PDBsum entry 1w3y

Lyase

PDB id: 1w3y

Contents

Protein chain

721 a.a. *

Ligands

PVC

XYL ×2

SO4 ×5

Waters ×564

* Residue conservation analysis

PDB id:

1w3y

Name:

Lyase

Title:

Crystal structure of s. Pneumoniae hyaluronate lyase in complex with palmitoyl-vitamin c

Structure:

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

Source:

Streptococcus pneumoniae. Organism_taxid: 1313. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.65Å R-factor: 0.192 R-free: 0.210

Authors:

D.J.Rigden,M.J.Jedrzejas

Key ref:

A.Botzki et al. (2004). L-Ascorbic acid 6-hexadecanoate, a potent hyaluronidase inhibitor. X-ray structure and molecular modeling of enzyme-inhibitor complexes. J Biol Chem, 279, 45990-45997. PubMed id: 15322107 DOI: 10.1074/jbc.M406146200

Date:

21-Jul-04 Release date: 26-Aug-04

Protein chain

Q54873  (HYSA_STRPN) -  Hyaluronate lyase from Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)

Seq: 1066 a.a.

Struc: 721 a.a.*

* PDB and UniProt seqs differ at 8 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 = PVC) matches with 43.24% similarity) + H2O

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

Key reference

DOI no: 10.1074/jbc.M406146200

J Biol Chem 279:45990-45997 (2004)

PubMed id: 15322107

L-Ascorbic acid 6-hexadecanoate, a potent hyaluronidase inhibitor. X-ray structure and molecular modeling of enzyme-inhibitor complexes.

A.Botzki, D.J.Rigden, S.Braun, M.Nukui, S.Salmen, J.Hoechstetter, G.Bernhardt, S.Dove, M.J.Jedrzejas, A.Buschauer.

ABSTRACT

Hyaluronidases are enzymes that degrade hyaluronan, an important component of the extracellular matrix. The mammalian hyaluronidases are considered to be involved in many (patho)physiological processes like fertilization, tumor growth, and metastasis. Bacterial hyaluronidases, also termed hyaluronate lyases, contribute to the spreading of microorganisms in tissues. Such roles for hyaluronidases suggest that inhibitors could be useful pharmacological tools. Potent and selective inhibitors are not known to date, although L-ascorbic acid has been reported to be a weak inhibitor of Streptococcus pneumoniae hyaluronate lyase (SpnHL). The x-ray structure of SpnHL complexed with L-ascorbic acid has been elucidated suggesting that additional hydrophobic interactions might increase inhibitory activity. Here we show that L-ascorbic acid 6-hexadecanoate (Vcpal) is a potent inhibitor of both streptococcal and bovine testicular hyaluronidase (BTH). Vcpal showed strong inhibition of Streptococcus agalactiae hyaluronate lyase with an IC(50) of 4 microM and weaker inhibition of SpnHL and BTH with IC(50) values of 100 and 56 microM, respectively. To date, Vcpal has proved to be one of the most potent inhibitors of hyaluronidase. We also determined the x-ray structure of the SpnHL-Vcpal complex and confirmed the hypothesis that additional hydrophobic interactions with Phe-343, His-399, and Thr-400 in the active site led to increased inhibition. A homology structural model of BTH was also generated to suggest binding modes of Vcpal to this hyaluronidase. The long alkyl chain seemed to interact with an extended, hydrophobic channel formed by mostly conserved amino acids Ala-84, Leu-91, Tyr-93, Tyr-220, and Leu-344 in BTH.

Selected figure(s)

Figure 1.
FIG. 1. Chemical structures of L-ascorbic acid and L-ascorbic acid 6-hexadecanoate.

Figure 3.
FIG. 3. A, the SpnHL binding site for L-ascorbic acid 6-hexadecanoate. Hydrogen bonds are represented as dotted lines. Shown is the final sigmaA-weighted omit map electron density calculated to a resolution of 1.65 Å when the inhibitor was excluded from the model and contoured at 2.0 . B, schematic diagram of interactions of L-ascorbic acid 6-hexadecanoate with SpnHL. Hydrogen bonds are represented as dotted lines. Other residues shown form hydrophobic interactions with the inhibitor. The figure was made with LIGPLOT (35). C, binding mode of hexasaccharide substrate. The coordinates of the hexasaccharide substrate originate from its complex with SpnHL (Protein Data Bank code 1loh [PDB] (54)). D, binding mode of L-ascorbic acid 6-hexadecanoate. The cryoprotectant xylitol molecule close to the inhibitor (see text) is also shown (bottom right corner).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 45990-45997) copyright 2004.

Figures were selected by an automated process.