Summary: Pectinesterase
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Pectinesterase Edit Wikipedia article
| pectinesterase | |||||||||
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| Identifiers | |||||||||
| EC number | 3.1.1.11 | ||||||||
| CAS number | 9025-98-3 | ||||||||
| Databases | |||||||||
| IntEnz | IntEnz view | ||||||||
| BRENDA | BRENDA entry | ||||||||
| ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDB PDBe PDBsum | ||||||||
| Gene Ontology | AmiGO / QuickGO | ||||||||
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Pectinesterase (PE) (EC 3.1.1.11) is a ubiquitous cell-wall-associated enzyme that presents several isoforms that facilitate plant cell wall modification and subsequent breakdown. It is found in all higher plants as well as in some bacteria and fungi. Pectinesterase functions primarily by altering the localised pH of the cell wall resulting in alterations in cell wall integrity.
Pectinesterase catalyses the de-esterification of pectin into pectate and methanol. Pectin is one of the main components of the plant cell wall. In plants, pectinesterase plays an important role in cell wall metabolism during fruit ripening. In plant bacterial pathogens such as Erwinia carotovora and in fungal pathogens such as Aspergillus niger, pectinesterase is involved in maceration and soft-rotting of plant tissue. Plant pectinesterases are regulated by pectinesterase inhibitors, which are ineffective against microbial enzymes.[2]
Contents
Function
Recent studies[citation needed] have shown that the manipulation of pectinesterase expression can influence numerous physiological processes. In plants, pectinesterase plays a role in the modulation of cell wall mechanical stability during fruit ripening, cell wall extension during pollen germination and pollen tube growth, abscission, stem elongation, tuber yield and root development. Pectinesterase has also been shown to play a role in a plants response to pathogen attack. A cell wall-associated pectinesterase of Nicotiana tabacum is involved in host cell receptor recognition for the tobacco mosaic virus movement protein and it has been shown that this interaction is required for cell-to-cell translocation of the virus.
Pectinesterase action on the components of the plant cell wall can produce two diametrically opposite effects. The first being a contribution to the stiffening of the cell wall by producing blocks of unesterified carboxyl groups that can interact with calcium ions forming a pectate gel. The other being that proton release may stimulate the activity of cell wall hydrolases contributing to cell wall loosening.
Esterification of pectin
Pectins form approximately 35% of the dry weight of dicot cell walls. They are polymerised in the cis Golgi, methylesterified in the medial Golgi and substituted with side chains in the trans Golgi cisternae. Pectin biochemistry can be rather complicated but put simply, the pectin backbone comprises 3 types of polymer: homogalacturonan (HGA); rhamnogalacturonan I (RGI); rhamnogalacturonan II (RGII).
Homogalacturonan is highly methyl-esterified when exported into cell walls and is subsequently de-esterified by the action of pectinesterase and other pectic enzymes. Pectinesterase catalyses the de-esterification of methyl-esterified D-galactosiduronic acid units in pectic compounds yielding substrates for depolymerising enzymes, particularly acidic pectins and methanol.
Most of the purified plant pectinesterases have neutral or alkaline isoelectric points and are bound to the cell wall via electrostatic interactions. Pectinesterases can however display acidic isoelectric points as detected in soluble fractions of plant tissues. Until recently, it was generally assumed that plant pectinesterases remove methyl esters in a progressive block-wise fashion, giving rise to long contiguous stretches of un-esterified GalA residues in homogalacturonan domains of pectin. Alternatively it was thought that fungal pectinesterases had a random activity resulting in the de-esterification of single GalA residues per enzyme/substrate interactions. It has now been shown that some plant pectinesterase isoforms may exhibit both mechanisms and that such mechanisms are driven by alterations in pH. The optimal pH of higher plants is usually between pH 7 and pH 8 although the pH of pectinesterase from fungi and bacteria is usually much lower than this.
Molecular biology and biochemistry
PE proteins are synthesised as pre-proteins of 540-580 amino acids possessing a signal sequence and a large amino-terminal extension of around 22 kDa. This terminal extension is eventually removed to yield a mature protein of 34-37 kDa. Most PEs lack consensus sequences for N-glycosylation in the mature protein, although at least one site is present in the amino-terminal extension region.
Spatial and temporal regulation of pectinesterase activity during plant development is based on a large family of isoforms. Recently, the systematic sequencing of the Arabidopsis thaliana genome has led to the identification of 66 open reading frames that are annotated as pectinesterases, most of which are encoded as large pre-proproteins. The signal peptide pre-region is required for targeting the enzyme to the endoplasmic reticulum and consists of about 25 amino acid residues. These N-terminal regions contain several glycosylation sites and it is thought that these sites also play a role in targeting.
Pectinesterase is thought to be secreted to the apoplasm with highly methylated pectin although at some point along this secretory pathway the N-terminal pro-peptide is cleaved off. Currently, the role of the pro-region is unknown although it has been hypothesised that it may act as an intramolecular chaperone, ensuring correct folding or deactivating activity until PE insertion in the cell wall is complete.
Recently, particular attention has been devoted to molecular studies of pectinesterase leading to the characterisation of several related isoforms in various higher plant species. Some of these pectinesterases were shown to be ubiquitously expressed, whereas others are specifically expressed during fruit ripening, germination of the pollen grain, or stem elongation. Such data suggests that pectinesterses are encoded by a family of genes that are differentially regulated in cell type in response to specific developmental or environmental cues.
Plant isoforms
Several pectinesterase isoforms differing in molecular weight, isoelectric point and biochemical activity have been identified in dicotyledonous plants. Pectinesterase isoforms are encoded by a family of genes, some of which are constitutively expressed throughout the plant, whereas others are differentially expressed in specific tissues and at different developmental stages. Isoforms of pectinesterase differ in various biochemical parameters such as relative molecular mass, isoelectric point, optimum pH, substrate affinity, ion-requirement and location.
Structure
| Pectinesterase, catalytic | |||||||||||
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| Identifiers | |||||||||||
| Symbol | Pectinesterase_cat | ||||||||||
| Pfam | PF01095 | ||||||||||
| InterPro | IPR000070 | ||||||||||
| PROSITE | PDOC00413 | ||||||||||
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The N-terminal pro-peptides of pectinesterase are variable in size and sequence and show a low level of amino acid identity. Alternatively the C-terminal catalytic region is highly conserved and constitutes the mature enzyme. The first three-dimensional structure solved for a plant pectinesterase was for an isoform from carrot (Daucus carota) root and consists of a right-handed parallel β-helix as seen in all the carbohydrate esterase family CE-8, a transmembrane domain and a pectin binding cleft.[3] Similarly several pectinesterase structures have been elucidated in fungi and E.coli and share most of the structural motifs seen in plants.
Prokaryotic and eukaryotic pectinesterases share a few regions of sequence similarity. The crystal structure of pectinesterase from Erwinia chrysanthemi revealed a beta-helix structure similar to that found in pectinolytic enzymes, though it is different from most structures of esterases.[4] The putative catalytic residues are in a similar location to those of the active site and substrate-binding cleft of pectate lyase.
References
- ^ Fries, M.; Ihrig, J.; Brocklehurst, K.; Shevchik, V. E.; Pickersgill, R. W. (2007). "Molecular basis of the activity of the phytopathogen pectin methylesterase". The EMBO Journal. 26 (17): 3879–3887. doi:10.1038/sj.emboj.7601816. PMC 2000356. PMID 17717531.
- ^ Giovane A, Tsernoglou D, Camardella L, Di Matteo A, Raiola A, Bonivento D, De Lorenzo G, Cervone F, Bellincampi D (2005). "Structural basis for the interaction between pectin methylesterase and a specific inhibitor protein". Plant Cell. 17 (3): 849–858. doi:10.1105/tpc.104.028886. PMC 1069703. PMID 15722470.
- ^ PDB: 1GQ8; Johansson K, El-Ahmad M, Friemann R, Jörnvall H, Markovic O, Eklund H (March 2002). "Crystal structure of plant pectin methylesterase". FEBS Lett. 514 (2–3): 243–9. doi:10.1016/S0014-5793(02)02372-4. PMID 11943159.
- ^ PDB: 1QJV; Pickersgill RW, Smith D, Jenkins J, Mayans O, Worboys K (2001). "Three-dimensional structure of Erwinia chrysanthemi pectin methylesterase reveals a novel esterase active site". J. Mol. Biol. 305 (4): 951–960. doi:10.1006/jmbi.2000.4324. PMID 11162105.
External links
- pectinesterase at the US National Library of Medicine Medical Subject Headings (MeSH)
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Pectinesterase Provide feedback
No Pfam abstract.
Internal database links
| SCOOP: | Beta_helix DUF1565 NosD Pectate_lyase_3 |
External database links
| CAZY: | CE8 |
| PROSITE: | PDOC00413 |
| SCOP: | 1qjv |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000070
Pectinesterase EC (pectin methylesterase) catalyses the de-esterification of pectin into pectate and methanol. Pectin is one of the main components of the plant cell wall. In plants, pectinesterase plays an important role in cell wall metabolism during fruit ripening. In plant bacterial pathogens such as Erwinia carotovora and in fungal pathogens such as Aspergillus niger, pectinesterase is involved in maceration and soft-rotting of plant tissue. Plant pectinesterases are regulated by pectinesterase inhibitors, which are ineffective against microbial enzymes [ PUBMED:15722470 ].
Prokaryotic and eukaryotic pectinesterases share a few regions of sequence similarity. The crystal structure of pectinesterase from Erwinia chrysanthemi revealed a beta-helix structure similar to that found in pectinolytic enzymes, though it is different from most structures of esterases [ PUBMED:11162105 ]. The putative catalytic residues are in a similar location to those of the active site and substrate-binding cleft of pectate lyase.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Molecular function | pectinesterase activity (GO:0030599) |
| Biological process | cell wall modification (GO:0042545) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Pec_lyase-like (CL0268), which has the following description:
This superfamily all contain a right handed beta helix similar to that first found in pectate lyase [1].
The clan contains the following 39 members:
AC_1 Adeno_E1B_55K AIDA B_solenoid_dext B_solenoid_ydck Bactofilin Beta_helix Beta_helix_2 Beta_helix_3 Chlam_PMP Chondroitinas_B Cthe_2159 Disaggr_assoc DUF1565 DUF2154 DUF2807 DUF3737 DUF4097 DUF4957 DUF5649 End_N_terminal FapA Fil_haemagg Fil_haemagg_2 Glyco_hydro_28 Glyco_hydro_49 Glyco_hydro_92 Haemagg_act IPU_b_solenoid NosD PATR Pectate_lyase Pectate_lyase_3 Pectate_lyase_4 Pectinesterase Pertactin PhageP22-tail Toast_rack_N VacAAlignments
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| Seed (26) |
Full (14934) |
Representative proteomes | UniProt (28650) |
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| RP15 (1516) |
RP35 (7642) |
RP55 (12519) |
RP75 (17937) |
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| PP/heatmap | 1 | ||||||
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| Seed (26) |
Full (14934) |
Representative proteomes | UniProt (28650) |
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| RP15 (1516) |
RP35 (7642) |
RP55 (12519) |
RP75 (17937) |
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| Raw Stockholm | |||||||
| Gzipped | |||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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Curation and family details
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Curation
| Seed source: | Prosite |
| Previous IDs: | none |
| Type: | Repeat |
| Sequence Ontology: | SO:0001068 |
| Author: |
Finn RD  , Bateman A
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| Number in seed: | 26 |
| Number in full: | 14934 |
| Average length of the domain: | 246.80 aa |
| Average identity of full alignment: | 31 % |
| Average coverage of the sequence by the domain: | 58.02 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 298 | ||||||||||||
| Family (HMM) version: | 21 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Pectinesterase domain has been found. There are 24 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
