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PDBsum entry 2e24

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protein ligands links
Lyase PDB id
2e24
Jmol
Contents
Protein chain
752 a.a. *
Ligands
PEG
Waters ×559
* Residue conservation analysis
PDB id:
2e24
Name: Lyase
Title: Crystal structure of a mutant (r612a) of xanthan lyase
Structure: Xanthan lyase. Chain: a. Fragment: residues 26-777. Engineered: yes. Mutation: yes
Source: Bacillus sp.. Organism_taxid: 84635. Strain: gl1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.15Å     R-factor:   0.175     R-free:   0.217
Authors: Y.Maruyama,B.Mikami,W.Hashimoto,K.Murata
Key ref:
Y.Maruyama et al. (2007). A structural factor responsible for substrate recognition by Bacillus sp. GL1 xanthan lyase that acts specifically on pyruvated side chains of xanthan. Biochemistry, 46, 781-791. PubMed id: 17223699 DOI: 10.1021/bi0619775
Date:
07-Nov-06     Release date:   30-Jan-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9AQS0  (XANLY_BACGL) -  Xanthan lyase
Seq:
Struc:
 
Seq:
Struc:
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.4.2.2.12  - 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: 10.1021/bi0619775 Biochemistry 46:781-791 (2007)
PubMed id: 17223699  
 
 
A structural factor responsible for substrate recognition by Bacillus sp. GL1 xanthan lyase that acts specifically on pyruvated side chains of xanthan.
Y.Maruyama, B.Mikami, W.Hashimoto, K.Murata.
 
  ABSTRACT  
 
Xanthan is a bacterial heteropolysaccharide composed of pentasaccharide repeating units, i.e., a cellobiose as a backbone and a trisaccharide consisting of two mannoses and one glucuronic acid as a side chain. Nonreducing terminal mannose residues of xanthan side chains are partially pyruvated. Bacillus sp. GL1 xanthan lyase, a member of polysaccharide lyase family 8, acts specifically on pyruvated side chains of xanthan and yields pyruvated mannose through a beta-elimination reaction by using a single Tyr255 residue as base and acid catalysts. Here we show structural factors for substrate recognition by xanthan lyase through X-ray crystallographic and mutational analyses. The enzyme accommodates mannose and pyruvated mannose at the -1 subsite, although both inhibitor and dissociation constants of the two monosaccharides indicated that the affinity of pyruvated mannose for xanthan lyase is much higher than that of mannose. The high affinity of pyruvated mannose is probably due to the formation of additional hydrogen bonds between the carboxyl group of pyruvated mannose and amino acid residues of Tyr315 and Arg612. Site-directed mutagenesis of the two residues demonstrated that Arg612 is a key residue in recognizing pyruvated mannose. Arg612 is located in the protruding loop covering the substrate, suggesting that the loop functions as a lid that is responsible for the proper accommodation of the substrate at the active site.
 

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
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).
A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER.
  J Biol Chem, 282, 37134-37145.
PDB codes: 2z8r 2z8s
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.