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This is the Wikipedia entry entitled "Pectinesterase". More...
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Pectinesterase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / QuickGO|
Pectinesterase (PE) (EC 184.108.40.206) 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.
Recent studies 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.
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.
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 Î²-helix as seen in all the carbohydrate esterase family CE-8, a transmembrane domain and a pectin binding cleft. 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. The putative catalytic residues are in a similar location to those of the active site and substrate-binding cleft of pectate lyase.
- 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): 3879â€“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): 849â€“858. doi:10.1105/tpc.104.028886. PMC 1069703. PMID 15722470.
- doi:10.1016/S0014-5793(02)02372-4. PMID 11943159. ; Johansson K, El-Ahmad M, Friemann R, JÃ¶rnvall H, Markovic O, Eklund H (March 2002). "Crystal structure of plant pectin methylesterase". FEBS Lett. 514 (2â€“3): 243â€“9.
- doi:10.1006/jmbi.2000.4324. PMID 11162105. ; 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): 951â€“960.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Pectinesterase Provide feedback
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Internal database links
|SCOOP:||Beta_helix DUF1565 NosD Pectate_lyase_3|
External database links
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.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||cell wall (GO:0005618)|
|Molecular function||pectinesterase activity (GO:0030599)|
|Biological process||cell wall modification (GO:0042545)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
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Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
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This superfamily all contain a right handed beta helix similar to that first found in pectate lyase .
The clan contains the following 29 members:Adeno_E1B_55K AIDA Beta_helix Chlam_PMP Chondroitinas_B Cthe_2159 Disaggr_assoc DUF1565 DUF2154 DUF2807 DUF3737 DUF4097 DUF4957 End_N_terminal Fil_haemagg Fil_haemagg_2 Glyco_hydro_28 Glyco_hydro_49 Glyco_hydro_92 Haemagg_act NosD Pec_lyase_C Pectate_lyase Pectate_lyase_3 Pectinesterase Pertactin PhageP22-tail Toast_rack_N VacA
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Author:||Finn RD , Bateman A|
|Number in seed:||28|
|Number in full:||9116|
|Average length of the domain:||253.80 aa|
|Average identity of full alignment:||30 %|
|Average coverage of the sequence by the domain:||58.16 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||19|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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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