PDBsum entry 1lxm

Lyase

PDB id: 1lxm

Contents

Protein chain

794 a.a. *

Ligands

NAG-BDP-NAG-BDP-NAG-BDP

Waters ×191

* Residue conservation analysis

PDB id:

1lxm

Name:

Lyase

Title:

Crystal structure of streptococcus agalactiae hyaluronate lyase complexed with hexasaccharide unit of hyaluronan

Structure:

Hyaluronate lyase. Chain: a. Synonym: hyaluronidase, hyase. Engineered: yes

Source:

Streptococcus agalactiae. Organism_taxid: 1311. Gene: hyl. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.20Å R-factor: 0.218 R-free: 0.271

Authors:

L.V.Mello,B.L.De Groot,S.Li,M.J.Jedrzejas

Key ref:

L.V.Mello et al. (2002). Structure and flexibility of Streptococcus agalactiae hyaluronate lyase complex with its substrate. Insights into the mechanism of processive degradation of hyaluronan. J Biol Chem, 277, 36678-36688. PubMed id: 12130645 DOI: 10.1074/jbc.M205140200

Date:

05-Jun-02 Release date: 30-Oct-02

Protein chain

Q53591  (HYSA_STRA3) -  Hyaluronate lyase from Streptococcus agalactiae serotype III (strain NEM316)

Seq: 984 a.a.

Struc: 794 a.a.*

* PDB and UniProt seqs differ at 15 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.2.2.1 - hyaluronate lyase.
• Reaction: [hyaluronan](n) = n 3-(4-deoxy-beta-D-gluc-4-enuronosyl)-N-acetyl-D- glucosamine + H2O

[hyaluronan](n) = n 3-(4-deoxy-beta-D-gluc-4-enuronosyl)-N-acetyl-D- glucosamine (Bound ligand (Het Group name = NAG) matches with 57.69% similarity) + H2O

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1074/jbc.M205140200

J Biol Chem 277:36678-36688 (2002)

PubMed id: 12130645

Structure and flexibility of Streptococcus agalactiae hyaluronate lyase complex with its substrate. Insights into the mechanism of processive degradation of hyaluronan.

L.V.Mello, B.L.De Groot, S.Li, M.J.Jedrzejas.

ABSTRACT

Streptococcus agalactiae hyaluronate lyase degrades primarily hyaluronan, the main polysaccharide component of the host connective tissues, into unsaturated disaccharide units as the end product. Such function of the enzyme destroys the normal connective tissue structure of the host and exposes the tissue cells to various bacterial toxins. The crystal structure of hexasaccharide hyaluronan complex with the S. agalactiae hyaluronate lyase was determined at 2.2 A resolution; the mechanism of the catalytic process, including the identification of specific residues involved in the degradation of hyaluronan, was clearly identified. The enzyme is composed structurally and functionally from two distinct domains, an alpha-helical alpha-domain and a beta-sheet beta-domain. The flexibility of the protein was investigated by comparing the crystal structures of the S. agalactiae and the Streptococcus pneumoniae enzymes, and by using essential dynamics analyses of CONCOORD computer simulations. These revealed important modes of flexibility, which could be related to the protein function. First, a rotation/twist of the alpha-domain relative to the beta-domain is potentially related to the mechanism of processivity of the enzyme; this twist motion likely facilitates shifting of the ligand along the catalytic site cleft in order to reposition it to be ready for further cleavage. Second, a movement of the alpha- and beta-domains with respect to each other was found to contribute to a change in electrostatic characteristics of the enzyme and appears to facilitate binding of the negatively charged hyaluronan ligand. Third, an opening/closing of the substrate binding cleft brings a catalytic histidine closer to the cleavable substrate beta1,4-glycosidic bond. This opening/closing mode also reflects the main conformational difference between the crystal structures of the S. agalactiae and the S. pneumoniae hyaluronate lyases.

Selected figure(s)

Figure 1.
Fig. 1. The structure of S. agalactiae hyaluronate lyase with bound hexasaccharide hyaluronan substrate. A, ribbon drawing of the structure of the complex. All three domains of the enzyme are shown, the N-terminal -sheet domain ( II-domain, top), the -helical domain ( -domain, middle), the C-terminal -sheet domain ( II-domain, bottom), as well as the cleft with the bound hexasaccharide unit of hyaluronan substrate (depicted in a ball and stick fashion with bonds colored in red). The structure of the enzyme is color-coded by the secondary structure elements ( -helices in blue, 3[10] helices in purple, -sheets in green), and the atoms of the substrate are colored by the atom type (carbon atoms in green, oxygen atoms in red, and nitrogen atoms in blue). Consecutive disaccharide units of HA starting from the reducing end are labeled as HA1 , HA2, and HA3. B, comparison of structures of S. agalactiae and S. pneumoniae hyaluronate lyases. The S. agalactiae enzyme (black) (domains labeled) has an additional domain at its N terminus ( I-domain). The cleft area in this enzyme is also wider than that of the S. pneumoniae hyaluronate lyase (blue) (maximum difference in width of ~7 Å). C, electrostatic potential distribution in the catalytic cleft. The positive potential is shown in blue and the negative potential in red. The majority of the cleft is highly positively charged (middle and the left side; positive patch) whereas at the product-releasing end of the cleft is negatively charged (right side of the cleft; a negative patch). The hydrophobic patch is also shown. Bound hexasaccharide hyaluronan is shown as sticks color-coded by atom type. Reducing and non-reducing ends of HA are labeled.

Figure 3.
Fig. 3. DynDom analysis of the difference between the S. pneumoniae and S. agalactiae hyaluronate lyase x-ray crystal structures. Shown is the x-ray structure of S. agalactiae HL, with the yellow arrow depicting the rotation axis for the domain transition toward the S. pneumoniae HL structure, in which the red domain rotates with respect to the blue domain. The domain motion corresponds to a closure motion (white arrows). The green residues provide the flexible linker between the two domains.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 36678-36688) copyright 2002.

Figures were selected by an automated process.