PDBsum entry: 2e24

Lyase

PDB id: 2e24

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

Protein chain

Q9AQS0  (Q9AQS0_BACGL) -  Xanthan lyase

Seq: 930 a.a.

Struc: 752 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• 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.