P05117 (PGLR_SOLLC) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Solanum lycopersicum (Tomato) (Lycopersicon esculentum) [Reference proteome]

Taxonomic identifier

4081 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › asterids › lamiids › Solanales › Solanaceae › Solanoideae › Solaneae › Solanum › Lycopersicon

Protein attributes

Sequence length	457 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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	Secreted › extracellular space › apoplast. Secreted › cell 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 process	Cell wall biogenesis/degradation Fruit ripening
Cellular component	Apoplast Cell wall Secreted
Domain	Repeat Signal
Molecular function	Glycosidase Hydrolase
PTM	Glycoprotein
Technical term	Complete proteome Direct protein sequencing Genetically modified food Reference proteome
Gene Ontology (GO)
Biological_process	carbohydrate metabolic process Inferred from electronic annotation. Source: InterPro fruit ripening Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	apoplast Inferred from electronic annotation. Source: UniProtKB-SubCell cell wall Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	polygalacturonase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Signal peptide	1 – 24	24	Ref.6
	Propeptide	25 – 71	47			PRO_0000024804
	Chain	72 – 444	373	Polygalacturonase-2		PRO_0000024805
	Propeptide	445 – 457	13			PRO_0000043095
Regions
	Repeat	228 – 255	28	PbH1 1
	Repeat	256 – 277	22	PbH1 2
	Repeat	309 – 330	22	PbH1 3
	Repeat	338 – 359	22	PbH1 4
Sites
	Active site	270	1	Proton donor By similarity
	Active site	293	1	By similarity
Amino acid modifications
	Glycosylation	189	1	N-linked (GlcNAc...) Potential
	Glycosylation	240	1	N-linked (GlcNAc...) Potential
	Glycosylation	286	1	N-linked (GlcNAc...) Potential
	Glycosylation	311	1	N-linked (GlcNAc...) Potential
Experimental info
	Sequence conflict	96	1	E → Q AA sequence Ref.1
	Sequence conflict	136	1	V → E in CAD44521. Ref.8
	Sequence conflict	169	1	G → E in CAD44521. Ref.8

Sequences

	Sequence		Length	Mass (Da)
	P05117 [UniParc]. Last modified August 13, 1987. Version 1. Checksum: 449E4DC36919B074	FASTA	457	50,052
	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

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.
PIR	A25534.
RefSeq	NP_001234021.1. NM_001247092.1.
UniGene	Les.17635. Les.4463.
3D structure databases
ProteinModelPortal	P05117.
ModBase	Search...
Protein family/group databases
Allergome	6157. Lyc e PG.
CAZy	GH28. Glycoside Hydrolase Family 28.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	Solyc10g080210.1.1; Solyc10g080210.1.1; Solyc10g080210.1.
GeneID	544051.
Family and domain databases
Gene3D	2.160.20.10. 1 hit.
InterPro	IPR000743. Glyco_hydro_28. IPR006626. PbH1. IPR012334. Pectin_lyas_fold. IPR011050. Pectin_lyase_fold/virulence. [Graphical view]
Pfam	PF00295. Glyco_hydro_28. 1 hit. [Graphical view]
SMART	SM00710. PbH1. 4 hits. [Graphical view]
SUPFAM	SSF51126. Pectin_lyas_like. 1 hit.
PROSITE	PS00502. POLYGALACTURONASE. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PGLR_SOLLC

Accession

Primary (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:	April 3, 2013
This is version 104 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program