group at the terminus of the side-chain.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     4 terms  


DOI no: 10.1074/jbc.M208100200 J Biol Chem 278:7663-7673 (2003)
PubMed id: 12475987  
Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan.
W.Hashimoto, H.Nankai, B.Mikami, K.Murata.
Xanthan lyase, a member of polysaccharide lyase family 8, is a key enzyme for complete depolymerization of a bacterial heteropolysaccharide, xanthan, in Bacillus sp. GL1. The enzyme acts exolytically on the side chains of the polysaccharide. The x-ray crystallographic structure of xanthan lyase was determined by the multiple isomorphous replacement method. The crystal structures of xanthan lyase and its complex with the product (pyruvylated mannose) were refined at 2.3 and 2.4 A resolution with final R-factors of 17.5 and 16.9%, respectively. The refined structure of the product-free enzyme comprises 752 amino acid residues, 248 water molecules, and one calcium ion. The enzyme consists of N-terminal alpha-helical and C-terminal beta-sheet domains, which constitute incomplete alpha(5)/alpha(5)-barrel and anti-parallel beta-sheet structures, respectively. A deep cleft is located in the N-terminal alpha-helical domain facing the interface between the two domains. Although the overall structure of the enzyme is basically the same as that of the family 8 lyases for hyaluronate and chondroitin AC, significant differences were observed in the loop structure over the cleft. The crystal structure of the xanthan lyase complexed with pyruvylated mannose indicates that the sugar-binding site is located in the deep cleft, where aromatic and positively charged amino acid residues are involved in the binding. The Arg(313) and Tyr(315) residues in the loop from the N-terminal domain and the Arg(612) residue in the loop from the C-terminal domain directly bind to the pyruvate moiety of the product through the formation of hydrogen bonds, thus determining the substrate specificity of the enzyme.
  Selected figure(s)  
Figure 5.
Fig. 5. Coordination of the calcium ion in the C-terminal domain (stereodiagram). The calcium ion (yellow ball) coordinates to the oxygen atoms of Asp515, Asp516, Asp517, Glu676, and WAT951, which are shown in purple. These interactions are indicated by dotted lines. This figure was prepared using the programs MOLSCRIPT (29) and RASTER3D (31).
Figure 9.
Fig. 9. Molecular surface of the active cleft. Aromatic, positively, and negatively charged aa residues are colored yellow, cyan, and purple, respectively. PyrMan is shown as a stick model. A, the mannose moiety of PyrMan is on the front side, and the pyruvate moiety of PyrMan on the back side. The catalytic site is thought to be located in front of the tunnel. B, this view is from the opposite direction of A. This figure was prepared using the program GRASP (32).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 7663-7673) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20805221 M.L.Garron, and M.Cygler (2010).
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
  Glycobiology, 20, 1547-1573.  
19579240 J.Calveras, M.Egido-Gabás, L.Gómez, J.Casas, T.Parella, J.Joglar, J.Bujons, and P.Clapés (2009).
Dihydroxyacetone phosphate aldolase catalyzed synthesis of structurally diverse polyhydroxylated pyrrolidine derivatives and evaluation of their glycosidase inhibitory properties.
  Chemistry, 15, 7310-7328.  
18256495 K.Murata, S.Kawai, B.Mikami, and W.Hashimoto (2008).
Superchannel of bacteria: biological significance and new horizons.
  Biosci Biotechnol Biochem, 72, 265-277.  
16495121 V.L.Yip, and S.G.Withers (2006).
Breakdown of oligosaccharides by the process of elimination.
  Curr Opin Chem Biol, 10, 147-155.  
15849405 W.Hashimoto, K.Momma, Y.Maruyama, M.Yamasaki, B.Mikami, and K.Murata (2005).
Structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules.
  Biosci Biotechnol Biochem, 69, 673-692.  
15090531 O.Miyake, A.Ochiai, W.Hashimoto, and K.Murata (2004).
Origin and diversity of alginate lyases of families PL-5 and -7 in Sphingomonas sp. strain A1.
  J Bacteriol, 186, 2891-2896.  
  16233728 W.Hashimoto, M.Yamasaki, T.Itoh, K.Momma, B.Mikami, and K.Murata (2004).
Super-channel in bacteria: structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules.
  J Biosci Bioeng, 98, 399-413.  
12876365 M.Yamasaki, S.Moriwaki, W.Hashimoto, B.Mikami, and K.Murata (2003).
Crystallization and preliminary X-ray analysis of alginate lyase, a member of family PL-7, from Pseudomonas aeruginosa.
  Acta Crystallogr D Biol Crystallogr, 59, 1499-1501.  
15224891 P.Michaud, A.Da Costa, B.Courtois, and J.Courtois (2003).
Polysaccharide lyases: recent developments as biotechnological tools.
  Crit Rev Biotechnol, 23, 233-266.  
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.