Polygalacturonase: Difference between revisions
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< | <StructureSection load='1czf' size='350' side='right' caption='Glycosylated structure of endo-polygalacturonase II complex with Zn+2 ion (grey) (PDB code [[1czf]])' scene=''> | ||
'''Polygalacturonases''' (PGs) catalyze the enzymatic depolymerization of pectates – polysaccharides that comprise the plant cell wall. Polymer disassembly of substrates by ''exo-'' and ''endo-'' PGs is carried out via a hydrolytic mechanism. Degradation of pectates in plant cell walls contributes to ripening of fruits, such as tomatoes and melons<ref>PMID:9625687</ref>. Microbial PGs have been identified to be a part of defense mechanisms because of their role in pathogen attack<ref name="crystal">PMID:9733763</ref>. | '''Polygalacturonases''' (PGs) catalyze the enzymatic depolymerization of pectates – polysaccharides that comprise the plant cell wall. Polymer disassembly of substrates by ''exo-'' and ''endo-'' PGs is carried out via a hydrolytic mechanism. Degradation of pectates in plant cell walls contributes to ripening of fruits, such as tomatoes and melons<ref>PMID:9625687</ref>. Microbial PGs have been identified to be a part of defense mechanisms because of their role in pathogen attack<ref name="crystal">PMID:9733763</ref>. | ||
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One must distinguish between pectate and pectin. Pectate is a galacturonate polymer, pectin has a polygalacturonate backbone, but some of the monomers are methylesterified on the sixth carbon. PG acts on pectate, not pectin. | One must distinguish between pectate and pectin. Pectate is a galacturonate polymer, pectin has a polygalacturonate backbone, but some of the monomers are methylesterified on the sixth carbon. PG acts on pectate, not pectin. | ||
== Structural highlights == | == Structural highlights == | ||
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A right-handed parallel beta helix is a tertiary fold. The secondary structure is the beta and the alpha structure. If you describe how the secondary structure folds in space, that becomes tertiary structure. The secondary structural elements of the core fold of the proteins are only beta structure, the beta strands form parallel beta sheets. There are three main parallel beta sheets, PG's often have a smaller parallel beta sheet of only three-four beta strands. Nomenclature on how the sheets and turns are labeled are described in Yoder et al<ref name="yoder">PMID:8081738</ref>. | A right-handed parallel beta helix is a tertiary fold. The secondary structure is the beta and the alpha structure. If you describe how the secondary structure folds in space, that becomes tertiary structure. The secondary structural elements of the core fold of the proteins are only beta structure, the beta strands form parallel beta sheets. There are three main parallel beta sheets, PG's often have a smaller parallel beta sheet of only three-four beta strands. Nomenclature on how the sheets and turns are labeled are described in Yoder et al<ref name="yoder">PMID:8081738</ref>. | ||
Not all PGs have ten coils in the parallel beta helix. They usually have approximately 10 coils. [[Image:PBH2.jpg|200px|left|thumb| Nomenclature for structural elements of the parallel beta helix<ref name="yoder" />. PB1 is Parallel Beta Sheet 1, T1 is Turn 1, between PB1 and PB2., | Not all PGs have ten coils in the parallel beta helix. They usually have approximately 10 coils. [[Image:PBH2.jpg|200px|left|thumb| Nomenclature for structural elements of the parallel beta helix<ref name="yoder" />. PB1 is Parallel Beta Sheet 1, T1 is Turn 1, between PB1 and PB2., PB3]] With the parallel beta helix fold, the three major beta sheets are call PB1, PB2, and PB3. The turns between strands are Turn 1 (T1) between PB1 and PB2, T2 is the turn between PB2 and PB3, and T3 is the turn between PB3 and PB1 of the next coil. For your reference, this is illustrated in the figure below. | ||
</StructureSection> | </StructureSection> | ||
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*Endopolygalacturonase | *Endopolygalacturonase | ||
**[[7b7a]] – AtEPGU – ''Arabidopsis thaliana''<br /> | |||
**[[7b8b]] – AtEPGU2<br /> | |||
**[[2iq7]] – EPGU – ''Colletotrichum lupini'' <br /> | **[[2iq7]] – EPGU – ''Colletotrichum lupini'' <br /> | ||
**[[1hg8]] – EPGU – ''Fusarium moniliforme'' <br /> | **[[1hg8]] – EPGU – ''Fusarium moniliforme'' <br /> | ||
**[[1nhc]] – AnEPGU I – ''Aspergillus niger'' <br /> | **[[1nhc]] – AnEPGU I – ''Aspergillus niger'' <br /> | ||
**[[1czf]] – AnEPGU II <br /> | **[[1czf]] – AnEPGU II <br /> | ||
**[[6kve]] – TlEPGU – ''Talaromyces leycettanus''<br /> | |||
**[[6kvh]], [[7e56]] – TlEPGU (mutant)<br /> | |||
*Exopolygalacturonase | |||
**[[2uve]] – YeEXPGU – ''Yersinia enterocolitica'' <br /> | |||
**[[2uvf]] – YeEXPGU + digalacturonic acid <br /> | |||
}} | }} | ||
== References == | == References == | ||
<references/> | <references/> | ||