O49006 · PME3_ARATH

Function

function

Acts in the modification of cell walls via demethylesterification of cell wall pectin (PubMed:21171891, PubMed:26183897).
Required for zinc Zn2+ homeostasis and to monitor Zn2+ influence on cell wall-controlled growth processes such as root cell elongation (PubMed:23826687).
Monitors seed germination and favors root hairs production (PubMed:28375469).
Prevents cruciferin seed storage proteins activity, but promotes the expression of genes involved in cell wall organization and remodeling as well as genes involved in lipid and protein metabolism, during post-germinative growth of seedlings (PubMed:28375469).
Confers sensitivity to Zn2+ when overexpressed (PubMed:23826687).
Acts as a susceptibility factor required for the initial colonization of the host tissue by virulent pathogens including Botrytis cinerea and Pectobacterium carotovorum, probably by facilitating cell wall pectine degradation by pathogen pectic enzymes after its demethylesterification (PubMed:21171891).

Miscellaneous

The PMEI region may act as an autoinhibitory domain and prevent untimely PME activity during transport.

Catalytic activity

Activity regulation

Regulated negatively by pectinesterase inhibitors (e.g. PMEI3, PMEI4, PMEI7 and PMEI9) in a pH-dependent manner, mainly in slightly acidic conditions (pH 6.0 and 5.0), especially in dark-grown hypocotyls; this processus relies on changes in the protonation of amino acids involved in intermolecular and intramolecular interactions.

Biotechnology

Mutant pme3 facilitates efficiency of viable mesophyll protoplast isolation probably as a result of reduced methylesterified homogalacturonan (HGA) level.

Kinetics

KM SUBSTRATE pH TEMPERATURE[C] NOTES EVIDENCE
12 μMHG96B82
5 μMHG96B69
9 μMHG96B20
6 μMHG97B77P63
224 μMHG96P64
Vmax pH TEMPERATURE[C] NOTES EVIDENCE
0.07 μmol/min/ugwith HG96B82 as substrate
0.05 μmol/min/ugwith HG96B69 as substrate
0.1 μmol/min/ugwith HG96B20 as substrate
0.05 μmol/min/ugwith HG97B77P63 as substrate
0.02 μmol/min/ugwith HG96P64 as substrate

pH Dependence

Optimum pH is 7.5 on homogalacturonan (HG) substrates with a degree of methylesterification between 60 and 80% and a random distribution of methyl esters.

Pathway

Glycan metabolism; pectin degradation; 2-dehydro-3-deoxy-D-gluconate from pectin: step 1/5.

Features

Showing features for binding site, site, active site.

Type
IDPosition(s)Description
Binding site356substrate; for pectinesterase activity
Binding site386substrate; for pectinesterase activity
Site408Transition state stabilizer
Active site409Proton donor; for pectinesterase activity
Active site430Nucleophile; for pectinesterase activity
Binding site454substrate; for pectinesterase activity
Binding site498substrate; for pectinesterase activity
Binding site500substrate; for pectinesterase activity

GO annotations

AspectTerm
Cellular Componentapoplast
Cellular Componentcytoplasm
Cellular Componentcytosol
Cellular Componentplant-type cell wall
Molecular Functionenzyme inhibitor activity
Molecular FunctionmRNA binding
Molecular Functionpectinesterase activity
Biological Processcell wall modification
Biological Processdefense response to bacterium
Biological Processdefense response to fungus
Biological Processdefense response to Gram-negative bacterium
Biological Processnegative regulation of seed germination
Biological Processpectin catabolic process
Biological Processregulation of gene expression
Biological Processregulation of unidimensional cell growth
Biological Processresponse to bacterium
Biological Processresponse to fungus
Biological Processresponse to nematode
Biological Processresponse to zinc ion
Biological Processroot development
Biological Processroot hair cell development

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

Including 2 domains:

  • Recommended name
    Pectinesterase inhibitor 3
  • Alternative names
    • Pectin methylesterase inhibitor 3
  • Recommended name
    Pectinesterase 3
  • EC number
  • Short names
    PE 3
  • Alternative names
    • Pectin methylesterase 27
      (AtPME27
      )
    • Pectin methylesterase 3
      (AtPME3
      )

Gene names

    • Name
      PME3
    • Synonyms
      ARATH27
      , OZS2
    • ORF names
      MLN21.10
    • Ordered locus names
      At3g14310

Organism names

  • Taxonomic identifier
  • Strain
    • cv. Columbia
  • Taxonomic lineage
    Eukaryota > Viridiplantae > Streptophyta > Embryophyta > Tracheophyta > Spermatophyta > Magnoliopsida > eudicotyledons > Gunneridae > Pentapetalae > rosids > malvids > Brassicales > Brassicaceae > Camelineae > Arabidopsis

Accessions

  • Primary accession
    O49006
  • Secondary accessions
    • Q56X61
    • Q93YZ2
    • Q9LUL7

Proteomes

Organism-specific databases

Genome annotation databases

Subcellular Location

Keywords

Phenotypes & Variants

Disruption phenotype

Early germination and reduced root hair production associated with lower expression of several pectin-degrading enzymes, genes involved in cell wall organization and remodeling and genes involved in lipid and protein metabolism, thus leading to a global decrease in proteolytic activity, however, cruciferin genes accumulate abnormally (PubMed:28375469).
Normal sensitivity to zinc Zn2+ (PubMed:23826687).
Increased resistance to Botrytis cinerea and Pectobacterium carotovorum associated with a reduced global pectin methylesterase (PME) activity, and correlating with an impaired ability of pathogens to grow on methylesterified pectin (PubMed:21171891).

Features

Showing features for mutagenesis.

TypeIDPosition(s)Description
Mutagenesis408Lost activity. Confers sensitivity to zinc Zn2+ when overexpressed.
Mutagenesis409Lost activity. Confers sensitivity to zinc Zn2+ when overexpressed.
Mutagenesis497In osz2; semi-dominant mutation with impaired proteolytic processing, and leading to an increased sensitivity to zinc Zn2+ characterized by Zn-triggered reduced root elongation due to a defect in cell elongation, but an increase number of root hairs; this phenotype is suppressed by calcium Ca2+ treatment. No obvious impact on pectin methylesterification.

Variants

We now provide the "Disease & Variants" viewer in its own tab.

The viewer provides 24 variants from UniProt as well as other sources including ClinVar and dbSNP.

Go to variant viewer

PTM/Processing

Features

Showing features for signal, propeptide, chain, glycosylation, disulfide bond.

Type
IDPosition(s)Description
Signal1-35
PropeptidePRO_000045896636-238Removed in mature 42 kDa form
PropeptidePRO_000045896536-273Removed in mature 38 kDa form
ChainPRO_000037166236-592Pectinesterase/pectinesterase inhibitor 3
Glycosylation96N-linked (GlcNAc...) asparagine
Glycosylation215N-linked (GlcNAc...) asparagine
ChainPRO_0000458967239-592Pectinesterase 3 of 42 kDa
ChainPRO_0000458968274-592Pectinesterase 3 of 38 kDa
Disulfide bond423↔443

Keywords

Proteomic databases

PTM databases

Expression

Tissue specificity

Expressed in roots, cotyledons, hypocotyls, seedlings, leaves, stems, flowers, dry seeds and siliques (PubMed:16622707, PubMed:28375469, PubMed:9767082).
Accumulates in etiolated hypocotyls (at protein level) (PubMed:26183897).

Induction

Induced by necrotrophic pathogens such as Pectobacterium carotovorum and Botrytis cinerea.

Developmental stage

Expressed throughout silique development.

Gene expression databases

Interaction

Subunit

Interacts with BIIDXI and At5g11420 (PubMed:25442819).
Binds reversibly to PMEI4, PMEI7 and PMEI8 to be inhibited; the stability of the PME3-PMEIs complexes and the inhibition of the pectin methylesterase (PME) activity is pH-dependent, based on protonation status of amino-acids at the complex interface (PubMed:26183897, PubMed:28034952, PubMed:29109147).

Protein-protein interaction databases

Structure

Family & Domains

Features

Showing features for region.

TypeIDPosition(s)Description
Region53-212Pectinesterase inhibitor 3
Region281-578Pectinesterase 3

Sequence similarities

In the N-terminal section; belongs to the PMEI family.
In the C-terminal section; belongs to the pectinesterase family.

Keywords

Phylogenomic databases

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Sequence processing
    The displayed sequence is further processed into a mature form.
  • Length
    592
  • Mass (Da)
    64,256
  • Last updated
    2009-05-05 v2
  • MD5 Checksum
    75D32BEF3D1B19C47C00B2821551AC9F
MAPSMKEIFSKDNFKKNKKLVLLSAAVALLFVAAVAGISAGASKANEKRTLSPSSHAVLRSSCSSTRYPELCISAVVTAGGVELTSQKDVIEASVNLTITAVEHNYFTVKKLIKKRKGLTPREKTALHDCLETIDETLDELHETVEDLHLYPTKKTLREHAGDLKTLISSAITNQETCLDGFSHDDADKQVRKALLKGQIHVEHMCSNALAMIKNMTDTDIANFEQKAKITSNNRKLKEENQETTVAVDIAGAGELDSEGWPTWLSAGDRRLLQGSGVKADATVAADGSGTFKTVAAAVAAAPENSNKRYVIHIKAGVYRENVEVAKKKKNIMFMGDGRTRTIITGSRNVVDGSTTFHSATVAAVGERFLARDITFQNTAGPSKHQAVALRVGSDFSAFYNCDMLAYQDTLYVHSNRQFFVKCLIAGTVDFIFGNAAVVLQDCDIHARRPNSGQKNMVTAQGRTDPNQNTGIVIQKCRIGATSDLQSVKGSFPTYLGRPWKEYSQTVIMQSAISDVIRPEGWSEWTGTFALNTLTYREYSNTGAGAGTANRVKWRGFKVITAAAEAQKYTAGQFIGGGGWLSSTGFPFSLGL

Sequence caution

The sequence AAL24278.1 differs from that shown. Reason: Frameshift
The sequence BAD94011.1 differs from that shown. Reason: Miscellaneous discrepancy Intron retention.

Features

Showing features for sequence conflict.

TypeIDPosition(s)Description
Sequence conflict81-82in Ref. 1; AAC72288
Sequence conflict280in Ref. 1; AAC72288

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
AF033204
EMBL· GenBank· DDBJ
AAC72288.1
EMBL· GenBank· DDBJ
Genomic DNA
AB022220
EMBL· GenBank· DDBJ
BAB01037.1
EMBL· GenBank· DDBJ
Genomic DNA
CP002686
EMBL· GenBank· DDBJ
AEE75500.1
EMBL· GenBank· DDBJ
Genomic DNA
AY037184
EMBL· GenBank· DDBJ
AAK59769.1
EMBL· GenBank· DDBJ
mRNA
AY052252
EMBL· GenBank· DDBJ
AAK97722.1
EMBL· GenBank· DDBJ
mRNA
AY143950
EMBL· GenBank· DDBJ
AAN28889.1
EMBL· GenBank· DDBJ
mRNA
AY058892
EMBL· GenBank· DDBJ
AAL24278.1
EMBL· GenBank· DDBJ
mRNA Frameshift
AK221816
EMBL· GenBank· DDBJ
BAD94011.1
EMBL· GenBank· DDBJ
mRNA Sequence problems.

Genome annotation databases

Similar Proteins

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