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Polysaccharide Lyase Family 17
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|Polysaccharide Lyase Family 17|
|3D structure||(α/α)6 barrel + anti-parallel β-sheet|
|Charge neutralizer||Asparagine and histidine|
|Active site residues||known|
|CAZy DB link|
PL17 contains 2 subfamilies  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 . 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 . Hyaluronan consisting of N-acetyl-D-glucoamine and 1,4 linked D-glucoronic acid .
Kinetics and Mechanism
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 .
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 .
One crystal structure is available in PL17, that of Alg17c from Saccharophagus degradans belonging to subfamily 2 . 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].
- 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 .
- 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) 
- 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) 
- First 3-D structure
- Alg17c crystal structure 
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- Lombard V, Bernard T, Rancurel C, Brumer H, Coutinho PM, and Henrissat B. (2010) A hierarchical classification of polysaccharide lyases for glycogenomics. Biochem J. 432, 437-44. DOI:10.1042/BJ20101185 |
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- 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
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- 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
- 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
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