Difference between revisions of "Polysaccharide Lyase Family 7"

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Polysaccharide Lyase Family PL7
3D Structure	β jelly roll
Mechanism	β-elimination
Active site residues	R, Q, H, 2xY
CAZy DB link
https://www.cazy.org/PL7.html

Mechanism

Figure 1. Multiple protein sequence alignment of Aly PL7 as well as a secondary structure prediction with the crystallized PL7 from Klabsiella pneumoniae (PDB ID 4OZX). Conserved residues in the homologues are colored in red and (putative) catalytic residues are indicated by a star. The multiple protein sequence alignment was done with Espript3.0 [].

Alginate lyases (Alys) from all families (PL5, PL6, PL7, PL14, PL15, PL17, and PL18), catalyze the depolymerization of alginate in three steps: (I) removal of the negative charge on the carboxylate anion, (II) general base-catalyzed abstraction of the proton on the C5 and (III) β-elimination of the 4-O-glycosidic bond [2]. Most PL7s are endo-active, i.e. acting within a poly- or oligosaccharide and releasing smaller alginate fragments. Some PL7 are exo-acting cleaving a monosaccharide from the non-reducing end of the polymer [3]. In both modes of action, a new non-reducing end with a 4-deoxy-L-erythro-hex-4-en pyranosyl uronate residue (Δ) is formed.

Some marine PL7 alginate lyases require a calcium cation for substrate recognition and binding [3]. Ca²⁺ is weakening the ionic interactions between substrate (polyanion) and PL7 (polycation) by reducing the surface density of the alginate charge and therefore increasing the enzyme activity [4]. However, there have also been reports of mono- or divalent (metal) cations not increasing or even decreasing enzymatic activity [5, 6]. Therefore, it is not clear if Ca²⁺ is required for recognition and / or binding of alginate PL7s. Nevertheless, one could speculate if cations like Ca²⁺ are creating a more accessible form of alginate. In the presence of divalent cations, the confirmation of alginate is changed due to cross linkages with guluronate residues from opposing chains forming a so-called egg box model [7]. Thereby, the 3D confirmation of alginate is changed, forming hydrogels which might be an easier target for the enzyme in the marine environment thanits dissolved form.

Kinetics and catalytic residues

Several structural and biochemical analyses of wild type and mutated PL7s revealed five residues forming the active site: arginine (R), glutamine (Q), histidine (H), 2x tyrosine (Y) [8, 9, 10], which are present in three highly conserved regions: R*ELR*ML, VIIGQ(I/V)H, YFKAG*Y*Q respectively (Figure 1) [11]. It has been proposed that in PL7 ALY-1 from Corynebacterium sp. Q117+Y195 interact near the reaction site of alginate to maintain proper orientation of the substrate, R72 interacts with alginate as a base to deprotonate the carboxyl groups at C5 and H119 forming a salt bridge between substrate and enzyme[12]. However, there can also be additional charged residues at the active site, which promote substrate recognition and binding [3]. Such residues can be found in the N-terminal R*ELREML and VIIGQIH regions. Both highly conserved regions are mainly characterized by hydrophobic amino acids (especially aromatic amino acids) such as leucine, tryptophan and methionine as well as residues with planar polar side chains (especially amino acids with charged side chains) such as arginine, glutamic acid, glutamine (Figure 2). These residues have been suggested to be substrate-binding molecules [11].

Substrate specificities

Figure 2. Subfamilies of PL7s []. Unrooted tree with bootstrap values after maximum likelihood analysis. Number refer to Uniprot accession numbers. Red dots indicate enzymes from Z. galactanivorans. Pink triangles indicate enzymes characterized biochemically. Blue squares indicate that the structure of the protein has been solved.

Polysaccharide lyase family 7 (PL7) contains five subfamilies (SF) based on their sequence similarities [13], plus a so far uncharacterized sixth subfamily, which consist only of marine representatives of the Flavobacteriaceae (Figure 2) [3]. The substrate specificity depends on the source of alginate, i.e. derived from brown seaweed or mucoid bacteria Pseudomonas spp. and Azotobacter vinelandii, as well as geographical and seasonal parameters. Alginate is a heteropolysaccharide, consisting of β-D-mannuronate (M) and α-L-guluronate (G). These monosaccharides can occur in homogenous and heterogenous blocks. In addition, bacterial alginate is often acetylated at the C2 and / or C3 of mannuronate, thereby shielding the substrate from degradation. Hence, PL7s can be mannuronate (EC 4.2.2.3), guluronate (EC 4.2.2.11) or mixed link (EC 4.2.2.-) specific lyases. Despite the preference for M- or G-enriched blocks, most PL7 also have a low to moderate activity at the other building block [3, 6, 14]. PolyG specific PL7 have been found in the SF3 and SF5 [3] with QIH in the second highly conserved region, while polyM specific PL7s are characterized by QVH [15, 16].

Three-dimensional structures

Figure 3. 3D Structure of endo- and exo-active PL7s []. (A,B) endo AlyA1 and (C, D) exo AlyA5 from Zobellia galaactinovorans DsijT shown as cartoon (A,C) and surface structure (B,D) with superimposed tetrasaccharide from PDB ID 2ZAA. The image was conducted in PyMOL [].

PL7 displays a jelly roll fold, which is also found in PL14 as well as in glycoside hydrolases of family GH16. Zobellia galactanivorans DsijT possess, among others, two PL7s with different modes of activity [3]. AlyA1 is an endo-acting PL7 belonging to SF3 with a wide open cleft harboring the active site (Figure 3A, B), whereas AlyA5 belongs to SF5 and is exo-active with an active site closed by three loops forming a small pocket (Figure 3C, D). The highly conserved 9-amino-acid-block YFKAGVY*Q (where * is a variable residue) at the C-terminus of PL7s (Figure 2) has also been found for an extracellular pectate lyase (PL1, PDB: 1AIR) in E. chrysanthemi. Alginate and pectate/pectin lyases share the β-elimination mechanism, the recognition of substrates of a similar structure, a Ca²⁺-binding site and primary sequence similarity, indicating that they probably possess a similar core structural fold probably important to maintain a stable 3D-confirmation [11]. Several alginate lyases have been reported to be multimodular enzymes with putative non-catalytic, carbohydrate-binding modules (CBMs). The first biochemically characterized CBM of an endo PL7 was an N-terminal CBM13 from Agarivorans sp. L11, which increased the substrate binding and therefore catalytic efficiency, influenced substrate specificity, the product profile and thermo stability of the lyase [18]. Opposite observations regarding catalytic efficiency and substrate specificity were made for an endo PL7 from Vibrio splendidus OU02 DNA with an N-terminal CBM32 linked by a unique alpha-helix linker. The CBM and linker were proposed to serve as a "pivot point" somehow just pushing the product profile towards trisaccharides [19]. The PL7 from Persicobacter sp. CCB-QB2 consists of three domains - an N-terminal CBM16 with unknown function, a CBM32 and the C-terminal PL7 [14]. Overall the role of CBMs from different families as part of PL7s still remains unclear. Another common structural feature found in PLs is a number of flexible loops facing above the active site [20], which have been demonstrated to influence substrate recognition, binding [3, 21] and potentially specificity [22].

Gene transfer of Alys among different habitats

Alginate degrading organisms often possess specified gene clusters for glycan utilization which contain, among other proteins such as transporters, several endo- and exo-acting Alys of different families. These gene clusters are called polysaccharide utilization loci (PULs) for Bacteriodetes [23] or alginolytic operons in case a SusCD pair transporter is missing or replaced by a different transporter system. It has been shown that these gene clusters can be transferred horizontally from one organism to another and thereby even cross different environmental habitats [24, 25]. The first alginate utilization system (AUS) was found in Zobellia galactinovorans which contains two clusters harboring five out of seven Alys (3x PL7). Those operons originated from an ancestral marine Flavobacterium and were independently transferred to marine Proteobacteria and Japanese gut Bacteriodetes by lateral gene transfer (LGT) [26].

A more detailed studied on horizontal gene transfer of PL7 between marine, ecophysiological different Vibrionaceae isolates revealed rapid adaptation of closely related but speciated bacterial populations, resulting in a fine scale of resource partitioning. The exchange of PL7 between marine microbes drove the evolution of polysaccharide degrading pathways, which might have led to three ecotypes – the pioneers, which degrade the polymer into oligomers, the harvesters (intermediate of the other two types) and the scavengers, which can only utilize very small oligosaccharides created by the pioneers [27].

Family Firsts

First catalytic endo-activity: polyM PL7 from Photobacterium ATCC 433367 [28], polyG PL7 from Klebsiella pneumoniae subbsp. aerogenes [29]
First catalytic exo-activity: AlyA5 from Zobellia galactanivorans DsijT [3]
First 3-D apo-structure: PA1167 from Pseudomonas aeruginosa [30]
First 3-D holo-structure: A1-II from Sphingomons sp. A1 [31]
First characterised CBM: AlyL2 containing a N-terminal CBM13 from Agarivorans sp. L11 [18]

References

All Medline abstracts: PubMed

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-* [[Author]]: ^^^Jan-Hendrik Hehemann^^^
+* [[Author]]s: [[User:Nadine Gerlach|Nadine Gerlach]]
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+* [[Responsible Curator]]:  [[User:Jan-Hendrik Hehemann|Jan-Hendrik Hehemann]]
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 |-
 |'''Active site residues'''
-|known
+|R, Q, H, 2xY
 |-
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
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 </div>
 <!-- This is the end of the table -->
+== Mechanism ==
+[[Image:AlyPL7 MultipleSequenceAlignment.JPG|thumb|400px|'''Figure 1. Multiple protein sequence alignment of Aly PL7 ''' as well as a secondary structure prediction with the crystallized PL7 from ''Klabsiella pneumoniae'' ([{{PDBlink}}4OZX PDB ID 4OZX]). Conserved residues in the homologues are colored in red and (putative) catalytic residues are indicated by a star. The multiple protein sequence alignment was done with Espript3.0 <cite>Robert2014</cite>.]]
+Alginate [[Polysaccharide_Lyases|lyases]] (Alys) from all families ([[PL5]], [[PL6]], PL7, [[PL14]], [[PL15]], [[PL17]], and [[PL18]]), catalyze the depolymerization of alginate in three steps: (I) removal of the negative charge on the carboxylate anion, (II) general base-catalyzed abstraction of the proton on the C5 and (III) β-elimination of the 4-O-glycosidic bond <cite>Gacesa1986</cite>. Most PL7s are endo-active, i.e. acting within a poly- or oligosaccharide and releasing smaller alginate fragments. Some PL7 are exo-acting cleaving a monosaccharide from the non-reducing end of the polymer <cite>Thomas2013</cite>. In both modes of action, a new non-reducing end with a 4-deoxy-L-erythro-hex-4-en pyranosyl uronate residue (Δ) is formed.
+Some marine PL7 alginate lyases require a calcium cation for substrate recognition and binding <cite>Thomas2013</cite>. Ca<sup>2+</sup> is weakening the ionic interactions between substrate (polyanion) and PL7 (polycation) by reducing the surface density of the alginate charge and therefore increasing the enzyme activity <cite>Favorov1979</cite>.  However, there have also been reports of mono- or divalent (metal) cations not increasing or even decreasing enzymatic activity <cite>Jagtap2014 Badur2015</cite>. Therefore, it is not clear if Ca<sup>2+</sup> is required for recognition and / or binding of alginate PL7s. Nevertheless, one could speculate if cations like Ca<sup>2+</sup> are creating a more accessible form of alginate. In the presence of divalent cations, the confirmation of alginate is changed due to cross linkages with guluronate residues from opposing chains forming a so-called egg box model <cite>Grant1973</cite>. Thereby, the 3D confirmation of alginate is changed, forming hydrogels which might be an easier target for the enzyme in the marine environment thanits dissolved form.
+== Kinetics and catalytic residues ==
+Several structural and biochemical analyses of wild type and mutated PL7s revealed five residues forming the active site: arginine (R), glutamine (Q), histidine (H), 2x tyrosine (Y) <cite>Preston2000 Yamasaki200 Yamasaki2005</cite>, which are present in three highly conserved regions: R*ELR*ML, VIIGQ(I/V)H, YFKAG*Y*Q respectively (Figure 1) <cite>Wong2000</cite>. It has been proposed that in PL7 ALY-1 from ''Corynebacterium'' sp. Q117+Y195 interact near the reaction site of alginate to maintain proper orientation of the substrate, R72            interacts with alginate as a base to deprotonate the carboxyl groups at C5 and H119 forming a salt bridge between substrate and enzyme<cite>Osawa2015</cite>. However, there can also be additional charged residues at the active site, which promote substrate recognition and binding <cite>Thomas2013</cite>. Such residues can be found in the N-terminal R*ELREML and VIIGQIH regions. Both highly conserved regions are mainly characterized by hydrophobic amino acids (especially aromatic amino acids) such as leucine, tryptophan and methionine as well as residues with planar polar side chains (especially amino acids with charged side chains) such as arginine, glutamic acid, glutamine (Figure 2). These residues have been suggested to be substrate-binding molecules <cite>Wong2000</cite>.
 == Substrate specificities ==
-The polysaccharide lyase family 7 (PL7) contains 5 subfamilies <cite>Lombard2010</cite>.  All characterized PL7 enzymes were alginate lyases specific for the anionic, gel forming polysaccharide alginate which is from brown seaweed such as kelps or from certain types of bacteria. Alginate consists of beta-D-mannuronate and alpha-L-guluronate, which occur in homogenous or heterogenous blocks. Hence, PL7 can be mannuronate, guluronate or mixed link lyases. PL7 enzymes are often found in marine bacteria such as the seaweed associated Flavobacterium Zobellia galactanivorans <cite>Thomas2013</cite> or in coastal, planktonic gammaproteobacteria such as Vibrio spp. PL7 alginate lyases also occur in terrestrial bacteria.
+[[Image:PL7SF_Thomasetal2013.JPG|thumb|400px|'''Figure 2. Subfamilies of PL7s''' <cite>Thomas2013</cite>. Unrooted tree with bootstrap values after maximum likelihood analysis. Number refer to Uniprot accession numbers. Red dots indicate enzymes from ''Z. galactanivorans''. Pink triangles indicate enzymes characterized biochemically. Blue squares indicate that the structure of the protein has been solved.]]
+[[Polysaccharide_Lyases|Polysaccharide lyase]] family 7 (PL7) contains five subfamilies (SF) based on their sequence similarities <cite>Lombard2010</cite>, plus a so far uncharacterized sixth subfamily, which consist only of marine representatives of the Flavobacteriaceae (Figure 2) <cite>Thomas2013</cite>. The substrate specificity depends on the source of alginate, i.e. derived from brown seaweed or mucoid bacteria ''Pseudomonas'' spp. and ''Azotobacter vinelandii'', as well as geographical and seasonal parameters. Alginate is a heteropolysaccharide, consisting of β-D-mannuronate (M) and α-L-guluronate (G). These monosaccharides can occur in homogenous and heterogenous blocks. In addition, bacterial alginate is often acetylated at the C2 and / or C3 of mannuronate, thereby shielding the substrate from degradation. Hence, PL7s can be mannuronate ([{{EClink}}4.2.2.3 EC 4.2.2.3]), guluronate ([{{EClink}}4.2.2.11 EC 4.2.2.11]) or mixed link (EC 4.2.2.-) specific lyases. Despite the preference for M- or G-enriched blocks, most PL7 also have a low to moderate activity at the other building block <cite>Thomas2013 Badur2015 Sim2017</cite>. PolyG specific PL7 have been found in the SF3 and SF5 <cite>Thomas2013</cite> with QIH in the second highly conserved region, while polyM specific PL7s are characterized by QVH <cite>Zhu2015 Deng2014</cite>.
-== Catalytic Residues ==
+== Three-dimensional structures ==
+[[Image:EndovsexoPL7_Thomas_et_al_2013.jpg|thumb|400px|'''Figure 3. 3D Structure of endo- and exo-active PL7s''' <cite>Thomas2013</cite>. (A,B) endo AlyA1 and (C, D) exo AlyA5 from ''Zobellia galaactinovorans'' DsijT shown as cartoon (A,C) and surface structure (B,D) with superimposed tetrasaccharide from [{{PDBlink}}2ZAA PDB ID 2ZAA]. The image was conducted in PyMOL <cite>DeLano2002</cite>.]]
+PL7 displays a jelly roll fold, which is also found in [[PL14]] as well as in glycoside hydrolases of family [[GH16]]. ''Zobellia galactanivorans'' DsijT possess, among others, two PL7s with different modes of activity <cite>Thomas2013</cite>. AlyA1 is an endo-acting PL7 belonging to SF3 with a wide open cleft harboring the active site (Figure 3A, B), whereas AlyA5 belongs to SF5 and is exo-active with an active site closed by three loops forming a small pocket (Figure 3C, D). The highly conserved 9-amino-acid-block YFKAGVY*Q (where * is a variable residue) at the C-terminus of PL7s (Figure 2) has also been found for an extracellular pectate lyase (PL1, PDB: 1AIR) in ''E. chrysanthemi''. Alginate and pectate/pectin lyases share the β-elimination mechanism, the recognition of substrates of a similar structure, a Ca<sup>2+</sup>-binding site and primary sequence similarity, indicating that they probably possess a similar core structural fold probably important to maintain a stable 3D-confirmation <cite>Wong2000</cite>.
+Several alginate lyases have been reported to be multimodular enzymes with putative non-catalytic, [[Carbohydrate_Binding_Module_Families|carbohydrate-binding modules (CBMs)]]. The first biochemically characterized CBM of an endo PL7 was an N-terminal [[CBM13]] from ''Agarivorans'' sp. L11, which increased the substrate binding and therefore catalytic efficiency, influenced substrate specificity, the product profile and thermo stability of the lyase <cite>Li2015</cite>. Opposite observations regarding catalytic efficiency and substrate specificity were made for an endo PL7 from ''Vibrio splendidus'' OU02 DNA with an N-terminal [[CBM32]] linked by a unique alpha-helix linker. The CBM and linker were proposed to serve as a "pivot point" somehow just pushing the product profile towards trisaccharides <cite>Lyu2018</cite>. The PL7 from ''Persicobacter'' sp. CCB-QB2 consists of three domains - an N-terminal [[CBM16]] with unknown function, a [[CBM32]] and the C-terminal PL7 <cite>Sim2017</cite>. Overall the role of [[CBM]]s from different families as part of PL7s still remains unclear. Another common structural feature found in PLs is a number of flexible loops facing above the active site <cite>Xu2018</cite>, which have been demonstrated to influence substrate recognition, binding <cite>Thomas2013 Ogura2008</cite> and potentially specificity <cite>Qin2018</cite>.
-== Three-dimensional structures ==
+== Gene transfer of Alys among different habitats ==
+Alginate degrading organisms often possess specified gene clusters for glycan utilization which contain, among other proteins such as transporters, several endo- and exo-acting Alys of different families. These gene clusters are called polysaccharide utilization loci (PULs) for Bacteriodetes <cite>Bjursell2016</cite> or alginolytic operons in case a SusCD pair transporter is missing or replaced by a different transporter system. It has been shown that these gene clusters can be transferred horizontally from one organism to another and thereby even cross different environmental habitats <cite>Hehemann2010 Mathieu2018</cite>. The first alginate utilization system (AUS) was found in ''Zobellia galactinovorans'' which contains two clusters harboring five out of seven Alys (3x PL7). Those operons originated from an ancestral marine Flavobacterium and were independently transferred to marine Proteobacteria and Japanese gut Bacteriodetes by lateral gene transfer (LGT) <cite>Thomas2012</cite>.
+A more detailed studied on horizontal gene transfer of PL7 between marine, ecophysiological different Vibrionaceae isolates revealed rapid adaptation of closely related but speciated bacterial populations, resulting in a fine scale of resource partitioning. The exchange of PL7 between marine microbes drove the evolution of polysaccharide degrading pathways, which might have led to three ecotypes – the pioneers, which degrade the polymer into oligomers, the harvesters (intermediate of the other two types) and the scavengers, which can only utilize very small oligosaccharides created by the pioneers <cite>Hehemann2016</cite>.
 == Family Firsts ==
+;First catalytic endo-activity: polyM PL7 from ''Photobacterium'' ATCC 433367 <cite>Malissard1993</cite>, polyG PL7 from ''Klebsiella pneumoniae subbsp. aerogenes''  <cite>Baron1994</cite>
+;First catalytic exo-activity: AlyA5 from ''Zobellia galactanivorans'' DsijT <cite>Thomas2013</cite>
+;First 3-D apo-structure: PA1167 from ''Pseudomonas aeruginosa'' <cite>Yamasaki2004</cite>
+;First 3-D holo-structure: A1-II from ''Sphingomons'' sp. A1 <cite>Ogura2007</cite>
+;First characterised CBM: AlyL2 containing a N-terminal CBM13 from ''Agarivorans'' sp. L11 <cite>Li2015</cite>
 == References ==
 <biblio>
 #Lombard2010 pmid=20925655
+#Lombard2014 pmid=24270786
+#Favorov1979 pmid=476128
+#Gacesa1986  Gacesa P. (1987) Alginate‐modifying enzymes: A proposed unified mechanism of action for the lyases and epimerases. ''FEBS Letters'', '''212''', 1873-3468. [http://dx.doi.org/10.1016/0014-5793(87)81344-3 DOI:10.1016/0014-5793(87)81344-3]
 #Thomas2013 pmid=23782694
+#Thomas2012 pmid=22513138
+#Hehemann2010 pmid=20376150
+#Yamasaki2004 pmid=15136569
+#Badur2015 pmid=25556193
+#Yamasaki2005 pmid=16081095
+#Deng2014 pmid=24050202
+#Li2015 pmid=25837818
+#Zhu2015 pmid=25831216
+#Wong2000 pmid=11018131
+#Sim2017 pmid=29057942
+#Lyu2018 pmid=29864445
+#Bjursell2016 pmid=16968696
+#Malissard1993 pmid=8319887
+#Baron1994 pmid=8200539
+#Osawa2015 pmid=15644208
+#Robert2014 pmid=24753421
+#DeLano2002 Delano WL. (2002) Pymol: An open-source molecular graphics tool. ''CCP4 Newsletter On Protein Crystallography'', '''40''', 82-92. [http://www.ccp4.ac.uk/newsletters/newsletter40.pdf#page=44 Direct link].
+#Preston2000 pmid=11029455
+#Jagtap2014 pmid=24795372
+#Hehemann2016 pmid=27653556
+#Mathieu2018 pmid=29795267
+#Ogura2008 pmid=18514736
+#Xu2018 pmid=29150496
+#Qin2018 pmid=29292806
+#Grant1973 Grant, G., Morris, E., Rees, D., Smith, P., and Thom, D.Biological interactions between polysaccharides and diva-lent cations: the egg-box model. FEBS Lett32,195, 1973.
 </biblio>
+[[Category:Polysaccharide Lyase Families|PL007]]