polygalacturonase

This enzyme's multiple parallel β sheets form a helical shape that is called a β helix. This highly stable structure, thanks to numerous hydrogen bonds and disulfide bonds between strands, is a common characteristic of enzymes involved in the degradation of pectin.{{cite journal | vauthors = D'Ovidio R, Mattei B, Roberti S, Bellincampi D | title = Polygalacturonases, polygalacturonase-inhibiting proteins and pectic oligomers in plant-pathogen interactions | journal = Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics | volume = 1696 | issue = 2 | pages = 237–44 | date = February 2004 | pmid = 14871664 | doi = 10.1016/j.bbapap.2003.08.012 }} The interior of the β helix is hydrophobic.

File:PG with active site.png (1HG8) showing active site in magenta]]

X-ray crystallography has been used to determine the three-dimensional structure of several PGs in different organisms. Fungal PGs from Colletotrichum lupini,{{cite journal | vauthors = Bonivento D, Pontiggia D, Matteo AD, Fernandez-Recio J, Salvi G, Tsernoglou D, Cervone F, Lorenzo GD, Federici L | title = Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins | journal = Proteins | volume = 70 | issue = 1 | pages = 294–9 | date = January 2008 | pmid = 17876815 | doi = 10.1002/prot.21610 | doi-access = free }} Aspergillus aculeatus, and Aspergillus niger (PG1{{cite journal | vauthors = van Pouderoyen G, Snijder HJ, Benen JA, Dijkstra BW | title = Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger | journal = FEBS Letters | volume = 554 | issue = 3 | pages = 462–6 | date = November 2003 | pmid = 14623112 | doi = 10.1016/s0014-5793(03)01221-3 | url = https://pure.rug.nl/ws/files/6675169/2003FEBSLettvPouderoyen.pdf | doi-access = free }} and PG2{{cite journal | vauthors = van Santen Y, Benen JA, Schröter KH, Kalk KH, Armand S, Visser J, Dijkstra BW | title = 1.68-A crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis | journal = The Journal of Biological Chemistry | volume = 274 | issue = 43 | pages = 30474–80 | date = October 1999 | pmid = 10521427 | doi = 10.1074/jbc.274.43.30474 | doi-access = free }}) have been crystallized. The PGs from bacteria like Erwinia carotovora{{cite journal | vauthors = Pickersgill R, Smith D, Worboys K, Jenkins J | title = Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora | journal = The Journal of Biological Chemistry | volume = 273 | issue = 38 | pages = 24660–4 | date = September 1998 | pmid = 9733763 | doi = 10.1074/jbc.273.38.24660 | doi-access =free }} and Bacillus subtilis have also been crystallized.

The active site of Fusarium moniliforme PG comprises six charged amino acid residues: H188, R267, and K269 are involved in substrate binding, D212 (a general acid) is responsible for proton donation to the glycosydic oxygen, and D213 and D191 activate H₂O for a nucleophilic attack.

Polygalacturonase is a pectinase, an enzyme that degrades pectin by hydrolyzing the O-glycosyl bonds in pectin's polygalacturonan network, resulting in α-1,4-polygalacturonic residues.{{cite web|title=Information on EC 3.2.1.15 - polygalacturonase|url=http://www.brenda-enzymes.org/enzyme.php?ecno=3.2.1.15|website=BRENDA}} The rate of hydrolysis is dependent on polysaccharide chain length. Low rates of hydrolysis are associated with very short chains (e.g. digalacturonic acid) and very long chains.{{cite journal|last1=Pressey|first1=Russell|last2=Reger|first2=Bonnie J. | name-list-style = vanc |title=Polygalacturonase in pollen from corn and other grasses|journal=Plant Science|date=1989|volume=59|issue=1|pages=57–62|doi=10.1016/0168-9452(89)90008-3}}

File:Polygalacturonase mechanism.png

Exo- vs Endo-polygalacturonases

Exo- and Endo-polygalacturonases utilize different hydrolytic modes of action. Endo-polygalacturonases hydrolyze in a random fashion along the polygalacturonan network. This method results in oligogalacturonides.{{cite journal | vauthors = Ferrari S, Savatin DV, Sicilia F, Gramegna G, Cervone F, Lorenzo GD | title = Oligogalacturonides: plant damage-associated molecular patterns and regulators of growth and development | journal = Frontiers in Plant Science | volume = 4 | issue = 49 | pages = 49 | date = 13 Mar 2013 | pmid = 23493833 | pmc = 3595604 | doi = 10.3389/fpls.2013.00049 | doi-access = free }} Exo-polygalacturonases hydrolyze at the non-reducing end of the polymer, generating a monosaccharide galacturonic acid. Occasionally, organisms employ both methods. In addition to different modes of action, polygalacturonases polymorphism allows fungal polygalacturonases to more effectively degrade a wider range of plant tissues. PG variety in optimal pH, substrate specificity, and other factors are likely helpful for phytopathogenic organisms like fungi.

Due to the applicability of this enzyme's activity on agricultural productivity and commercial success, much of the research on PGs has revolved around the role of PGs in the fruit ripening process, pollen, and abscission.

Pectin is one of the three polysaccharides present in the plant cell wall, and it plays a role in maintaining the barrier between the inside and outside environment and gives strength to the plant cell walls.{{cite journal | vauthors = Harholt J, Suttangkakul A, Vibe Scheller H | title = Biosynthesis of pectin | journal = Plant Physiology | volume = 153 | issue = 2 | pages = 384–95 | date = June 2010 | pmid = 20427466 | doi = 10.1104/pp.110.156588 | pmc = 2879803 }} Specifically, pectin in the middle lamella holds neighboring cells together.{{cite journal | vauthors = Orfila C, Seymour GB, Willats WG, Huxham IM, Jarvis MC, Dover CJ, Thompson AJ, Knox JP | title = Altered middle lamella homogalacturonan and disrupted deposition of (1→5)-α-L-arabinan in the pericarp of Cnr, a ripening mutant of tomato | journal = Plant Physiology | volume = 126 | issue = 1 | pages = 210–21 | date = May 2001 | pmid = 11351084 | pmc = 102295 | doi = 10.1104/pp.126.1.210 }}

Fruit ripening

The first GM food available in stores was a genetically modified tomato (also known as Flavr Savr) that had a longer shelf life and was ideal for shipping. Its delayed ripening was achieved by preventing polygalacturonase from destroying pectin, which makes tomatoes firm. An antisense PG gene was introduced, preventing polygalacturonase from ripening and softening the tomato.{{cite book|last1=Berg|first1=Jeremy M.|last2= Tymoczko|first2=John L.|last3=Stryer|first3=Lubert | name-list-style = vanc |title=Biochemistry|date=2012|publisher=W. H. Freeman and Company|isbn=9781429229364|page=167|edition=7}} Although this method has been shown to reduce PG enzymatic activity by 70 to 90%, the PG antisense RNA did not hinder normal color development.{{cite journal | vauthors = Sheehy RE, Kramer M, Hiatt WR | title = Reduction of polygalacturonase activity in tomato fruit by antisense RNA | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 85 | issue = 23 | pages = 8805–9 | date = December 1988 | pmid = 16593997 | pmc = 282595 | doi = 10.1073/pnas.85.23.8805| bibcode = 1988PNAS...85.8805S | doi-access = free }}

Depolymerization of pectin is largely involved in the later stages of fruit ripening, especially as the fruit becomes overripe.{{cite journal | vauthors = Hadfield KA, Bennett AB | title = Polygalacturonases: many genes in search of a function | journal = Plant Physiology | volume = 117 | issue = 2 | pages = 337–43 | date = June 1998 | pmid = 9625687 | pmc = 1539180 | doi = 10.1104/pp.117.2.337 }} While tomatoes are the prime example of high PG activity, this enzyme is also very active in avocado and peach ripening. PG enzymes in peach, two exo-PGs and one endo-PG, become active when the fruit is already soft.{{cite journal|last1=G. Downs|first1=Christopher|last2=J. Brady|first2=Colin|last3=Gooley|first3=Andrew | name-list-style = vanc |title=Exopolygalacturonase protein accumulates late in peach fruit ripening|journal=Physiologia Plantarum|date=June 1992|volume=85|issue=2|pages=133–140|doi=10.1111/j.1399-3054.1992.tb04715.x}}

Fruits like persimmons may either lack PG enzymes or have very low levels of PG and as such they have not been detected yet. In these cases, other enzymes may catalyze the ripening process.

Pollen

Exo-PGs play a role in enabling pollen tube elongation since pectin rearrangement is necessary for the growth of pollen tubes. This PG activity has been found in grasses like maize as well as in trees, particularly in the Eastern cottonwood.{{cite journal|last1=Pressey|first1=Russell|title=Polygalacturonase in tree pollens|journal=Phytochemistry|date=1991|volume=30|issue=6|pages=1753–1755|doi=10.1016/0031-9422(91)85006-L|url=https://zenodo.org/record/1258252}} Exo-PGs involved in pollen tube growth need Ca²⁺ for maximal enzymatic activity and can be inhibited by high concentrations of NaCl, citrate, and EDTA.

Abscission zones

It is largely unclear whether PGs play a role in facilitating abscission in certain plants, and if they do, whether they are exo- or endo-acting. Conflicting research has been published on, for example, whether PG is involved in citrus fruit abscission. One particular issue has been the usage of assays that are not able to measure exo-PG activity.{{cite journal|last1=Berger|first1=Richard K.|last2=Reid|first2=Philip D. | name-list-style = vanc |title=Role of Polygalacturonase in Bean Leaf Abscission|journal=Plant Physiology|date=15 January 1979|volume=63|issue=6|pages=1133–1137|doi=10.1104/pp.63.6.1133|pmid=16660870|pmc=542983}} An additional complication is the difference in PG enzymatic activity between fruit and leaf cell-separation zones. In peach, PG activity was only detected in fruit abscission zones.{{cite journal|last1=Bonghi|first1=C.|last2=Rascio|first2=N.|last3=Ramina|first3=A.|last4=Casadoro|first4=G. | name-list-style = vanc |title=Cellulase and polygalacturonase involvement in the abscission of leaf and fruit explants of peach|journal=Plant Molecular Biology|date=December 1992|volume=20|issue=5|pages=839–848|doi=10.1007/bf00027155|pmid=1281437|s2cid=12409373}}

Other

Agricultural pests like Lygus hesperus damage cotton and other crops because they secrete PGs in their saliva that digest plant tissue. They employ both exo- and endo-PGs.{{cite journal | vauthors = Celorio-Mancera Mde L, Carl Greve L, Teuber LR, Labavitch JM | title = Identification of endo- and exo-polygalacturonase activity in Lygus hesperus (Knight) salivary glands | journal = Archives of Insect Biochemistry and Physiology | volume = 70 | issue = 2 | pages = 122–35 | date = February 2009 | pmid = 19085947 | doi = 10.1002/arch.20282 | url = http://www.plantsciences.ucdavis.edu/faculty/labavitch/PDFs/Celorio-Mancera%20et%20al.2009.pdf }}

File:PGIP competitive inhibition.png (1OGQ). Residues that interact with PG active site are highlighted in blue.]]

Phytopathogenic fungi expose plant cell walls to cell wall degrading enzymes (CWDEs) like PGs.

In response, most plants have natural inhibitor proteins that slow the hydrolytic activity of PG. These inhibitors also prompt long chain oligogalacturonide accumulation in order to encourage a defense mechanism against the attack. The polygalacturonase inhibitor proteins (PGIPs) are leucine-rich repeat proteins that have been reported to demonstrate both

non-competitiveDaniel King, Carl Bergmann, Ron Orlando, Jacques A. E. Benen, Harry C. M. Kester, and Jaap Visser; "Use of Amide Exchange Mass Spectrometry To Study Conformational Changes within the Endopolygalacturonase II – Polygalacturonic Acid – Polygalacturonase Inhibiting Protein System", Biochem. 41, 10225-10233, 2002 and competitiveFederici L, Caprari C, Mattei B, Savino C, Di Matteo A, De Lorenzo G, Cervone F, Tsernoglou D. Structural requirements of endopolygalacturonase for the interaction with PGIP (polygalacturonase-inhibiting protein). Proc Natl Acad Sci U S A. 2001 Nov 6;98(23):13425-30. inhibition of PGs. The active site of PG interacts with a pocket containing multiple polar amino acids in Phaseolus vulgaris PGIP2. The inhibitor prevents substrate binding by occupying the active site, resulting in competitive inhibition.

The crystal structures for PGIP and PGIP2 have been determined for the bean P. vulgaris. The charged and polar residues that interact with the PG active site have been identified in P. vulgaris as D131, S133, T155, D157, T180, and D203.{{cite journal | vauthors = Di Matteo A, Federici L, Mattei B, Salvi G, Johnson KA, Savino C, De Lorenzo G, Tsernoglou D, Cervone F | title = The crystal structure of polygalacturonase-inhibiting protein (PGIP), a leucine-rich repeat protein involved in plant defense | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 100 | issue = 17 | pages = 10124–8 | date = August 2003 | pmid = 12904578 | pmc = 187787 | doi = 10.1073/pnas.1733690100 | bibcode = 2003PNAS..10010124D | doi-access = free }} Using PGIP2 as a template, the theoretical structures of other PGIPs have been determined for some other common crops.

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{{reflist|32em}}

• [http://www.pg-pgip.info PG & PGIP Structural Database]
• [http://pec.biodbs.info/ Pectinase Database]

{{Sugar hydrolases}}

{{Enzymes}}

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Category:EC 3.2.1