PDBsum entry 1x1i

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Lyase PDB id
Protein chain
752 a.a. *
Waters ×795
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of xanthan lyase (n194a) complexed with a product
Structure: Xanthan lyase. Chain: a. Fragment: residues 26-777. Engineered: yes. Mutation: yes
Source: Bacillus sp. Gl1. Organism_taxid: 84635. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.80Å     R-factor:   0.176     R-free:   0.204
Authors: Y.Maruyama,W.Hashimoto,B.Mikami,K.Murata
Key ref:
Y.Maruyama et al. (2005). Crystal structure of Bacillus sp. GL1 xanthan lyase complexed with a substrate: insights into the enzyme reaction mechanism. J Mol Biol, 350, 974-986. PubMed id: 15979090 DOI: 10.1016/j.jmb.2005.05.055
04-Apr-05     Release date:   19-Jul-05    
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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: 10.1016/j.jmb.2005.05.055 J Mol Biol 350:974-986 (2005)
PubMed id: 15979090  
Crystal structure of Bacillus sp. GL1 xanthan lyase complexed with a substrate: insights into the enzyme reaction mechanism.
Y.Maruyama, W.Hashimoto, B.Mikami, K.Murata.
Bacillus sp. GL1 xanthan lyase, a member of polysaccharide lyase family 8 (PL-8), acts exolytically on the side-chains of pentasaccharide-repeating polysaccharide xanthan and cleaves the glycosidic bond between glucuronic acid (GlcUA) and pyruvylated mannose (PyrMan) through a beta-elimination reaction. To clarify the enzyme reaction mechanism, i.e. its substrate recognition and catalytic reaction, we determined crystal structures of a mutant enzyme, N194A, in complexes with the product (PyrMan) and a substrate (pentasacharide) and in a ligand-free form at 1.8, 2.1, and 2.3A resolution. Based on the structures of the mutant in complexes with the product and substrate, we found that xanthan lyase recognized the PyrMan residue at subsite -1 and the GlcUA residue at +1 on the xanthan side-chain and underwent little interaction with the main chain of the polysaccharide. The structure of the mutant-substrate complex also showed that the hydroxyl group of Tyr255 was close to both the C-5 atom of the GlcUA residue and the oxygen atom of the glycosidic bond to be cleaved, suggesting that Tyr255 likely acts as a general base that extracts the proton from C-5 of the GlcUA residue and as a general acid that donates the proton to the glycosidic bond. A structural comparison of catalytic centers of PL-8 lyases indicated that the catalytic reaction mechanism is shared by all members of the family PL-8, while the substrate recognition mechanism differs.
  Selected figure(s)  
Figure 4.
Figure 4. Active center of xanthan lyase (stereo diagram). (a) Superpositioning of wild-type/PyrMan (grey), N194A/PyrMan (cyan), and N194A/pentasaccharide (yellow). Bound sugar residues and surrounding amino acid residues are shown as a stick model. Red indicates oxygen and blue nitrogen atoms of amino acid residues. (b) Structure and interaction of xanthan disaccharide (PyrMan-GlcUA) and neighboring amino acid residues in the N194A/pentasaccharide complex. Thin lines indicate hydrogen bond interactions.
Figure 6.
Figure 6. Proposed model of the xanthan lyase reaction mechanism. (a) The substrate is bound to the active site cleft of xanthan lyase and orientated in the proper conformation via interactions with amino acid residues including hydrogen bonds of Asn194 and His246 with the carboxyl group of GlcUA. The hydroxyl group of Tyr255 is located close to the oxygen atom of the glycosidic bond to be cleaved and the C-5 atom of GlcUA. (b) Tyr255 extracts the C-5 proton of the GlcUA residue and subsequently donates the proton to the oxygen atom of the glycosidic bond, cleaving the glycosidic bond and forming a double bond between the C-4 and C-5 atoms of GlcUA.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 350, 974-986) copyright 2005.  
  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.  
19193638 A.Ochiai, T.Itoh, B.Mikami, W.Hashimoto, and K.Murata (2009).
Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases.
  J Biol Chem, 284, 10181-10189.
PDB codes: 2zux 2zuy
18978091 N.Konno, K.Igarashi, N.Habu, M.Samejima, and A.Isogai (2009).
Cloning of the Trichoderma reesei cDNA encoding a glucuronan lyase belonging to a novel polysaccharide lyase family.
  Appl Environ Microbiol, 75, 101-107.  
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.  
17947240 A.Ochiai, T.Itoh, Y.Maruyama, A.Kawamata, B.Mikami, W.Hashimoto, and K.Murata (2007).
  J Biol Chem, 282, 37134-37145.
PDB codes: 2z8r 2z8s
16521140 C.S.Rye, A.Matte, M.Cygler, and S.G.Withers (2006).
An atypical approach identifies TYR234 as the key base catalyst in chondroitin AC lyase.
  Chembiochem, 7, 631-637.  
16893885 T.Itoh, W.Hashimoto, B.Mikami, and K.Murata (2006).
Crystal structure of unsaturated glucuronyl hydrolase complexed with substrate: molecular insights into its catalytic reaction mechanism.
  J Biol Chem, 281, 29807-29816.
PDB codes: 2ahf 2ahg 2d5j
16495121 V.L.Yip, and S.G.Withers (2006).
Breakdown of oligosaccharides by the process of elimination.
  Curr Opin Chem Biol, 10, 147-155.  
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.