PDBsum entry: 1j0m

Lyase

PDB id: 1j0m

Contents

Protein chain

752 a.a. *

Metals

_CA

Waters ×247

* Residue conservation analysis

PDB id:

1j0m

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.

Resolution:

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

Date:

19-Nov-02 Release date: 01-Apr-03

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: 10.1074/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.

ABSTRACT

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.