CAZypedia - User contributions [en-ca]

Polysaccharide Lyase Family 6

2020-11-17T13:21:06Z

Emil Stender:

{{CuratorApproved}}
* [[Author]]: [[User:Emil Stender|Emil G.P. Stender]]
* [[Responsible Curator]]: ^^^Birte Svensson^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family 6'''
|-
|'''3D structure'''
|parallel β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutralizer'''
|calcium or water
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL6.html
|}
</div>


== Substrate specificities ==
PL6 contains 3 subfamilies <cite>Lombard2010 Mathieu2016</cite> all of which contain members catalyzing the depolymerisation of alginate <cite>Mathieu2016</cite>. Alginate consist of 1,4 linked β-{{Smallcaps|D}}-mannuronic acid and α-{{Smallcaps|L}}-guluronic acid arranged in poly-mannuronic acid blocks, poly-guluronic acid blocks or poly-mannuronic/guluronic acid blocks <cite>Haug1966 Haug1967</cite>. Subfamily 2 and 3 have so far only shown specificity for poly-mannuronic/guluronic acid blocks <cite>Mathieu2016</cite>, while subfamily 1 has been demonstrated to depolymerize poly-guluronic acid <cite>Lyu2019 Xu2017</cite>, poly-mannuronic acid <cite>Maki1993 Stender2019</cite>, poly-mannuronic/guluronic acid <cite>Mathieu2016</cite> as well as dermatan sulfate (formerly chrondroitin B) <cite>Mathieu2016 #Huang1999 #Michel2004</cite>. Dermatan sulfate consist of N-acetyl galactosamine (GalNAc) and glucuronic acid (GlcA) joined by β 1,4 or 1,3 linkages respectively with a variable sulfation pattern <cite>Trowbridge2002</cite>.

== Kinetics and Mechanism ==
[[Image:PL6_lyase_mechanism.png|thumb|600px| '''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. In both cases the catalytic base abstracts the C5 proton and an acid donates one resulting in the β-elimination of the 1,4 glycosidic linkage.]]
The β-elimination catalyzed by the PL6 enzymes results in the formation of a C4-C5 unsaturated sugar residue at the new non-reducing end. The first step is the neutralization of the acid group in the +1 subsite by a calcium <cite>Xu2017 Michel2004</cite> or by water <cite>Lyu2019</cite>. This lowers the p''K''<sub>a</sub> 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 {{Smallcaps|D}}-mannuronic acid) or ''anti'' where they are on opposite sides of the sugar ring (the case for {{Smallcaps|L}}-guluronic acid) <cite>Garron2010 Xu2018</cite>.

== Catalytic Residues ==
After charge neutralization a lysine functions as the catalytic base and an arginine as the acid. They were originally identified as K253 and R273 in chondroitinase B from ''Pedobacter heparinus'' <cite>Huang1999</cite>. PL6 is so far the only discovered alginate lyase family that uses K/R as a catalytic base/acid pair <cite>Xu2018</cite>.
== Three-dimensional structures ==
[[Image:PL6_structures.png|thumb|600px|'''Figure 2.''' Crystal structures of the monomeric chrondroitinase B and AlyF as well 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 active site 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) <cite>Huang1999</cite> later it was shown that this enzyme is calcium dependent <cite>Michel2004</cite>. The first alginate lyase structure solved was the exolytic, guluronic acid-specific, homo-dimeric AlyGC in complex with tetra-mannuronic acid (2.6 Å) <cite>Xu2017</cite>. The first monomeric alginate lyase structure solved was the guluronic acid-specific AlyF in complex with tetra-guluronic acid (1.8 Å) <cite>Lyu2019</cite>. The first mannuronic acid specific alginate lyase structure was ''Bcel''PL6 (1.3Å) from human gut ''Bacteroides cellulosilyticus'' <cite>Stender2019</cite>. All four structures 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 <cite>Maki1993</cite>
;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) <cite>Michel2004</cite>. The catalytic lysine was identified later based on conservation, mutagenesis and activity analysis <cite>Xu2017</cite>
;First charge neutralizer: Calcium in Chondroitinase B from ''Pedobacter Heparinus'' by by crystallography and assaying the effect of calcium on enzyme activity <cite>Michel2004</cite>.
;First 3-D structure: Chondroitinase B from ''Pedobacter Heparinus'' <cite>Huang1999</cite>.

== References ==
<biblio>
#Lombard2010 pmid=20925655
#Mathieu2016 pmid=27438604
#Haug1967 Haug, A., Larsen, B., and Smidsrod, O. (1967) Studies on sequence of uronic acid residues in alginic acid. Acta Chem. Scand. 21, 691–704. [http://dx.doi.org/10.3891/acta.chem.scand.21-0691 DOI:10.3891/acta.chem.scand.21-0691]
#Haug1966 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. [http://dx.doi.org/10.3891/acta.chem.scand.20-0183 DOI:10.3891/acta.chem.scand.20-0183]
#Lyu2019 pmid=31004719
#Xu2017 pmid=28154171
#Stender2019 pmid=31530640
#Maki1993 pmid=8336113
#Huang1999 pmid=10600383
#Trowbridge2002 pmid=12213784
#Michel2004 pmid=15155751
#Garron2010 pmid=20805221
#Xu2018 pmid=29150496

</biblio>

[[Category:Polysaccharide Lyase Families|PL006]]

Polysaccharide Lyase Family 17

2020-06-15T08:49:54Z

Emil Stender:

Polysaccharide Lyase Family 15

2020-06-15T08:34:44Z

Emil Stender:

Polysaccharide Lyase Family 15

2020-06-15T08:34:23Z

Emil Stender:

Polysaccharide Lyase Family 6

2020-06-15T08:21:58Z

Emil Stender:

Polysaccharide Lyase Family 6

2020-03-12T11:34:44Z

Emil Stender:

Polysaccharide Lyase Family 17

2020-02-26T12:39:33Z

Emil Stender:

Polysaccharide Lyase Family 6

2020-02-26T12:06:37Z

Emil Stender:

Polysaccharide Lyase Family 6

2020-02-26T12:04:05Z

Emil Stender:

User:Emil Stender

2020-02-21T13:12:20Z

Emil Stender:

[[Image:Emil_Stender.png|200px|right]]
Emil G. P. Stender obtained his M.Sc. in biochemistry from University of Copenhagen - Denmark in 2014 and completed his PhD in 2018 at Technical University of Denmark (DTU) under supervision of ^^^Birte Svensson^^^ and co-supervised by Maher Abou Hachem. The project involved characterization of whey protein-alginate interactions and identification of alginate binding sites on the surface of β-lactoglobulin <cite>Stender2019 Stender2017</cite>. He has since been employed as a postdoc at DTU – Bioengineering in a project identifying and characterizing enzymes enabling human gut microbiota to utilize alginate. His main research interests are protein biophysics, [[Polysaccharide Lyases]] and alginate modifying enzymes. He published the first structure of an mannuronic acid specific alginate lyase in polysaccharide lyase family 6 from the human gut microbe ''Bacteroides cellulosilyticus'' <cite>Stender2019_2</cite>.

----

<biblio>
#Stender2019_2 pmid=31530640
#Stender2019 Stender, E. G. P., Birch, J., Kjeldsen, C., Nielsen, L. D., Duus, J. O., Kragelund, B. B., and Svensson, B. (2019) Alginate trisaccharide binding sites on the surface of β-Lactoglobulin identified by NMR spectroscopy: implications for molecular network formation. ACS Omega. 4, 6165–6174
#Stender2017 Stender, E. G. P., Khan, S., Ipsen, R., Madsen, F., Hägglund, P., Abou Hachem, M., Almdal, K., Westh, P., and Svensson, B. (2017) Effect of alginate size, mannuronic/guluronic acid content and pH on particle size, thermodynamics and composition of complexes with β-lactoglobulin. Food Hydrocoll. 75, 157–163
#Stender2018 pmid=29327016
#Stender2015 pmid=26107850
#OShea2015 pmid=25348421

</biblio>


[[Category:Contributors|Stender,Emil]]

Polysaccharide Lyase Family 6

2020-02-21T13:03:57Z

Emil Stender:

File:PL6 lyase mechanism.png

2019-07-09T07:36:04Z

Emil Stender: Emil Stender uploaded a new version of File:PL6 lyase mechanism.png

Polysaccharide Lyase Family 17

2019-07-08T07:42:34Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-08T07:36:35Z

Emil Stender:

Polysaccharide Lyase Family 6

2019-07-05T11:31:31Z

Emil Stender:

Polysaccharide Lyase Family 6

2019-07-05T09:34:13Z

Emil Stender:

Polysaccharide Lyase Family 6

2019-07-05T09:23:06Z

Emil Stender:

Polysaccharide Lyase Family 6

2019-07-05T09:21:55Z

Emil Stender:

Polysaccharide Lyase Family 6

2019-07-05T09:21:25Z

Emil Stender:

Polysaccharide Lyase Family 6

2019-07-05T08:34:48Z

Emil Stender:

Polysaccharide Lyase Family 15

2019-07-05T08:22:38Z

Emil Stender:

Polysaccharide Lyase Family 15

2019-07-05T08:12:00Z

Emil Stender:

Polysaccharide Lyase Family 15

2019-07-04T11:24:14Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T11:20:58Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T11:19:08Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T11:18:26Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T11:18:08Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T11:17:57Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T11:10:40Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T11:06:39Z

Emil Stender:

File:PL17 structure.png

2019-07-04T11:00:50Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T10:49:21Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T10:47:53Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T10:47:06Z

Emil Stender:

File:Cat res PL17.png

2019-07-04T10:43:17Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T09:32:01Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T09:29:04Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T09:26:48Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T09:23:45Z

Emil Stender:

Polysaccharide Lyase Family 17

2019-07-04T09:21:58Z

Emil Stender:

Polysaccharide Lyase Family 15

2019-07-03T14:06:47Z

Emil Stender:

Polysaccharide Lyase Family 15

2019-07-03T12:30:31Z

Emil Stender:

Polysaccharide Lyase Family 15

2019-07-03T12:28:31Z

Emil Stender:

File:Atu3025 structure.png

2019-07-03T12:21:12Z

Emil Stender:

Polysaccharide Lyase Family 15

2019-07-03T12:15:54Z

Emil Stender:

File:Catalytic PL15.png

2019-07-03T12:02:12Z

Emil Stender:

Polysaccharide Lyase Family 15

2019-07-03T12:01:39Z

Emil Stender:

Polysaccharide Lyase Family 15

2019-07-03T11:58:34Z

Emil Stender:

Polysaccharide Lyase Family 15

2019-07-03T11:47:32Z

Emil Stender:

{{UnderConstruction}}
* [[Author]]: ^^^Emil Stender^^^
* [[Responsible Curator]]: ^^^Birte Svensson^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family 15'''
|-
|'''3D structure'''
|(α/α)<sub>6</sub> barrel + anti-parallel β-sheet
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutralizer'''
|Arginine and histidine
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL15.html
|}
</div>


== Substrate specificities ==
PL15 currently contains 2 subfamilies <cite>Lombard2010</cite> as well as several proteins currently not assigned to any subfamily. Subfamily 1 has been shown to only degrade alginate ADDIN CSL_CITATION {"citationItems":[{"id":"ITEM-1","itemData":{"DOI":"10.1016/S1046-5928(03)00018-4","ISSN":"10465928","PMID":"12729723","abstract":"Sphingomonas sp. A1 (strain A1) cells contain three kinds of endotype alginate lyases [A1-I, A1-II, and A1-III], all of which are formed from a common precursor through posttranslational processing. In addition to these lyases, another type of lyase (A1-IV) that acts on oligoalginates exists in the bacterium. A1-IV was overexpressed in Escherichia coli cells through control of its gene under the T7 promoter. The expression level of the enzyme in E. coli cells was 8.6 U/L-culture, which was about 270-fold higher than that in strain A1 cells. The enzyme was purified to homogeneity through three steps with an activity yield of 10.9%. The optimal pH and temperature, thermal stability, and mode of action of the purified enzyme were similar to those of the native enzyme from strain A1 cells. A1-IV exolytically degraded oligoalginates, which were produced from alginate through the reaction of A1-I, A1-II, or A1-III, into monosaccharides, indicating that the cooperative actions of these four enzymes cause the complete depolymerization of alginate in strain A1 cells. © 2003 Elsevier Science (USA). All rights reserved.","author":[{"dropping-particle":"","family":"Miyake","given":"Osamu","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Hashimoto","given":"Wataru","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Murata","given":"Kousaku","non-dropping-particle":"","parse-names":false,"suffix":""}],"container-title":"Protein Expression and Purification","id":"ITEM-1","issue":"1","issued":{"date-parts":[["2003"]]},"page":"33-41","title":"An exotype alginate lyase in <i>Sphingomonas sp.</i> A1: overexpression in Escherichia coli, purification, and characterization of alginate lyase IV (A1-IV)","type":"article-journal","volume":"29"},"uris":["http://www.mendeley.com/documents/?uuid=a10b46a4-bdd2-4166-90b1-4a4c7c369462"]},{"id":"ITEM-2","itemData":{"DOI":"10.1074/jbc.M110.125450","ISBN":"0021-9258","ISSN":"1083351X","PMID":"20507980","abstract":"Alginate, a major component of the cell wall matrix in brown seaweeds, is degraded by alginate lyases through a beta-elimination reaction. Almost all alginate lyases act endolytically on substrate, thereby yielding unsaturated oligouronic acids having 4-deoxy-l-erythro-hex-4-enepyranosyluronic acid at the nonreducing end. In contrast, Agrobacterium tumefaciens alginate lyase Atu3025, a member of polysaccharide lyase family 15, acts on alginate polysaccharides and oligosaccharides exolytically and releases unsaturated monosaccharides from the substrate terminal. The crystal structures of Atu3025 and its inactive mutant in complex with alginate trisaccharide (H531A/DeltaGGG) were determined at 2.10- and 2.99-A resolutions with final R-factors of 18.3 and 19.9%, respectively, by x-ray crystallography. The enzyme is comprised of an alpha/alpha-barrel + anti-parallel beta-sheet as a basic scaffold, and its structural fold has not been seen in alginate lyases analyzed thus far. The structural analysis of H531A/DeltaGGG and subsequent site-directed mutagenesis studies proposed the enzyme reaction mechanism, with His(311) and Tyr(365) as the catalytic base and acid, respectively. Two structural determinants, i.e. a short alpha-helix in the central alpha/alpha-barrel domain and a conformational change at the interface between the central and C-terminal domains, are essential for the exolytic mode of action. This is, to our knowledge, the first report on the structure of the family 15 enzyme.","author":[{"dropping-particle":"","family":"Ochiai","given":"Akihito","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Yamasaki","given":"Masayuki","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Mikami","given":"Bunzo","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Hashimoto","given":"Wataru","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Murata","given":"Kousaku","non-dropping-particle":"","parse-names":false,"suffix":""}],"container-title":"Journal of Biological Chemistry","id":"ITEM-2","issue":"32","issued":{"date-parts":[["2010"]]},"page":"24519-24528","title":"Crystal Structure of exotype alginate lyase Atu3025 from <i>Agrobacterium tumefaciens</i>","type":"article-journal","volume":"285"},"uris":["http://www.mendeley.com/documents/?uuid=68ef39c9-91a5-484b-b750-19b4460ae650"]},{"id":"ITEM-3","itemData":{"DOI":"10.1128/AEM.01285-14","ISSN":"10985336","PMID":"24795372","abstract":"Marine microbes use alginate lyases to degrade and catabolize alginate, a major cell wall matrix polysaccharide of brown seaweeds. Microbes frequently contain multiple, apparently redundant alginate lyases, raising the question of whether these enzymes have complementary functions. We report here on the molecular cloning and functional characterization of three exo-type oligoalginate lyases (OalA, OalB, and OalC) from Vibrio splendidus 12B01 (12B01), a marine bacterioplankton species. OalA was most active at 16°C, had a pH optimum of 6.5, and displayed activities toward poly-β-d-mannuronate [poly(M)] and poly-α-l-guluronate [poly(G)], indicating that it is a bifunctional enzyme. OalB and OalC were most active at 30 and 35°C, had pH optima of 7.0 and 7.5, and degraded poly(M·G) and poly(M), respectively. Detailed kinetic analyses of oligoalginate lyases with poly(G), poly(M), and poly(M·G) and sodium alginate as substrates demonstrated that OalA and OalC preferred poly(M), whereas OalB preferred poly(M·G). The catalytic efficiency (kcat/Km) of OalA against poly(M) increased with decreasing size of the substrate. OalA showed kcat/Km from 2,130 mg(-1) ml s(-1) for the trisaccharide to 224 mg(-1) ml s(-1) for larger oligomers of ∼50 residues, and 50.5 mg(-1) ml s(-1) for high-molecular-weight alginate. Although OalA was most active on the trisaccharide, OalB and OalC preferred dimers. Taken together, our results indicate that these three Oals have complementary substrate scopes and temperature and pH adaptations.","author":[{"dropping-particle":"","family":"Jagtap","given":"Sujit Sadashiv","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Hehemann","given":"Jan Hendrik","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Polz","given":"Martin F.","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Lee","given":"Jung Kul","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Zhao","given":"Huimin","non-dropping-particle":"","parse-names":false,"suffix":""}],"container-title":"Applied and Environmental Microbiology","id":"ITEM-3","issue":"14","issued":{"date-parts":[["2014"]]},"page":"4207-4214","title":"Comparative biochemical characterization of three exolytic oligoalginate lyases from <i>Vibrio splendidus</i> reveals complementary substrate scope, temperature, and pH adaptations","type":"article-journal","volume":"80"},"uris":["http://www.mendeley.com/documents/?uuid=dcde9ba3-b1cf-4f7d-b9a8-ebdcd84a07fa"]},{"id":"ITEM-4","itemData":{"DOI":"10.1263/jbb.99.048","ISSN":"1389-1723","PMID":"16233753","abstract":"Sphingomonas sp. A1 (strain A1) produces three endotypes (A1-I [65 kDa], A1-II [25 kDa], and A1-III [40 kDa]) and an exotype (A1-IV [86 kDa]) alginate lyases in cytoplasm. These four enzymes cooperatively depolymerize alginate into constituent monosaccharides. In addition to the genes for these lyases, novel genes encoding hypothetical proteins homologous with A1-IV were found in the genomes of many bacteria including strain A1. One such protein, A1-IV' (90 kDa) of strain A1, was overexpressed in Escherichia coli cells, purified, and characterized. A1-IV' catalyzed the cleavage of glycosidic bonds in alginate through a beta-elimination reaction and released unsaturated di- and trisaccharides as main products, thus indicating that the enzyme is an endotype alginate lyase. A1-IV', which differed from A1-IV in some enzymatic properties, was not expressed in strain A1, suggesting that A1-IV' has no significant role in alginate metabolism. A1-IV' and other A1-IV homologs facilitate the creation of novel polysaccharide lyase family 15 based on their primary structures, implying the evolution route of alginate lyases in family PL-15.","author":[{"dropping-particle":"","family":"Hashimoto","given":"Wataru","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Miyake","given":"Osamu","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Ochiai","given":"Akihito","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Murata","given":"Kousaku","non-dropping-particle":"","parse-names":false,"suffix":""}],"container-title":"Journal of bioscience and bioengineering","id":"ITEM-4","issue":"1","issued":{"date-parts":[["2005"]]},"page":"48-54","title":"Molecular identification of <i>Sphingomonas sp.</i> A1 alginate lyase (A1-IV') as a member of novel polysaccharide lyase family 15 and implications in alginate lyase evolution.","type":"article-journal","volume":"99"},"uris":["http://www.mendeley.com/documents/?uuid=51cad4de-8e15-475c-acec-a6942bed1400"]}],"mendeley":{"formattedCitation":"(2–5)","plainTextFormattedCitation":"(2–5)","previouslyFormattedCitation":"(2–5)"},"properties":{"noteIndex":0},"schema":"https://github.com/citation-style-language/schema/raw/master/csl-citation.json"}(2–5) while subfamily 2 has been found to be heparin and heparan sulfate lyases ADDIN CSL_CITATION {"citationItems":[{"id":"ITEM-1","itemData":{"DOI":"10.1073/pnas.1704367114","ISSN":"0027-8424","PMID":"28630303","abstract":"The human microbiota, which plays an important role in health and disease, uses complex carbohydrates as a major source of nutrients. Utilization hierarchy indicates that the host glycosaminoglycans heparin (Hep) and heparan sulfate (HS) are high-priority carbohydrates for Bacteroides thetaiotaomicron, a prominent member of the human microbiota. The sulfation patterns of these glycosaminoglycans are highly variable, which presents a significant enzymatic challenge to the polysaccharide lyases and sulfatases that mediate degradation. It is possible that the bacterium recruits lyases with highly plastic specificities and expresses a repertoire of enzymes that target substructures of the glycosaminoglycans with variable sulfation or that the glycans are desulfated before cleavage by the lyases. To distinguish between these mechanisms, the components of the B. thetaiotaomicron Hep/HS degrading apparatus were analyzed. The data showed that the bacterium expressed a single-surface endo-acting lyase that cleaved HS, reflecting its higher molecular weight compared with Hep. Both Hep and HS oligosaccharides imported into the periplasm were degraded by a repertoire of lyases, with each enzyme displaying specificity for substructures within these glycosaminoglycans that display a different degree of sulfation. Furthermore, the crystal structures of a key surface glycan binding protein, which is able to bind both Hep and HS, and periplasmic sulfatases reveal the major specificity determinants for these proteins. The locus described here is highly conserved within the human gut Bacteroides, indicating that the model developed is of generic relevance to this important microbial community.","author":[{"dropping-particle":"","family":"Cartmell","given":"Alan","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Lowe","given":"Elisabeth C.","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Baslé","given":"Arnaud","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Firbank","given":"Susan J.","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Ndeh","given":"Didier A.","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Murray","given":"Heath","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Terrapon","given":"Nicolas","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Lombard","given":"Vincent","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Henrissat","given":"Bernard","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Turnbull","given":"Jeremy E.","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Czjzek","given":"Mirjam","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Gilbert","given":"Harry J.","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Bolam","given":"David N.","non-dropping-particle":"","parse-names":false,"suffix":""}],"container-title":"Proceedings of the National Academy of Sciences","id":"ITEM-1","issue":"27","issued":{"date-parts":[["2017"]]},"page":"7037-7042","title":"How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans","type":"article-journal","volume":"114"},"uris":["http://www.mendeley.com/documents/?uuid=338ab035-66d5-4197-9ce8-779b9805b183"]},{"id":"ITEM-2","itemData":{"DOI":"10.1073/pnas.1815791116","ISSN":"0027-8424","abstract":"Over the last two decades, the number of gene/protein sequences gleaned from sequencing projects of individual genomes and environmental DNA has grown exponentially. Only a tiny fraction of these predicted proteins has been experimentally characterized, and the function of most proteins remains hypothetical or only predicted based on sequence similarity....","author":[{"dropping-particle":"","family":"Helbert","given":"William","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Poulet","given":"Laurent","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Drouillard","given":"Sophie","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Mathieu","given":"Sophie","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Loiodice","given":"Mélanie","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Couturier","given":"Marie","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Lombard","given":"Vincent","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Terrapon","given":"Nicolas","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Turchetto","given":"Jeremy","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Vincentelli","given":"Renaud","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Henrissat","given":"Bernard","non-dropping-particle":"","parse-names":false,"suffix":""}],"container-title":"Proceedings of the National Academy of Sciences of the United States of America","id":"ITEM-2","issue":"13","issued":{"date-parts":[["2019"]]},"page":"6063-6068","title":"Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space","type":"article-journal","volume":"116"},"uris":["http://www.mendeley.com/documents/?uuid=e0b9a3a0-aadb-49af-ad30-b5ef4878a6df"]}],"mendeley":{"formattedCitation":"(6, 7)","plainTextFormattedCitation":"(6, 7)","previouslyFormattedCitation":"(6, 7)"},"properties":{"noteIndex":0},"schema":"https://github.com/citation-style-language/schema/raw/master/csl-citation.json"}(6, 7). 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 ADDIN CSL_CITATION {"citationItems":[{"id":"ITEM-1","itemData":{"DOI":"10.3891/acta.chem.scand.21-0691","ISSN":"0904-213X","author":[{"dropping-particle":"","family":"Haug","given":"A","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Larsen","given":"B","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Smidsrod","given":"O","non-dropping-particle":"","parse-names":false,"suffix":""}],"container-title":"Acta Chemica Scandinavica","id":"ITEM-1","issue":"3","issued":{"date-parts":[["1967"]]},"page":"691-704","title":"Studies on sequence of uronic acid residues in alginic acid","type":"article-journal","volume":"21"},"uris":["http://www.mendeley.com/documents/?uuid=bbbac0a0-1a50-4d81-91fb-b5ea25ba38b7"]},{"id":"ITEM-2","itemData":{"DOI":"10.3891/acta.chem.scand.20-0183","ISSN":"0904-213X","author":[{"dropping-particle":"","family":"Haug","given":"A","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Larsen","given":"B","non-dropping-particle":"","parse-names":false,"suffix":""},{"dropping-particle":"","family":"Smidsrod","given":"O","non-dropping-particle":"","parse-names":false,"suffix":""}],"container-title":"Acta Chemica Scandinavica","id":"ITEM-2","issue":"1","issued":{"date-parts":[["1966"]]},"page":"183-190","title":"A study of constitution of alginic acid by partial acid hydrolysis","type":"article-journal","volume":"20"},"uris":["http://www.mendeley.com/documents/?uuid=e8a81ee7-106f-4eef-a522-8f1ce49ea0a7"]}],"mendeley":{"formattedCitation":"(8, 9)","plainTextFormattedCitation":"(8, 9)","previouslyFormattedCitation":"(8, 9)"},"properties":{"noteIndex":0},"schema":"https://github.com/citation-style-language/schema/raw/master/csl-citation.json"}(8, 9). Heparin consisting of disaccharide repeating units of which the most common is 2-O-sulfated 1,4 linked α-L-iduronic acid and 6-O-sulfated, N-sulfated glucosamine [IdoA(2S)-GlcNS(6S)]. Heparan sulfate being very similar to heparin having the IdoA replaced with β-D-glucuronic acid with a considerably more variable sulfation and acetylation pattern.
Authors may get an idea of what to put in each field from ''Curator Approved'' [[Glycoside Hydrolase Families]]. ''(TIP: Right click with your mouse and open this link in a new browser window...)''

In the meantime, please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>.

== Kinetics and Mechanism ==
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== Catalytic Residues ==
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== Three-dimensional structures ==
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== Family Firsts ==
;First stereochemistry determination: Content is to be added here.
;First catalytic nucleophile identification: Content is to be added here.
;First general acid/base residue identification: Content is to be added here.
;First 3-D structure: Content is to be added here.

== References ==
<biblio>
#Lombard2010 pmid=20925655
#Miyake2003 pmid=12729723
#Ochiai2010 pmid=20507980
#Jagtap2014 pmid=24795372
#Hashimoto20005 pmid=16233753
#Cartmell2017 pmid=28630303
#Helbert2019 pmid=30850540

#Cantarel2009 pmid=18838391
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
</biblio>

[[Category:Polysaccharide Lyase Families|PL015]]

Polysaccharide Lyase Family 15

2019-07-03T11:35:28Z

Emil Stender: