Proteopedia - User contributions [en]

Polygalacturonase

2017-07-18T00:18:42Z

Krishna Amin:

<Structure load='1czf' size='350' frame='true' align='right' caption='Tertiary structure of ''endo''-polygalacturonase II' scene='Tertiary structure of ''endo''-polygalacturonase II' />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>DOI: 10.1104/pp.117.2.337</ref>. Microbial PGs have been identified to be a part of defense mechanisms because of their role in pathogen attack <ref>DOI: 10.1074/jbc.273.38.24660</ref>.

--MDY -- this is a bit confusing. PG's are found in bacteria, fungi, plants, and animals. Plant PG's are involved in fruit ripening. Bacteria and fungal PG are involved in plant pathogenesis, often acting as plant virulence factors and involved in some of the initial pathogenic effects through their action of degrading the plant cell wall. -- MDY

== Function ==

Polygalacturonases hydrolyze α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues in polygalacturonic acids. Structural variation has been identified among differing PGs depending on organismal origins and catalytic functions. For example, endo-polygalacturonases produced from Erwinia carotovora demonstrate functional similarity to pectate lyases in that they cleave polygalacturonic acids in a calcium-depended manner via β-elimination<ref>DOI: 10.1074/jbc.273.38.24660</ref>.

MDY -- we need to 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 -- MDY

== Disease ==

== Relevance ==

== Structural highlights ==

The tertiary fold of PGs varies in its composition of coils, approximating at 10 coils in a right-handed parallel beta helix domain along with loop regions that together form the substrate-binding cleft, which appears to have a tunnel-like shape. The active site of PGs is found between the looped regions of the protein. Located within the looped regions are two conserved aspartate residues that are predicted to participate in catalytic activity <ref>DOI: 10.1074/jbc.273.38.24660</ref>.

MDY- 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>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>PMID:8081738</ref>. PB1 is Parallel Beta Sheet 1, T1 is Turn 1, between PB1 and PB2., [[PBH2]]]] 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.
--MDY

== References ==
<references/>
<ref>Pickersgill, R., Smith D., Worboys K., and Jenkins, J. "Crystal Structure of Polygalacturonase from Erwinia carotovora ssp. carotovora." The Jorunal of Biological Chemistry June (1998). [http://dx.doi.org/10.1074/jbc.273.38.24660 DOI: 10.1074/jbc.273.38.24660]</ref>

Polygalacturonase

2017-07-18T00:15:16Z

Krishna Amin:

<Structure load='1czf' size='350' frame='true' align='right' caption='Tertiary structure of ''endo''-polygalacturonase II' scene='Tertiary structure of ''endo''-polygalacturonase II' />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 (Polygalacturonases: many genes in search of a function). Microbial PGs have been identified to be a part of defense mechanisms because of their role in pathogen attack <ref>DOI: 10.1074/jbc.273.38.24660</ref>.

--MDY -- this is a bit confusing. PG's are found in bacteria, fungi, plants, and animals. Plant PG's are involved in fruit ripening. Bacteria and fungal PG are involved in plant pathogenesis, often acting as plant virulence factors and involved in some of the initial pathogenic effects through their action of degrading the plant cell wall. -- MDY

== Function ==

Polygalacturonases hydrolyze α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues in polygalacturonic acids. Structural variation has been identified among differing PGs depending on organismal origins and catalytic functions. For example, endo-polygalacturonases produced from Erwinia carotovora demonstrate functional similarity to pectate lyases in that they cleave polygalacturonic acids in a calcium-depended manner via β-elimination (crystal structure).

MDY -- we need to 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 -- MDY

== Disease ==

== Relevance ==

== Structural highlights ==

The tertiary fold of PGs varies in its composition of coils, approximating at 10 coils in a right-handed parallel beta helix domain along with loop regions that together form the substrate-binding cleft, which appears to have a tunnel-like shape. The active site of PGs is found between the looped regions of the protein. Located within the looped regions are two conserved aspartate residues that are predicted to participate in catalytic activity (crystal structure).

MDY- 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>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>PMID:8081738</ref>. PB1 is Parallel Beta Sheet 1, T1 is Turn 1, between PB1 and PB2., [[PBH2]]]] 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.
--MDY

== References ==
<references/>
<ref>Pickersgill, R., Smith D., Worboys K., and Jenkins, J. "Crystal Structure of Polygalacturonase from Erwinia carotovora ssp. carotovora." The Jorunal of Biological Chemistry June (1998). [http://dx.doi.org/10.1074/jbc.273.38.24660 DOI: 10.1074/jbc.273.38.24660]</ref>

Polygalacturonase

2017-07-18T00:14:36Z

Krishna Amin:

<Structure load='1czf' size='350' frame='true' align='right' caption='Tertiary structure of ''endo''-polygalacturonase II' scene='Tertiary structure of ''endo''-polygalacturonase II' />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 (Polygalacturonases: many genes in search of a function). Microbial PGs have been identified to be a part of defense mechanisms because of their role in pathogen attack <ref>DOI: 10.1074/jbc.273.30.24660</ref>.

--MDY -- this is a bit confusing. PG's are found in bacteria, fungi, plants, and animals. Plant PG's are involved in fruit ripening. Bacteria and fungal PG are involved in plant pathogenesis, often acting as plant virulence factors and involved in some of the initial pathogenic effects through their action of degrading the plant cell wall. -- MDY

== Function ==

Polygalacturonases hydrolyze α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues in polygalacturonic acids. Structural variation has been identified among differing PGs depending on organismal origins and catalytic functions. For example, endo-polygalacturonases produced from Erwinia carotovora demonstrate functional similarity to pectate lyases in that they cleave polygalacturonic acids in a calcium-depended manner via β-elimination (crystal structure).

MDY -- we need to 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 -- MDY

== Disease ==

== Relevance ==

== Structural highlights ==

The tertiary fold of PGs varies in its composition of coils, approximating at 10 coils in a right-handed parallel beta helix domain along with loop regions that together form the substrate-binding cleft, which appears to have a tunnel-like shape. The active site of PGs is found between the looped regions of the protein. Located within the looped regions are two conserved aspartate residues that are predicted to participate in catalytic activity (crystal structure).

MDY- 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>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>PMID:8081738</ref>. PB1 is Parallel Beta Sheet 1, T1 is Turn 1, between PB1 and PB2., [[PBH2]]]] 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.
--MDY

== References ==
<references/>
<ref>Pickersgill, R., Smith D., Worboys K., and Jenkins, J. "Crystal Structure of Polygalacturonase from Erwinia carotovora ssp. carotovora." The Jorunal of Biological Chemistry June (1998). [http://dx.doi.org/10.1074/jbc.273.38.24660 DOI: 10.1074/jbc.273.38.24660]</ref>

Polygalacturonase

2017-07-13T16:55:20Z

Krishna Amin:

<Structure load='1czf' size='350' frame='true' align='right' caption='Tertiary structure of ''endo''-polygalacturonase II' scene='Tertiary structure of ''endo''-polygalacturonase II' />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 (Polygalacturonases: many genes in search of a function). Microbial PGs have been identified to be a part of defense mechanisms because of their role in pathogen attack (crystal structure).

--MDY -- this is a bit confusing. PG's are found in bacteria, fungi, plants, and animals. Plant PG's are involved in fruit ripening. Bacteria and fungal PG are involved in plant pathogenesis, often acting as plant virulence factors and involved in some of the initial pathogenic effects through their action of degrading the plant cell wall. -- MDY

== Function ==

Polygalacturonases hydrolyze α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues in polygalacturonic acids. Structural variation has been identified among differing PGs depending on organismal origins and catalytic functions. For example, endo-polygalacturonases produced from Erwinia carotovora demonstrate functional similarity to pectate lyases in that they cleave polygalacturonic acids in a calcium-depended manner via β-elimination (crystal structure).

MDY -- we need to 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 -- MDY

== Disease ==

== Relevance ==

== Structural highlights ==

The tertiary fold of PGs varies in its composition of coils, approximating at 10 coils in a right-handed parallel beta helix domain along with loop regions that together form the substrate-binding cleft, which appears to have a tunnel-like shape. The active site of PGs is found between the looped regions of the protein. Located within the looped regions are two conserved aspartate residues that are predicted to participate in catalytic activity (crystal structure).

MDY- 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.

Not all PGs have ten coils in the parallel beta helix. They usually have approximately 10 coils. [[Image:Phb.jpg|200px|left|thumb| Nomenclature for structural elements of the parallel beta helix. PB1 is Parallel Beta Sheet 1, T1 is Turn 1, between PB1 and PB2., [[Pbh]]]] 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.
--MDY

== References ==
<references/>
<ref>Pickersgill, R., Smith D., Worboys K., and Jenkins, J. "Crystal Structure of Polygalacturonase from Erwinia carotovora ssp. carotovora." The Jorunal of Biological Chemistry June (1998). [http://dx.doi.org/10.1074/jbc.273.38.24660 DOI: 10.1074/jbc.273.38.24660]</ref>

Polygalacturonase

2017-07-13T16:50:04Z

Krishna Amin:

<Structure load='1czf' size='350' frame='true' align='right' caption='Tertiary structure of ''endo''-polygalacturonase II' scene='Tertiary structure of ''endo''-polygalacturonase II' />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 (Polygalacturonases: many genes in search of a function). Microbial PGs have been identified to be a part of defense mechanisms because of their role in pathogen attack [1].

--MDY -- this is a bit confusing. PG's are found in bacteria, fungi, plants, and animals. Plant PG's are involved in fruit ripening. Bacteria and fungal PG are involved in plant pathogenesis, often acting as plant virulence factors and involved in some of the initial pathogenic effects through their action of degrading the plant cell wall. -- MDY

== Function ==

Polygalacturonases hydrolyze α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues in polygalacturonic acids. Structural variation has been identified among differing PGs depending on organismal origins and catalytic functions. For example, endo-polygalacturonases produced from Erwinia carotovora demonstrate functional similarity to pectate lyases in that they cleave polygalacturonic acids in a calcium-depended manner via β-elimination (crystal structure).

MDY -- we need to 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 -- MDY

== Disease ==

== Relevance ==

== Structural highlights ==

The tertiary fold of PGs varies in its composition of coils, approximating at 10 coils in a right-handed parallel beta helix domain along with loop regions that together form the substrate-binding cleft, which appears to have a tunnel-like shape. The active site of PGs is found between the looped regions of the protein. Located within the looped regions are two conserved aspartate residues that are predicted to participate in catalytic activity (crystal structure).

MDY- 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.

Not all PGs have ten coils in the parallel beta helix. They usually have approximately 10 coils. [[Image:Phb.jpg|200px|left|thumb| Nomenclature for structural elements of the parallel beta helix. PB1 is Parallel Beta Sheet 1, T1 is Turn 1, between PB1 and PB2., [[Pbh]]]] 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.
--MDY

== References ==
<references/>
<ref>Pickersgill, R., Smith D., Worboys K., and Jenkins, J. "Crystal Structure of Polygalacturonase from Erwinia carotovora ssp. carotovora." The Jorunal of Biological Chemistry June (1998). [http://dx.doi.org/10.1074/jbc.273.38.24660 DOI: 10.1074/jbc.273.38.24660]</ref>

Polygalacturonase

2017-07-13T16:35:10Z

Krishna Amin:

<Structure load='1czf' size='350' frame='true' align='right' caption='Secondary structure of ''endo''-polygalacturonase II' scene='Insert optional scene name here' />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 (Polygalacturonases: many genes in search of a function). Microbial PGs have been identified to be a part of defense mechanisms because of their role in pathogen attack [1].

--MDY -- this is a bit confusing. PG's are found in bacteria, fungi, plants, and animals. Plant PG's are involved in fruit ripening. Bacteria and fungal PG are involved in plant pathogenesis, often acting as plant virulence factors and involved in some of the initial pathogenic effects through their action of degrading the plant cell wall. -- MDY

== Function ==

Polygalacturonases hydrolyze α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues in polygalacturonic acids. Structural variation has been identified among differing PGs depending on organismal origins and catalytic functions. For example, endo-polygalacturonases produced from Erwinia carotovora demonstrate functional similarity to pectate lyases in that they cleave polygalacturonic acids in a calcium-depended manner via β-elimination (crystal structure).

MDY -- we need to 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 -- MDY

== Disease ==

== Relevance ==

== Structural highlights ==

The tertiary fold of PGs varies in its composition of coils, approximating at 10 coils in a right-handed parallel beta helix domain along with loop regions that together form the substrate-binding cleft, which appears to have a tunnel-like shape. The active site of PGs is found between the looped regions of the protein. Located within the looped regions are two conserved aspartate residues that are predicted to participate in catalytic activity (crystal structure).

MDY- 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.

Not all PGs have ten coils in the parallel beta helix. They usually have approximately 10 coils. [[Image:Phb.jpg|200px|left|thumb| Nomenclature for structural elements of the parallel beta helix. PB1 is Parallel Beta Sheet 1, T1 is Turn 1, between PB1 and PB2., [[Pbh]]]] 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.
--MDY

== References ==
<references/>
<ref>Pickersgill, R., Smith D., Worboys K., and Jenkins, J. "Crystal Structure of Polygalacturonase from Erwinia carotovora ssp. carotovora." The Jorunal of Biological Chemistry June (1998). [http://dx.doi.org/10.1074/jbc.273.38.24660 DOI: 10.1074/jbc.273.38.24660]</ref>

Polygalacturonase

2017-07-13T16:33:52Z

Krishna Amin:

<Structure load='1czf' size='350' frame='true' align='right' caption='Secondary structure of ''endo''-polygalacturonase II' scene='Insert optional scene name here' />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 (Polygalacturonases: many genes in search of a function). Microbial PGs have been identified to be a part of defense mechanisms because of their role in pathogen attack (crystal structure).

--MDY -- this is a bit confusing. PG's are found in bacteria, fungi, plants, and animals. Plant PG's are involved in fruit ripening. Bacteria and fungal PG are involved in plant pathogenesis, often acting as plant virulence factors and involved in some of the initial pathogenic effects through their action of degrading the plant cell wall. -- MDY

== Function ==

Polygalacturonases hydrolyze α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues in polygalacturonic acids. Structural variation has been identified among differing PGs depending on organismal origins and catalytic functions. For example, endo-polygalacturonases produced from Erwinia carotovora demonstrate functional similarity to pectate lyases in that they cleave polygalacturonic acids in a calcium-depended manner via β-elimination (crystal structure).

MDY -- we need to 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 -- MDY

== Disease ==

== Relevance ==

== Structural highlights ==

The tertiary fold of PGs varies in its composition of coils, approximating at 10 coils in a right-handed parallel beta helix domain along with loop regions that together form the substrate-binding cleft, which appears to have a tunnel-like shape. The active site of PGs is found between the looped regions of the protein. Located within the looped regions are two conserved aspartate residues that are predicted to participate in catalytic activity (crystal structure).

MDY- 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.

Not all PGs have ten coils in the parallel beta helix. They usually have approximately 10 coils. [[Image:Phb.jpg|200px|left|thumb| Nomenclature for structural elements of the parallel beta helix. PB1 is Parallel Beta Sheet 1, T1 is Turn 1, between PB1 and PB2., [[Pbh]]]] 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.
--MDY

== References ==
<references/>
<ref>Pickersgill, R., Smith D., Worboys K., and Jenkins, J. "Crystal Structure of Polygalacturonase from Erwinia carotovora ssp. carotovora." The Jorunal of Biological Chemistry June (1998). [http://dx.doi.org/10.1074/jbc.273.38.24660 DOI: 10.1074/jbc.273.38.24660]</ref>

Polygalacturonase

2017-07-13T16:28:55Z

Krishna Amin:

<Structure load='1czf' size='350' frame='true' align='right' caption='Secondary structure of ''endo''-polygalacturonase II' scene='Insert optional scene name here' />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 (Polygalacturonases: many genes in search of a function). Microbial PGs have been identified to be a part of defense mechanisms because of their role in pathogen attack (crystal structure).

--MDY -- this is a bit confusing. PG's are found in bacteria, fungi, plants, and animals. Plant PG's are involved in fruit ripening. Bacteria and fungal PG are involved in plant pathogenesis, often acting as plant virulence factors and involved in some of the initial pathogenic effects through their action of degrading the plant cell wall. -- MDY

== Function ==

Polygalacturonases hydrolyze α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues in polygalacturonic acids. Structural variation has been identified among differing PGs depending on organismal origins and catalytic functions. For example, endo-polygalacturonases produced from Erwinia carotovora demonstrate functional similarity to pectate lyases in that they cleave polygalacturonic acids in a calcium-depended manner via β-elimination (crystal structure).

MDY -- we need to 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 -- MDY

== Disease ==

== Relevance ==

== Structural highlights ==

The tertiary fold of PGs varies in its composition of coils, approximating at 10 coils in a right-handed parallel beta helix domain along with loop regions that together form the substrate-binding cleft, which appears to have a tunnel-like shape. The active site of PGs is found between the looped regions of the protein. Located within the looped regions are two conserved aspartate residues that are predicted to participate in catalytic activity (crystal structure).

MDY- 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.

Not all PGs have ten coils in the parallel beta helix. They usually have approximately 10 coils. [[Image:Phb.jpg|200px|left|thumb| Nomenclature for structural elements of the parallel beta helix. PB1 is Parallel Beta Sheet 1, T1 is Turn 1, between PB1 and PB2., [[Pbh]]]] 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.
--MDY

== References ==
<references/>
<ref>Pickersgill, R., Smith D., Worboys K., and Jenkins, J. "Crystal Structure of Polygalacturonase from Erwinia carotovora ssp. carotovora." The Jorunal of Biological Chemistry June 1998. DOI: 10.1074/jbc.273.38.24660</ref>

Polygalacturonase

2017-07-13T16:24:33Z

Krishna Amin:

<Structure load='1czf' size='350' frame='true' align='right' caption='Secondary structure of ''endo''-polygalacturonase II' scene='Insert optional scene name here' />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 (Polygalacturonases: many genes in search of a function). Microbial PGs have been identified to be a part of defense mechanisms because of their role in pathogen attack (crystal structure).

--MDY -- this is a bit confusing. PG's are found in bacteria, fungi, plants, and animals. Plant PG's are involved in fruit ripening. Bacteria and fungal PG are involved in plant pathogenesis, often acting as plant virulence factors and involved in some of the initial pathogenic effects through their action of degrading the plant cell wall. -- MDY

== Function ==

Polygalacturonases hydrolyze α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues in polygalacturonic acids. Structural variation has been identified among differing PGs depending on organismal origins and catalytic functions. For example, endo-polygalacturonases produced from Erwinia carotovora demonstrate functional similarity to pectate lyases in that they cleave polygalacturonic acids in a calcium-depended manner via β-elimination (crystal structure).

MDY -- we need to 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 -- MDY

== Disease ==

== Relevance ==

== Structural highlights ==

The tertiary fold of PGs varies in its composition of coils, approximating at 10 coils in a right-handed parallel beta helix domain along with loop regions that together form the substrate-binding cleft, which appears to have a tunnel-like shape. The active site of PGs is found between the looped regions of the protein. Located within the looped regions are two conserved aspartate residues that are predicted to participate in catalytic activity (crystal structure).

MDY- 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.

Not all PGs have ten coils in the parallel beta helix. They usually have approximately 10 coils. [[Image:Phb.jpg|200px|left|thumb| Nomenclature for structural elements of the parallel beta helix. PB1 is Parallel Beta Sheet 1, T1 is Turn 1, between PB1 and PB2., [[Pbh]]]] 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.
--MDY

== References ==
<references/>
<ref>DOI: 10.1074/jbc.273.38.24660</ref>

Polygalacturonase

2017-07-13T16:23:51Z

Krishna Amin:

<Structure load='1czf' size='350' frame='true' align='right' caption='Secondary structure of ''endo''-polygalacturonase II' scene='Insert optional scene name here' />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 (Polygalacturonases: many genes in search of a function). Microbial PGs have been identified to be a part of defense mechanisms because of their role in pathogen attack (crystal structure).

--MDY -- this is a bit confusing. PG's are found in bacteria, fungi, plants, and animals. Plant PG's are involved in fruit ripening. Bacteria and fungal PG are involved in plant pathogenesis, often acting as plant virulence factors and involved in some of the initial pathogenic effects through their action of degrading the plant cell wall. -- MDY

== Function ==

Polygalacturonases hydrolyze α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues in polygalacturonic acids. Structural variation has been identified among differing PGs depending on organismal origins and catalytic functions. For example, endo-polygalacturonases produced from Erwinia carotovora demonstrate functional similarity to pectate lyases in that they cleave polygalacturonic acids in a calcium-depended manner via β-elimination (crystal structure).

MDY -- we need to 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 -- MDY

== Disease ==

== Relevance ==

== Structural highlights ==

The tertiary fold of PGs varies in its composition of coils, approximating at 10 coils in a right-handed parallel beta helix domain along with loop regions that together form the substrate-binding cleft, which appears to have a tunnel-like shape. The active site of PGs is found between the looped regions of the protein. Located within the looped regions are two conserved aspartate residues that are predicted to participate in catalytic activity (crystal structure).

MDY- 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.

Not all PGs have ten coils in the parallel beta helix. They usually have approximately 10 coils. [[Image:Phb.jpg|200px|left|thumb| Nomenclature for structural elements of the parallel beta helix. PB1 is Parallel Beta Sheet 1, T1 is Turn 1, between PB1 and PB2., [[Pbh]]]] 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.
--MDY

== References ==
<references/>
<ref>DOI: 10.1074/jbc.273.38.24660

Polygalacturonase

2017-07-12T19:28:52Z

Krishna Amin:

Polygalacturonase

2017-07-12T19:22:27Z

Krishna Amin:

Polygalacturonase

2017-07-12T19:12:57Z

Krishna Amin:

Polygalacturonase

2017-07-12T19:12:31Z

Krishna Amin:

Polygalacturonase

2017-07-12T18:36:25Z

Krishna Amin:

Polygalacturonase

2017-07-11T22:51:41Z

Krishna Amin:

Polygalacturonase

2017-07-11T22:50:31Z

Krishna Amin:

Polygalacturonase

2017-07-11T22:48:39Z

Krishna Amin:

<Structure load='1czf' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />Polygalacturonases (PGs) catalyze the enzymatic depolymerization of pectins – 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 pectins in plant cell walls contributes to ripening of fruits, such as tomatoes and melons '''(Polygalacturonases: many genes in search of a function)'''.
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
== Function ==
PGs cleave α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues.
== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Polygalacturonase

2017-07-11T22:48:03Z

Krishna Amin:

<Structure load='10.2210/pdb1czf/pdb' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />Polygalacturonases (PGs) catalyze the enzymatic depolymerization of pectins – 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 pectins in plant cell walls contributes to ripening of fruits, such as tomatoes and melons '''(Polygalacturonases: many genes in search of a function)'''.
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
== Function ==
PGs cleave α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues.
== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Polygalacturonase

2017-07-01T21:30:01Z

Krishna Amin:

Polygalacturonases (PGs) catalyze the enzymatic depolymerization of pectins – 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 pectins in plant cell walls contributes to ripening of fruits, such as tomatoes and melons '''(Polygalacturonases: many genes in search of a function)'''.
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
== Function ==
PGs cleave α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues.
== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Polygalacturonase

2017-07-01T21:28:40Z

Krishna Amin:

Polygalacturonases (PGs) catalyze the enzymatic depolymerization of pectins – 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 pectins in plant cell walls contributes to ripening of fruits, such as tomatoes and melons '''(Polygalacturonases: many genes in search of a function)'''.
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox Reserved 354'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
PGs cleave α-(1-4) – glycosidic bonds between consecutive galacturonic acid residues.
== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Polygalacturonase

2017-07-01T21:23:42Z

Krishna Amin:

Polygalacturonases (PGs) catalyze the enzymatic depolymerization of pectins – 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 pectins in plant cell walls contributes to ripening of fruits, such as tomatoes and melons '''(Polygalacturonases: many genes in search of a function)'''.
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox Reserved 354'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
this is where you describe the function
== Disease ==
Hi Krishna !!

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Polygalacturonase

2017-07-01T21:22:53Z

Krishna Amin:

Polygalacturonases (PGs) catalyze the enzymatic depolymerization of pectins – polysaccharides that comprise the plant cell wall. Polymer disassembly of substrates by exo- and endo- PGs is carried out via hydrolytic mechanisms. Degradation of pectins in plant cell walls contributes to ripening of fruits, such as tomatoes and melons '''(Polygalacturonases: many genes in search of a function)'''.
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox Reserved 354'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
this is where you describe the function
== Disease ==
Hi Krishna !!

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox Reserved 354

2017-06-28T21:10:59Z

Krishna Amin: Sandbox Reserved 354 moved to Polygalacturonase

#REDIRECT [[Polygalacturonase]]

Polygalacturonase

2017-06-28T21:10:59Z

Krishna Amin: Sandbox Reserved 354 moved to Polygalacturonase

Polygalacturonase
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox Reserved 354'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
this is where you describe the function
== Disease ==
Hi Krishna !!

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Polygalacturonase

2017-06-28T20:05:41Z

Krishna Amin:

Polygalacturonase

2017-06-28T20:04:38Z

Krishna Amin:

==Polygalactoranase== 0
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox Reserved 354'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
this is where you describe the function
== Disease ==
Hi Krishna !!

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>