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PL6 contains 3 subfamilies [1] all of which contain members catalyzing the depolymerisation of alginate [2]. Alginate consisting of 1,4 linked β-D-mannuronic acid and α-L-guluronic acid arranged in poly-mannuronic acid blocks, poly-guluronic acid blocks or poly-mannuronic/guluronic acid blocks [3, 4]. Subfamily 2 and 3 have so far only shown specificity for poly-mannuronic/guluronic acid blocks [2], while subfamily 1 has been demonstrated to depolymerize poly-guluronic acid [5, 6], poly-mannuronic acid [7], poly-mannuronic/guluronic acid [2] as well as dermatan sulfate (formerly chrondroitin B) [2, 8, 9]. Dermatan sulfate consiting of N-acetyl galactosamine (GalNAc) or glucuronic acid (GlcA) joined by β 1,4 or 1,3 linkages respectively with a variable sulfation pattern [10].
Kinetics and Mechanism
Figure 1.Syn – or anti – β-elimination catalyzed by PL6 enzymes acting on alginate. M represents mannuronic acid and G guluronic acid. n represents the continued sugar chain.
The β-elimination catalyzed by the PL6 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 a calcium [6, 9] or by water [5]. 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. This can be done in syn with the acid and base on the same side of the sugar ring in the transition state (the case for D-mannuronic acid) or anti where they are on opposite sides of the sugar ring (the case for L-guluronic acid) [11, 12].
Catalytic Residues
After charge neutralization a lysine functions as the catalytic base and an arginine the acid. They were originally identified as K253 and R273 in chondroitinase B from Pedobacter Heparinus [8]. PL6 is the only discovered alginate lyase family that uses K/R as a catalytic base/acid pair [12].
Three-dimensional structures
Figure 2. Crystal structures of the monomeric chrondroitinase B and AlyF aswell as the dimeric AlyGC. Catalytic residues and substrates are in green the neutralizing calcium is the red sphere.
PL6 catalytic domain adopts a parallel β-helix fold with the activesite located on the surface of one of the β-sheets (Figure 2). The first PL6 structure solved was the chrondoitinase B from Pedobacter Heparinus (1.7 Å) [8] later it was shown that this enzyme is calcium dependent [9]. The first alginate lyase structure solved was the exolytic, guluronic acid-specific, homo-dimeric AlyGC in complex with tetra-mannuronic acid (2.6 Å) [6]. The first monomeric alginate lyase structure solved was the guluronic acid-specific AlyF in complex with tetra-guluronic acid (1.8 Å) [5]. All three structure belong to subfamily 1. There are no available crystal structures from subfamilies 2 and 3.
Family Firsts
First catalytic activity
OS-ALG-9 from Pseudomonas sp. on non-purified recombinant enzyme by the thiobarbituric acid method [7]
First catalytic base/acid
The catalytic arginine was originally identified in Chondroitinase B from Pedobacter Heparinus based on the crystal structure, concervation, mutagenesis and activity analysis (R271E no activity, R271K 0.09 % activity) [9]. The catalytic lysine was identified later by conservation, mutagenesis and activity analysis [6]
First charge neutralizer
Calcium in Chondroitinase B from Pedobacter Heparinus by by crystallography and assaying the effect of calcium on enzyme activity [9].
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 [Haug1966]
Haug, A., Larsen, B., and Smidsrod, O. (1967) Studies on sequence of uronic acid residues in alginic acid. Acta Chem. Scand. 21, 691–704 [Haug1967]
