Polysaccharide Lyase Family 8

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• Author: ^^^Michael Suits^^^
• Responsible Curator: ^^^Michael Suits^^^

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Polysaccharide Lyase Family PL8
3D Structure	(α/α)6 barrel + anti-parallel β-sheet
Mechanism	β-elimination
Active site residues	Pneumonococcal hyaluronidase: Asn249, His399, Tyr408.
CAZy DB link
http://www.cazy.org/PL8.html

Known Activities

Depending on the subfamily, PL8s display a broad range of enzymatic activities including: hyaluronate lyase (EC 4.2.2.1); chondroitin AC lyase (EC 4.2.2.5); xanthan lyase (EC 4.2.2.12); and chondroitin ABC lyase (EC 4.2.2.20).

Substrate specificities

PL8s are active on a variety of uronic acid-containing polysaccharides including hyaluronan [4)-β-D-Glucuronate-1,3-β -D-N-Acetyl-Glucosamine(1]_n, chondroitin AC [4)-β-D-Glucuronate-1,3-β-D-N-Acetyl-GalactosamineΔ4,6S(1]_n, xanthan [4)-β-D-Glucuronate-1,4-β-D-Glucuronate (1]_n, and chondroitin ABC [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-β-L-Iduronate2S-1,3-β-D-N-Acetyl-Galactosamine4S(1]_n.

Kinetics and Mechanism

One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas et al. proposed that in the S. pneumoniae hyaluronidase His399 acts as the general base, Asn349 act to neutralize the C5-carboxylate group, and Tyr408 is the protein donor [1, 2]. However, for two other PL8 family members: the Bacillus sp. GL1 xanthanase and Streptomyces coelicolor A3 hyaluronidase, it was suggested that equivalent tyrosine residues served as the general acid and general base throughout the reaction [3, 4]. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggest the latter hypothesis is favored, with H399 participating in the neutralization of the C5 [5]. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that opening/closing and twisting domain motions of the (α/α)₆ barrel and anti-parallel β-sheet domains underly processive substrate translocation [6].

Catalytic Residues

In Streptococcus pneumoniae, mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation [1]. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng et al. for discussions [4, 5]. An Asp for Asn mutation in Proteus vulgaris was suggested to provide the mechanism for distinguishing between the two epimers [7].

Three-dimensional structures

Structure by Activity: Hyaluronidase – 'Streptococcus pneumoniae' R6 [2](PDB 1OJM). Chondroitin AC lyase – 'Bacteroides stercoris' HJ-15 [8](PDB 1CB8). Xanthanase – 'Bacillus' sp GL1 [9](PDB 1J0M). Chondroitin ABC lyase – 'Proteus vulgaris' [7](PDB 1HN0).

Family Firsts

First stereochemistry determination

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First catalytic nucleophile identification

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First general acid/base residue identification

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First 3-D structure

Chondroitin AC lyase – “Bacteroides stercoris” HJ-15 [8](PDB 1CB8).

First Structure by Activity

Hyaluroniate lyase

Streptococcus pneumoniae R6 [2](PDB 1OJM).

Chondroitin AC lyase

Bacteroides stercoris HJ-15 [8](PDB 1CB8).

Xanthan lyase

Bacillus sp GL1 [9](PDB 1J0M).

Chondroitin ABC lyase

Proteus vulgaris [7](PDB 1HN0).

References

<biblio>

1. Rapport1951 pmid=14917676
2. Li2000 pmid=10716923
3. Fethiere1999 pmid=10329169
4. Sato1994 pmid=7512814
5. Huang2003 pmid=12706721
6. Hashimoto1998 pmid=9758797
7. Hashimoto2003 pmid=16348550
8. Maruyama2005 pmid=15979090
9. Kelly2001 pmid=11358878
10. Elmabrouk2011 pmid=21287626
11. Zheng2013 pmid=23944739
12. Joshi2009 pmid=19089975