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Protein

Endopolygalacturonase II

Gene

pgaII

Organism
Aspergillus niger
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in maceration and soft-rotting of plant tissue. Hydrolyzes the 1,4-alpha glycosidic bonds of de-esterified pectate in the smooth region of the plant cell wall.

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei201 – 2011Proton donor
Active sitei223 – 2231

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
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Cell wall biogenesis/degradation

Enzyme and pathway databases

SABIO-RKP26214.

Protein family/group databases

CAZyiGH28. Glycoside Hydrolase Family 28.
mycoCLAPiPGA28II_ASPNG.

Names & Taxonomyi

Protein namesi
Recommended name:
Endopolygalacturonase II (EC:3.2.1.15)
Short name:
EPG-II
Alternative name(s):
Pectinase 2
Polygalacturonase II
Short name:
PG-II
Polygalacturonase X2
Gene namesi
Name:pgaII
Synonyms:pg2
OrganismiAspergillus niger
Taxonomic identifieri5061 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaPezizomycotinaEurotiomycetesEurotiomycetidaeEurotialesAspergillaceaeAspergillus

Subcellular locationi

Secreted Curated

GO - Cellular componenti

  1. extracellular region Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi180 – 1801D → E or N: Reduces activity by 99.9%. No effect on Km for substrate. 1 Publication
Mutagenesisi201 – 2011D → E or N: Reduces activity by 99.9%. No effect on Km for substrate. 1 Publication
Mutagenesisi202 – 2021D → E: Reduces activity by 99.4%. No effect on Km for substrate. 1 Publication
Mutagenesisi202 – 2021D → N: Reduces activity by 99.9%. No effect on Km for substrate. 1 Publication
Mutagenesisi223 – 2231H → A: Reduces activity by 99.5%. No effect on Km for substrate. 1 Publication
Mutagenesisi256 – 2561R → N: Reduces activity by 86%. Reduces Km for substrate 10-fold. 1 Publication
Mutagenesisi258 – 2581K → N: Reduces activity by 99.2%. Reduces Km for substrate 10-fold. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2121Sequence AnalysisAdd
BLAST
Propeptidei22 – 276Sequence AnalysisPRO_0000024770
Chaini28 – 362335Endopolygalacturonase IIPRO_0000024771Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi30 ↔ 45
Disulfide bondi203 ↔ 219
Glycosylationi240 – 2401N-linked (GlcNAc...) (high mannose)CAR_000232
Disulfide bondi329 ↔ 334
Disulfide bondi353 ↔ 362

Keywords - PTMi

Disulfide bond, Glycoprotein, Zymogen

PTM databases

UniCarbKBiP26214.

Structurei

Secondary structure

1
362
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi29 – 346Combined sources
Helixi35 – 417Combined sources
Helixi42 – 443Combined sources
Beta strandi46 – 527Combined sources
Beta strandi61 – 633Combined sources
Beta strandi71 – 8010Combined sources
Beta strandi89 – 968Combined sources
Beta strandi98 – 1014Combined sources
Beta strandi106 – 1083Combined sources
Helixi111 – 1133Combined sources
Beta strandi121 – 1233Combined sources
Beta strandi129 – 1357Combined sources
Beta strandi137 – 1415Combined sources
Beta strandi143 – 1453Combined sources
Beta strandi152 – 1554Combined sources
Beta strandi157 – 1637Combined sources
Beta strandi165 – 1673Combined sources
Helixi169 – 1724Combined sources
Turni173 – 1753Combined sources
Beta strandi181 – 1844Combined sources
Beta strandi188 – 1947Combined sources
Beta strandi196 – 1983Combined sources
Beta strandi203 – 21614Combined sources
Beta strandi218 – 2225Combined sources
Beta strandi225 – 2306Combined sources
Beta strandi232 – 2343Combined sources
Beta strandi237 – 26024Combined sources
Beta strandi265 – 29228Combined sources
Beta strandi302 – 31817Combined sources
Beta strandi322 – 3287Combined sources
Turni331 – 3333Combined sources
Beta strandi334 – 34815Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CZFX-ray1.68A/B1-362[»]
ProteinModelPortaliP26214.
SMRiP26214. Positions 28-362.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP26214.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati156 – 18631PbH1 1Add
BLAST
Repeati209 – 22921PbH1 2Add
BLAST
Repeati238 – 25922PbH1 3Add
BLAST
Repeati267 – 28923PbH1 4Add
BLAST
Repeati301 – 32222PbH1 5Add
BLAST

Sequence similaritiesi

Belongs to the glycosyl hydrolase 28 family.Curated
Contains 5 PbH1 repeats.Curated

Keywords - Domaini

Repeat, Signal

Phylogenomic databases

eggNOGiCOG5434.

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. 5 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.

P26214-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHSFASLLAY GLVAGATFAS ASPIEARDSC TFTTAAAAKA GKAKCSTITL
60 70 80 90 100
NNIEVPAGTT LDLTGLTSGT KVIFEGTTTF QYEEWAGPLI SMSGEHITVT
110 120 130 140 150
GASGHLINCD GARWWDGKGT SGKKKPKFFY AHGLDSSSIT GLNIKNTPLM
160 170 180 190 200
AFSVQANDIT FTDVTINNAD GDTQGGHNTD AFDVGNSVGV NIIKPWVHNQ
210 220 230 240 250
DDCLAVNSGE NIWFTGGTCI GGHGLSIGSV GDRSNNVVKN VTIEHSTVSN
260 270 280 290 300
SENAVRIKTI SGATGSVSEI TYSNIVMSGI SDYGVVIQQD YEDGKPTGKP
310 320 330 340 350
TNGVTIQDVK LESVTGSVDS GATEIYLLCG SGSCSDWTWD DVKVTGGKKS
360
TACKNFPSVA SC
Length:362
Mass (Da):37,684
Last modified:May 1, 1992 - v1
Checksum:i952A79F612BC8000
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X58893 Genomic DNA. Translation: CAA41694.1.
PIRiS12895.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X58893 Genomic DNA. Translation: CAA41694.1.
PIRiS12895.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CZFX-ray1.68A/B1-362[»]
ProteinModelPortaliP26214.
SMRiP26214. Positions 28-362.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

CAZyiGH28. Glycoside Hydrolase Family 28.
mycoCLAPiPGA28II_ASPNG.

PTM databases

UniCarbKBiP26214.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiCOG5434.

Enzyme and pathway databases

SABIO-RKP26214.

Miscellaneous databases

EvolutionaryTraceiP26214.

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. 5 hits.
[Graphical view]
SUPFAMiSSF51126. SSF51126. 1 hit.
PROSITEiPS00502. POLYGALACTURONASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Molecular cloning, nucleotide sequence and expression of the gene encoding prepro-polygalacturonase II of Aspergillus niger."
    Bussink H.J.D., Kester H.C.M., Visser J.
    FEBS Lett. 273:127-130(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 28-40 AND 151-161.
    Strain: ATCC 9029 / NRRL 3 / CBS 120.49 / DSM 2466 / N400.
  2. "Identification of the glycosylation site and glycan structures of recombinant endopolygalacturonase II by mass spectrometry."
    Yang Y., Bergmann C., Benen J., Orlando R.
    Rapid Commun. Mass Spectrom. 11:1257-1262(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE OF CARBOHYDRATE ON ASN-240, IDENTIFICATION BY MASS SPECTROMETRY.
  3. "1.68-A crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis."
    van Santen Y., Benen J.A.E., Schroeter K.-H., Kalk K.H., Armand S., Visser J., Dijkstra B.W.
    J. Biol. Chem. 274:30474-30480(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS), MUTAGENESIS OF ASP-180; ASP-201; ASP-202; HIS-223; ARG-256 AND LYS-258.

Entry informationi

Entry nameiPGLR2_ASPNG
AccessioniPrimary (citable) accession number: P26214
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: May 1, 1992
Last modified: January 7, 2015
This is version 94 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. Glycosyl hydrolases
    Classification of glycosyl hydrolase families and list of entries
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.