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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
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

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  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. 432, 437-44. DOI:10.1042/BJ20101185 | PubMed ID:20925655 | HubMed [Lombard2010]
  2. Error fetching PMID 24795372: [Jagtap2014]
  3. Error fetching PMID 24478312: [Park2014]
  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
    [Shin2015]
  5. Error fetching PMID 25335746: [Wang2015]
  6. Error fetching PMID 29795267: [Mathieu2018]
  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
    [Haug1967]
  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
    [Haug1966]
  9. Error fetching PMID 19870951: [Meyer1940]
  10. Error fetching PMID 21826589: [Park2012]
All Medline abstracts: PubMed | HubMed