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P05117 (PGLR_SOLLC) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 109. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Polygalacturonase-2

Short name=PG
EC=3.2.1.15
Alternative name(s):
PG-2A
PG-2B
Pectinase
Gene names
Name:PG2
Synonyms:PG, PG2A, PG2B
OrganismSolanum lycopersicum (Tomato) (Lycopersicon esculentum) [Reference proteome]
Taxonomic identifier4081 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeasteridslamiidsSolanalesSolanaceaeSolanoideaeSolaneaeSolanumLycopersicon

Protein attributes

Sequence length457 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.13 Ref.15 Ref.18

Catalytic activity

Random hydrolysis of (1->4)-alpha-D-galactosiduronic linkages in pectate and other galacturonans. Ref.19

Subunit structure

Monomer PG2 (isoenzymes PG2A and PG2B). Also forms heterodimers called polygalacturonase 1 (PG1) with the beta subunit GP1. Ref.9 Ref.10 Ref.17

Subcellular location

Secretedextracellular spaceapoplast. Secretedcell wall. Note: Associated to the cell wall. Ref.13

Tissue specificity

Expressed only in ripening fruits (at protein level). Ref.2 Ref.4 Ref.16 Ref.17

Developmental stage

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. Ref.9 Ref.15 Ref.16

Induction

By ethylene. Ref.16

Post-translational modification

N-glycosylated. PG2B isozyme has a greater degree of glycosylation than PG2A. Ref.6 Ref.11 Ref.13

Biotechnological use

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.

Miscellaneous

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

Sequence similarities

Belongs to the glycosyl hydrolase 28 family.

Contains 4 PbH1 repeats.

Biophysicochemical properties

Absorption:

Abs(max)=276 nm Ref.9 Ref.11 Ref.12 Ref.20

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

Kinetic parameters:

KM=38 µM for polygalacturonic acid (for PG2 at pH 4.6 and 35 degrees Celsius)

KM=75 µM for polygalacturonic acid (for PG1 at pH 4.6 and 35 degrees Celsius)

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

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

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

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

pH dependence:

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.

Temperature dependence:

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

Sequence caution

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

Ontologies

Keywords
   Biological processCell wall biogenesis/degradation
Fruit ripening
   Cellular componentApoplast
Cell wall
Secreted
   DomainRepeat
Signal
   Molecular functionGlycosidase
Hydrolase
   PTMGlycoprotein
   Technical termComplete proteome
Direct protein sequencing
Genetically modified food
Reference proteome
Gene Ontology (GO)
   Biological_processcarbohydrate metabolic process

Inferred from electronic annotation. Source: InterPro

fruit ripening

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentapoplast

Inferred from electronic annotation. Source: UniProtKB-SubCell

cell wall

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionpolygalacturonase activity

Inferred from electronic annotation. Source: UniProtKB-EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2424 Ref.6
Propeptide25 – 7147
PRO_0000024804
Chain72 – 444373Polygalacturonase-2
PRO_0000024805
Propeptide445 – 45713
PRO_0000043095

Regions

Repeat228 – 25528PbH1 1
Repeat256 – 27722PbH1 2
Repeat309 – 33022PbH1 3
Repeat338 – 35922PbH1 4

Sites

Active site2701Proton donor By similarity
Active site2931 By similarity

Amino acid modifications

Glycosylation1891N-linked (GlcNAc...) Potential
Glycosylation2401N-linked (GlcNAc...) Potential
Glycosylation2861N-linked (GlcNAc...) Potential
Glycosylation3111N-linked (GlcNAc...) Potential

Experimental info

Sequence conflict961E → Q AA sequence Ref.1
Sequence conflict1361V → E in CAD44521. Ref.8
Sequence conflict1691G → E in CAD44521. Ref.8

Sequences

Sequence LengthMass (Da)Tools
P05117 [UniParc].

Last modified August 13, 1987. Version 1.
Checksum: 449E4DC36919B074

FASTA45750,052
        10         20         30         40         50         60 
MVIQRNSILL LIIIFASSIS TCRSNVIDDN LFKQVYDNIL EQEFAHDFQA YLSYLSKNIE 

        70         80         90        100        110        120 
SNNNIDKVDK NGIKVINVLS FGAKGDGKTY DNIAFEQAWN EACSSRTPVQ FVVPKNKNYL 

       130        140        150        160        170        180 
LKQITFSGPC RSSISVKIFG SLEASSKISD YKDRRLWIAF DSVQNLVVGG GGTINGNGQV 

       190        200        210        220        230        240 
WWPSSCKINK SLPCRDAPTA LTFWNCKNLK VNNLKSKNAQ QIHIKFESCT NVVASNLMIN 

       250        260        270        280        290        300 
ASAKSPNTDG VHVSNTQYIQ ISDTIIGTGD DCISIVSGSQ NVQATNITCG PGHGISIGSL 

       310        320        330        340        350        360 
GSGNSEAYVS NVTVNEAKII GAENGVRIKT WQGGSGQASN IKFLNVEMQD VKYPIIIDQN 

       370        380        390        400        410        420 
YCDRVEPCIQ QFSAVQVKNV VYENIKGTSA TKVAIKFDCS TNFPCEGIIM ENINLVGESG 

       430        440        450 
KPSEATCKNV HFNNAEHVTP HCTSLEISED EALLYNY 

« Hide

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRA25534.
RefSeqNP_001234021.1. NM_001247092.2.
UniGeneLes.17635.
Les.4463.

3D structure databases

ProteinModelPortalP05117.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

Allergome6157. Sola l PG.
CAZyGH28. Glycoside Hydrolase Family 28.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsSolyc10g080210.1.1; Solyc10g080210.1.1; Solyc10g080210.1.
GeneID544051.
KEGGsly:544051.

Family and domain databases

Gene3D2.160.20.10. 1 hit.
InterProIPR000743. Glyco_hydro_28.
IPR006626. PbH1.
IPR012334. Pectin_lyas_fold.
IPR011050. Pectin_lyase_fold/virulence.
[Graphical view]
PfamPF00295. Glyco_hydro_28. 1 hit.
[Graphical view]
SMARTSM00710. PbH1. 4 hits.
[Graphical view]
SUPFAMSSF51126. SSF51126. 1 hit.
PROSITEPS00502. POLYGALACTURONASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePGLR_SOLLC
AccessionPrimary (citable) accession number: P05117
Secondary accession number(s): P94004, Q70Y18, Q7DM56
Entry history
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: February 19, 2014
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Glycosyl hydrolases

Classification of glycosyl hydrolase families and list of entries