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This is the Wikipedia entry entitled "Cutinase". More...
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Cutinase Edit Wikipedia article
Structure of Fusarium solani cutinase. PDB .
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / QuickGO|
|SCOPe||1cex / SUPFAM|
- cutin + H2O cutin monomers
Aerial plant organs are protected by a cuticle composed of an insoluble polymeric structural compound, cutin, which is a polyester composed of hydroxy and hydroxyepoxy fatty acids. Plant pathogenic fungi produce extracellular degradative enzymes that play an important role in pathogenesis. They include cutinase, which hydrolyses cutin, facilitating fungus penetration through the cuticle. Inhibition of the enzyme can prevent fungal infection through intact cuticles. Cutin monomers released from the cuticle by small amounts of cutinase on fungal spore surfaces can greatly increase the amount of cutinase secreted by the spore, the mechanism for which is as yet unknown.
Cutinase is a serine esterase containing the classical Ser, His, Asp triad of serine hydrolases. The protein belongs to the alpha-beta class, with a central beta-sheet of 5 parallel strands covered by 5 helices on either side of the sheet. The active site cleft is partly covered by 2 thin bridges formed by amino acid side chains, by contrast with the hydrophobic lid possessed by other lipases. The protein also contains 2 disulfide bridges, which are essential for activity, their cleavage resulting in complete loss of enzymatic activity. Two cutinase-like proteins (MtCY39.35 and MtCY339.08c) have been found in the genome of the bacteria Mycobacterium tuberculosis.
- Longhi S, Czjzek M, Lamzin V, Nicolas A, Cambillau C (May 1997). "Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis". J. Mol. Biol. 268 (4): 779â€“99. doi:10.1006/jmbi.1997.1000. PMID 9175860.
- Ettinger WF, Thukral SK, Kolattukudy PE (1987). "Structure of cutinase gene, cDNA, and the derived amino acid sequence from phytopathogenic fungi". Biochemistry. 26 (24): 7883â€“7892. doi:10.1021/bi00398a052.
- Sweigard JA, Chumley FG, Valent B (1992). "Cloning and analysis of CUT1, a cutinase gene from Magnaporthe grisea". Mol. Gen. Genet. 232 (2): 174â€“182. doi:10.1007/BF00279994. PMID 1557023.
- Cambillau C, Martinez C, De Geus P, Lauwereys M, Matthyssens G (1992). "Fusarium solani cutinase is a lipolytic enzyme with a catalytic serine accessible to solvent". Nature. 356 (6370): 615â€“618. doi:10.1038/356615a0. PMID 1560844.
- Garcia-Lepe R, Nuero OM, Reyes F, Santamaria F (1997). "Lipases in autolysed cultures of filamentous fungi". Lett. Appl. Microbiol. 25 (2): 127â€“30. doi:10.1046/j.1472-765X.1997.00187.x. PMID 9281862.
- Purdy RE, Kolattukudy PE (1975). "Hydrolysis of plant cuticle by plant pathogens. Purification, amino acid composition, and molecular weight of two isozymes of cutinase and a nonspecific esterase from Fusarium solani f. pisi". Biochemistry. 14 (13): 2824â€“31. doi:10.1021/bi00684a006. PMID 1156575.
- Purdy RE, Kolattukudy PE (1975). "Hydrolysis of plant cuticle by plant pathogens. Properties of cutinase I, cutinase II, and a nonspecific esterase isolated from Fusarium solani pisi". Biochemistry. 14 (13): 2832â€“40. doi:10.1021/bi00684a007. PMID 239740.
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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.
Cutinase Provide feedback
No Pfam abstract.
Longhi S, Czjzek M, Lamzin V, Nicolas A, Cambillau C; , J Mol Biol 1997;268:779-799.: Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis. PUBMED:9175860 EPMC:9175860
Internal database links
|SCOOP:||Abhydrolase_1 Abhydrolase_2 Abhydrolase_6 Abhydrolase_8 DUF2974 DUF676 Hydrolase_4 Lipase_3 PE-PPE Thioesterase VirJ|
|Similarity to PfamA using HHSearch:||VirJ PE-PPE|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000675
Plant pathogenic fungi produce extracellular degradative enzymes [PUBMED:1557023] that play an important role in pathogenesis. They include cutinase, which hydrolyses cutin, facilitating fungus penetration through the cuticle. Cutinase is a serine esterase containing the classical Ser, His, Asp triad of serine hydrolases. The protein belongs to the alpha-beta class, with a central beta-sheet of 5 parallel strands covered by 5 helices on either side of the sheet. The active site cleft is partly covered by 2 thin bridges formed by amino acid side chains, by contrast with the hydrophobic lid possessed by other lipases [PUBMED:1560844]. The protein also contains 2 disulphide bridges, which are essential for activity, their cleavage resulting in complete loss of enzymatic activity.
Acetylxylan esterase removes acetyl side groups from xylan. The catalytic core of the enzyme has an alpha/beta/alpha sandwich fold, similar to that of cutinase [PUBMED:11243887].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||hydrolase activity (GO:0016787)|
|Biological process||metabolic process (GO:0008152)|
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
- the Pfam graphic itself.
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 catalytic domain is found in a very wide range of enzymes.
The clan contains the following 70 members:Abhydro_lipase Abhydrolase_1 Abhydrolase_2 Abhydrolase_3 Abhydrolase_4 Abhydrolase_5 Abhydrolase_6 Abhydrolase_7 Abhydrolase_8 Abhydrolase_9 Acyl_transf_2 Asp2 AXE1 BAAT_C Chlorophyllase Chlorophyllase2 COesterase Cutinase DLH DUF1057 DUF1100 DUF1350 DUF1400 DUF1749 DUF2048 DUF2235 DUF2920 DUF2974 DUF3089 DUF3141 DUF3530 DUF452 DUF676 DUF726 DUF818 DUF829 DUF900 DUF915 EHN Esterase Esterase_phd FSH1 Hydrolase_4 LCAT LIDHydrolase LIP Lipase Lipase3_N Lipase_2 Lipase_3 Ndr PAE PAF-AH_p_II Palm_thioest PE-PPE Peptidase_S10 Peptidase_S15 Peptidase_S28 Peptidase_S37 Peptidase_S9 PGAP1 PhaC_N PHB_depo_C PhoPQ_related Say1_Mug180 Ser_hydrolase Tannase Thioesterase UPF0227 VirJ
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:
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- the alignment generated by searching the sequence database using the HMM
- 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 can download (or view in your browser) a text representation of a Pfam alignment in various formats:
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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:||15|
|Number in full:||3992|
|Average length of the domain:||185.80 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||67.40 %|
|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:||22|
|Download:||download the raw HMM for this family|
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- 0 sequences
- 0 species
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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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There is 1 interaction 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 Cutinase domain has been found. There are 100 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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