Polysaccharide Lyase Family 17

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• Author: Emil Stender
• Responsible Curator: Birte Svensson

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Polysaccharide Lyase Family 17
3D structure	(α/α)6 barrel + anti-parallel β-sheet
Mechanism	β-elimination
Charge neutralizer	Asparagine and histidine
Active site residues	known
CAZy DB link
http://www.cazy.org/PL17.html

Substrate specificities

PL17 contains 2 subfamilies [1] as well as several proteins currently not assigned to any subfamily. Subfamily 2 has been shown to be exolytic alginate lyases [2, 3, 4, 5] with activity for all three block structures observed [6]. Alginate consisting of 1,4 linked β-D-mannuronic acid and α-L-guluronic acid arranged in poly-mannuronic acid , poly-guluronic acid or poly-mannuronic/guluronic acid blocks [7, 8]. Subfamily 1 has been found to be hyaluroran endo-lyases or poly-glucuronic acid lyases [6]. Hyaluronan consisting of N-acetyl-D-glucoamine and 1,4 linked D-glucoronic acid [9].

Kinetics and Mechanism

Figure 1. +1 subsite of the alginate lyase Alg17c (PDB: 4OJZ)

The β-elimination catalyzed by the PL17 enzymes results in the formation of a C4-C5 unsaturated sugar at the new non-reducing end. The first step is the neutralization of the acid group in the +1 subsite by the conserved histidine and asparagine. This lowers the pKa value of the C5-proton allowing for abstraction by the catalytic base (Figure 1). A catalytic acid then donates a proton to the glycosidic linkage resulting in the β-elimination [3].

Catalytic Residues

After charge neutralization a tyrosine functions as the catalytic base and another tyrosine as the acid. These were originally identified as Y456 and Y258 in Alg17c from Saccharophagus degradans [3].

Three-dimensional structures

Figure 2. Crystal structures of the substrate complex of the homo-dimeric Alg17c (PDB: 4OJZ) with the substrate in blue.

One crystal structure is available in PL17, that of Alg17c from Saccharophagus degradans belonging to subfamily 2 [3]. It is an (α/α)6 barrel + anti-parallel β-sheet with the catalytic machinery located in the (α/α)₆ barrel (Figure 2). Alg17c is a homodimer, though that does not appear to be a general feature of PL17 [2, 3, 4, 5].

Family Firsts

First catalytic activity

MJ-3 alginate lyase assayed by monitoring the absorbance at 235 nm and characterizing the degradation products by TLC and ¹H-NMR [10].

First catalytic base/acid

Y456 and Y258 in Alg17c crystal structure identified by their conservation in PL17, mutagenesis and kinetic analysis of mutants (Y258A and Y450A inactive) [3]

First charge neutralizer

N201 and H202 in the Alg17c crystal structure identified by their conservation in PL17, mutagenesis and kinetic analysis (N201A inactive and H202L 4.6 % activity remaining) [3]

First 3-D structure

Alg17c crystal structure [3]

References

1. Lombard V, Bernard T, Rancurel C, Brumer H, Coutinho PM, and Henrissat B. (2010). A hierarchical classification of polysaccharide lyases for glycogenomics. Biochem J. 2010;432(3):437-44. DOI:10.1042/BJ20101185 |
2. Jagtap SS, Hehemann JH, Polz MF, Lee JK, and Zhao H. (2014). Comparative biochemical characterization of three exolytic oligoalginate lyases from Vibrio splendidus reveals complementary substrate scope, temperature, and pH adaptations. Appl Environ Microbiol. 2014;80(14):4207-14. DOI:10.1128/AEM.01285-14 |
3. Park D, Jagtap S, and Nair SK. (2014). Structure of a PL17 family alginate lyase demonstrates functional similarities among exotype depolymerases. J Biol Chem. 2014;289(12):8645-55. DOI:10.1074/jbc.M113.531111 |

4. Shin, J. W., Lee, O. K., Park, H. H., Kim, H. S., and Lee, E. Y. (2015) Molecular characterization of a novel oligoalginate lyase consisting of AlgL- and heparinase II/III-like domains from Stenotrophomonas maltophilia KJ-2 and its application to alginate saccharification. Korean J. Chem. Eng. 32, 917–924 DOI:10.1007/s11814-014-0282-1

5. Wang L, Li S, Yu W, and Gong Q. (2015). Cloning, overexpression and characterization of a new oligoalginate lyase from a marine bacterium, Shewanella sp. Biotechnol Lett. 2015;37(3):665-71. DOI:10.1007/s10529-014-1706-z |
6. Mathieu S, Touvrey-Loiodice M, Poulet L, Drouillard S, Vincentelli R, Henrissat B, Skjåk-Bræk G, and Helbert W. (2018). Ancient acquisition of "alginate utilization loci" by human gut microbiota. Sci Rep. 2018;8(1):8075. DOI:10.1038/s41598-018-26104-1 |

7. Haug, A., Larsen, B., and Smidsrod, O. (1967) Studies on sequence of uronic acid residues in alginic acid. Acta Chem. Scand. 21, 691–704 DOI:10.3891/acta.chem.scand.21-0691

8. Haug, A., Larsen, B., and Smidsrod, O. (1966) A study of constitution of alginic acid by partial acid hydrolysis. Acta Chem. Scand. 20, 183–190 DOI:10.3891/acta.chem.scand.20-0183

9. Meyer K, Hobby GL, Chaffee E, and Dawson MH. (1940). THE HYDROLYSIS OF HYALURONIC ACID BY BACTERIAL ENZYMES. J Exp Med. 1940;71(2):137-46. DOI:10.1084/jem.71.2.137 |
10. Park HH, Kam N, Lee EY, and Kim HS. (2012). Cloning and characterization of a novel oligoalginate lyase from a newly isolated bacterium Sphingomonas sp. MJ-3. Mar Biotechnol (NY). 2012;14(2):189-202. DOI:10.1007/s10126-011-9402-7 |