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P05117

- PGLR_SOLLC

UniProt

P05117 - PGLR_SOLLC

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Protein

Polygalacturonase-2

Gene

PG2

Organism
Solanum lycopersicum (Tomato) (Lycopersicon esculentum)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalytic subunit of the polygalacturonase isozyme 1 and 2 (PG1 and PG2). Acts in concert with the pectinesterase, in the ripening process. Is involved in cell wall metabolism, specifically in polyuronide degradation. The depolymerization and solubilization of cell wall polyuronides mediated by PG2 during ripening seems to be limited by the beta subunit GP1, probably by recruiting PG2 to form PG1.3 Publications

Catalytic activityi

Random hydrolysis of (1->4)-alpha-D-galactosiduronic linkages in pectate and other galacturonans.1 Publication

Absorptioni

Abs(max)=276 nm4 Publications

The ratio of Abs(276)/Abs(260)=1.35. These values are for PG1.

Kineticsi

  1. KM=38 µM for polygalacturonic acid (for PG2 at pH 4.6 and 35 degrees Celsius)4 Publications
  2. KM=75 µM for polygalacturonic acid (for PG1 at pH 4.6 and 35 degrees Celsius)4 Publications

Vmax=58.8 µmol/min/mg enzyme (for PG2 at pH 4.6 and 35 degrees Celsius)4 Publications

Vmax=7 µmol/min/mg enzyme (for PG2 at pH 3.8 and 25 degrees Celsius)4 Publications

Vmax=27.7 µmol/min/mg enzyme (for PG1 at pH 4.6 and 35 degrees Celsius)4 Publications

Vmax=4 µmol/min/mg enzyme (for PG1 at pH 3.8 and 25 degrees Celsius)4 Publications

pH dependencei

Optimum pH is 4.4-4.8 at 35 degrees Celsius. PG1 is resistant to acidic but not to alkaline conditions, at which PG2 is released from the beta subunit.4 Publications

Temperature dependencei

Optimum temperature is 55-60 degrees Celsius at pH 4.4. PG1 is more thermostable than PG2.4 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei270 – 2701Proton donorPROSITE-ProRule annotation
Active sitei293 – 2931PROSITE-ProRule annotation

GO - Molecular functioni

  1. polygalacturonase activity Source: UniProtKB-EC

GO - Biological processi

  1. carbohydrate metabolic process Source: InterPro
  2. cell wall organization Source: UniProtKB-KW
  3. fruit ripening Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Cell wall biogenesis/degradation, Fruit ripening

Protein family/group databases

CAZyiGH28. Glycoside Hydrolase Family 28.

Names & Taxonomyi

Protein namesi
Recommended name:
Polygalacturonase-2 (EC:3.2.1.15)
Short name:
PG
Alternative name(s):
PG-2A
PG-2B
Pectinase
Gene namesi
Name:PG2
Synonyms:PG, PG2A, PG2B
OrganismiSolanum lycopersicum (Tomato) (Lycopersicon esculentum)
Taxonomic identifieri4081 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeasteridslamiidsSolanalesSolanaceaeSolanoideaeSolaneaeSolanumLycopersicon
ProteomesiUP000004994: Chromosome 10

Subcellular locationi

Secretedextracellular spaceapoplast 1 Publication. Secretedcell wall 1 Publication
Note: Associated to the cell wall.

GO - Cellular componenti

  1. apoplast Source: UniProtKB-KW
  2. cell wall Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Apoplast, Cell wall, Secreted

Pathology & Biotechi

Biotechnological usei

The effect of PG can be neutralized by introducing an antisense PG gene by genetic manipulation. The Flavr Savr tomato produced by Calgene (Monsanto) in such a manner has a longer shelf life due to delayed ripening.

Protein family/group databases

Allergomei6157. Sola l PG.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 24241 PublicationAdd
BLAST
Propeptidei25 – 7147PRO_0000024804Add
BLAST
Chaini72 – 444373Polygalacturonase-2PRO_0000024805Add
BLAST
Propeptidei445 – 457131 PublicationPRO_0000043095Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi189 – 1891N-linked (GlcNAc...)Sequence Analysis
Glycosylationi240 – 2401N-linked (GlcNAc...)Sequence Analysis
Glycosylationi286 – 2861N-linked (GlcNAc...)Sequence Analysis
Glycosylationi311 – 3111N-linked (GlcNAc...)Sequence Analysis

Post-translational modificationi

N-glycosylated. PG2B isozyme has a greater degree of glycosylation than PG2A.3 Publications

Keywords - PTMi

Glycoprotein

Expressioni

Tissue specificityi

Expressed only in ripening fruits (at protein level).4 Publications

Developmental stagei

PG1 appears when fruits start to be coloured. When fruits are orange, both PG2 and PG1 are present. In fully ripe fruit, mostly PG2 is expressed.3 Publications

Inductioni

By ethylene.1 Publication

Interactioni

Subunit structurei

Monomer PG2 (isoenzymes PG2A and PG2B). Also forms heterodimers called polygalacturonase 1 (PG1) with the beta subunit GP1.3 Publications

Structurei

3D structure databases

ProteinModelPortaliP05117.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati228 – 25528PbH1 1Add
BLAST
Repeati256 – 27722PbH1 2Add
BLAST
Repeati309 – 33022PbH1 3Add
BLAST
Repeati338 – 35922PbH1 4Add
BLAST

Sequence similaritiesi

Belongs to the glycosyl hydrolase 28 family.Curated
Contains 4 PbH1 repeats.Curated

Keywords - Domaini

Repeat, Signal

Phylogenomic databases

InParanoidiP05117.
OMAiKANGNDD.

Family and domain databases

Gene3Di2.160.20.10. 1 hit.
InterProiIPR000743. Glyco_hydro_28.
IPR006626. PbH1.
IPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
[Graphical view]
PfamiPF00295. Glyco_hydro_28. 1 hit.
[Graphical view]
SMARTiSM00710. PbH1. 4 hits.
[Graphical view]
SUPFAMiSSF51126. SSF51126. 1 hit.
PROSITEiPS00502. POLYGALACTURONASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P05117-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MVIQRNSILL LIIIFASSIS TCRSNVIDDN LFKQVYDNIL EQEFAHDFQA
60 70 80 90 100
YLSYLSKNIE SNNNIDKVDK NGIKVINVLS FGAKGDGKTY DNIAFEQAWN
110 120 130 140 150
EACSSRTPVQ FVVPKNKNYL LKQITFSGPC RSSISVKIFG SLEASSKISD
160 170 180 190 200
YKDRRLWIAF DSVQNLVVGG GGTINGNGQV WWPSSCKINK SLPCRDAPTA
210 220 230 240 250
LTFWNCKNLK VNNLKSKNAQ QIHIKFESCT NVVASNLMIN ASAKSPNTDG
260 270 280 290 300
VHVSNTQYIQ ISDTIIGTGD DCISIVSGSQ NVQATNITCG PGHGISIGSL
310 320 330 340 350
GSGNSEAYVS NVTVNEAKII GAENGVRIKT WQGGSGQASN IKFLNVEMQD
360 370 380 390 400
VKYPIIIDQN YCDRVEPCIQ QFSAVQVKNV VYENIKGTSA TKVAIKFDCS
410 420 430 440 450
TNFPCEGIIM ENINLVGESG KPSEATCKNV HFNNAEHVTP HCTSLEISED

EALLYNY
Length:457
Mass (Da):50,052
Last modified:August 13, 1987 - v1
Checksum:i449E4DC36919B074
GO

Sequence cautioni

The sequence CAD44521.1 differs from that shown. Reason: Frameshift at positions 156 and 161. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti96 – 961E → Q AA sequence (PubMed:3786135)Curated
Sequence conflicti136 – 1361V → E in CAD44521. 1 PublicationCurated
Sequence conflicti169 – 1691G → E in CAD44521. 1 PublicationCurated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04583 mRNA. Translation: CAA28254.1.
X05656 mRNA. Translation: CAA29148.1.
X14074 Genomic DNA. Translation: CAA32235.1.
M37304 Genomic DNA. Translation: AAA34178.1.
A15981 Unassigned RNA. Translation: CAA01256.1.
A24194 Unassigned DNA. Translation: CAA01720.1.
M20269 mRNA. Translation: AAA34177.1.
X07410 Genomic DNA. Translation: CAA30308.1.
AJ505947 mRNA. Translation: CAD44521.1. Frameshift.
PIRiA25534.
RefSeqiNP_001234021.1. NM_001247092.2.
UniGeneiLes.17635.
Les.4463.

Genome annotation databases

EnsemblPlantsiSolyc10g080210.1.1; Solyc10g080210.1.1; Solyc10g080210.1.
GeneIDi544051.
KEGGisly:544051.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04583 mRNA. Translation: CAA28254.1 .
X05656 mRNA. Translation: CAA29148.1 .
X14074 Genomic DNA. Translation: CAA32235.1 .
M37304 Genomic DNA. Translation: AAA34178.1 .
A15981 Unassigned RNA. Translation: CAA01256.1 .
A24194 Unassigned DNA. Translation: CAA01720.1 .
M20269 mRNA. Translation: AAA34177.1 .
X07410 Genomic DNA. Translation: CAA30308.1 .
AJ505947 mRNA. Translation: CAD44521.1 . Frameshift.
PIRi A25534.
RefSeqi NP_001234021.1. NM_001247092.2.
UniGenei Les.17635.
Les.4463.

3D structure databases

ProteinModelPortali P05117.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

Allergomei 6157. Sola l PG.
CAZyi GH28. Glycoside Hydrolase Family 28.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi Solyc10g080210.1.1 ; Solyc10g080210.1.1 ; Solyc10g080210.1 .
GeneIDi 544051.
KEGGi sly:544051.

Phylogenomic databases

InParanoidi P05117.
OMAi KANGNDD.

Family and domain databases

Gene3Di 2.160.20.10. 1 hit.
InterProi IPR000743. Glyco_hydro_28.
IPR006626. PbH1.
IPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
[Graphical view ]
Pfami PF00295. Glyco_hydro_28. 1 hit.
[Graphical view ]
SMARTi SM00710. PbH1. 4 hits.
[Graphical view ]
SUPFAMi SSF51126. SSF51126. 1 hit.
PROSITEi PS00502. POLYGALACTURONASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Sequencing and identification of a cDNA clone for tomato polygalacturonase."
    Grierson D., Tucker G.A., Keen J., Ray J., Bird C.R., Schuch W.
    Nucleic Acids Res. 14:8595-8603(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 72-96.
    Strain: cv. Ailsa Craig.
  2. "Molecular characterization of tomato fruit polygalacturonase."
    Sheehy R.E., Pearson J., Brady C.J., Hiatt W.R.
    Mol. Gen. Genet. 208:30-36(1987)
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, TISSUE SPECIFICITY.
  3. Hiatt W.R.
    Submitted (OCT-1987) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION.
  4. "The tomato polygalacturonase gene and ripening-specific expression in transgenic plants."
    Bird C.R., Smith C.J.S., Ray J.A., Moureau P., Bevan M.W., Bird A.S., Hughes S., Morris P.C., Grierson D., Schuch W.
    Plant Mol. Biol. 11:651-662(1988)
    [AGRICOLA] [Europe PMC]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], TISSUE SPECIFICITY.
    Strain: cv. Ailsa Craig.
  5. "Anti-sense regulation of plant gene expression."
    Bridges I.G., Schuch W.W., Grierson D.
    Patent number EP0271988, 22-JUN-1988
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: cv. Ailsa Craig.
  6. "In vitro synthesis and processing of tomato fruit polygalacturonase."
    DellaPenna D., Bennett A.B.
    Plant Physiol. 86:1057-1063(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-115, PROTEIN SEQUENCE OF N-TERMINUS, PROTEIN SEQUENCE OF 72-92, GLYCOSYLATION.
  7. "The nucleotide sequence of the 5' flanking region of a tomato polygalacturonase gene."
    Rose R.E., Houck C.M., Monson E.K., DeJesus C.E., Sheehy R.E., Hiatt W.R.
    Nucleic Acids Res. 16:7191-7191(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-93.
  8. "Isolation, cloning and characterization of polygalacturonase gene from fruit tissue of Lycopersicum esculentum cv. Arka vikas."
    Saiprasad G.V.S.
    Submitted (AUG-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 96-294.
    Strain: cv. Arka vikas.
    Tissue: Fruit.
  9. "Changes in polygalacturonase isoenzymes during the 'ripening' of normal and mutant tomato fruit."
    Tucker G.A., Robertson N.G., Grierson D.
    Eur. J. Biochem. 112:119-124(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, DEVELOPMENTAL STAGE.
  10. "The conversion of tomato-fruit polygalacturonase isoenzyme 2 into isoenzyme 1 in vitro."
    Tucker G.A., Robertson N.G., Grierson D.
    Eur. J. Biochem. 115:87-90(1981) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  11. "Carbohydrate composition and electrophoretic properties of tomato polygalacturonase isoenzymes."
    Moshrefi M., Luh B.S.
    Eur. J. Biochem. 135:511-514(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: BIOPHYSICOCHEMICAL PROPERTIES, GLYCOSYLATION.
  12. "Purification and characterization of tomato polygalacturonase converter."
    Pressey R.
    Eur. J. Biochem. 144:217-221(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH GP1, BIOPHYSICOCHEMICAL PROPERTIES.
  13. "Analysis of tomato polygalacturonase expression in transgenic tobacco."
    Osteryoung K.W., Toenjes K., Hall B., Winkler V., Bennett A.B.
    Plant Cell 2:1239-1248(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, GLYCOSYLATION.
  14. "Accumulation of the beta-subunit of polygalacturonase 1 in normal and mutant tomato fruit."
    Pogson B.J., Brady C.J.
    Planta 191:71-78(1993)
    Cited for: INTERACTION WITH GP1.
  15. "Reduction of tomato polygalacturonase beta subunit expression affects pectin solubilization and degradation during fruit ripening."
    Watson C.F., Zheng L., DellaPenna D.
    Plant Cell 6:1623-1634(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DEVELOPMENTAL STAGE.
  16. "Differential expression of the two subunits of tomato polygalacturonase isoenzyme 1 in wild-type and in tomato fruit."
    Zheng L., Watson C.F., DellaPenna D.
    Plant Physiol. 105:1189-1195(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEVELOPMENTAL STAGE, TISSUE SPECIFICITY, INDUCTION BY ETHYLENE.
  17. "Tomato fruit polygalacturonase isozyme 1 -- characterization of the beta subunit and its state of assembly in vivo."
    Moore T., Bennett A.B.
    Plant Physiol. 106:1461-1469(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT, TISSUE SPECIFICITY.
  18. "Insertional inactivation of the tomato polygalacturonase gene."
    Cooley M.B., Yoder J.I.
    Plant Mol. Biol. 38:521-530(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  19. "Polygalacturonase-mediated solubilization and depolymerization of pectic polymers in tomato fruit cell walls. Regulation By ph and ionic conditions."
    Chun J.-P., Huber D.J.
    Plant Physiol. 117:1293-1299(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME ACTIVITY.
  20. "Purified tomato polygalacturonase activity during thermal and high-pressure treatment."
    Verlent I., van Loey A., Smout C., Duvetter T., Hendrickx M.E.
    Biotechnol. Bioeng. 86:63-71(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
  21. "Resolving the space-group ambiguity of crystals of tomato fruit polygalacturonase."
    Heffron S., Watkins S., Moeller R., Taban A.H., Butowt R., DellaPenna D., Jurnak F.
    Acta Crystallogr. D 59:2088-2093(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.87 ANGSTROMS) OF 2-368.

Entry informationi

Entry nameiPGLR_SOLLC
AccessioniPrimary (citable) accession number: P05117
Secondary accession number(s): P94004, Q70Y18, Q7DM56
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: October 29, 2014
This is version 113 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

To avoid liquid rheology of tomato juice, temperature and pressure can be increased to inactivate selectively PG2 during the process.

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Genetically modified food, Reference proteome

Documents

  1. Glycosyl hydrolases
    Classification of glycosyl hydrolase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3