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This is the Wikipedia entry entitled "Pancreatic lipase family". More...
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Pancreatic lipase family Edit Wikipedia article
At least three tissue-specific isozymes exist in higher vertebrates, pancreatic, hepatic and gastric/lingual. These lipases are closely related to each other and to lipoprotein lipase (EC 18.104.22.168), which hydrolyses triglycerides of chylomicrons and very low density lipoproteins (VLDL).
The most conserved region in all these proteins is centred on a serine residue which has been shown to participate, with an histidine and an aspartic acid residue, in a charge relay system. Such a region is also present in lipases of prokaryotic origin and in lecithin-cholesterol acyltransferase (EC 22.214.171.124) (LCAT), which catalyzes fatty acid transfer between phosphatidylcholine and cholesterol.
Human pancreatic lipase
Pancreatic lipase, also known as pancreatic triacylglycerol lipase, is an enzyme secreted from the pancreas. As the primary lipase enzyme that hydrolyzes (breaks down) dietary fat molecules in the human digestive system, it is one of the main digestive enzymes, converting triglyceride substrates found in ingested oils to monoglycerides and free fatty acids.
- Triacylglycerol + 2 H2O 2-monoacylglycerol + 2 fatty acid anions
Bile salts secreted from the liver and stored in gallbladder are released into the duodenum, where they coat and emulsify large fat droplets into smaller droplets, thus increasing the overall surface area of the fat, which allows the lipase to break apart the fat more effectively. The resulting monomers (2 free fatty acids and one 2-monoacylglycerol) are then moved by way of peristalsis along the small intestine to be absorbed into the lymphatic system by a specialized vessel called a lacteal. This protein belongs to the pancreatic lipase family.
Unlike some pancreatic enzymes that are activated by proteolytic cleavage (e.g., trypsinogen), pancreatic lipase is secreted in its final form. However, it becomes efficient only in the presence of colipase in the duodenum.
Human proteins containing this domain
Pancreatic lipase is secreted into the duodenum through the duct system of the pancreas. Its concentration in serum is normally very low. Under extreme disruption of pancreatic function, such as pancreatitis or pancreatic adenocarcinoma, the pancreas may begin to autolyse and release pancreatic enzymes including pancreatic lipase into serum. Thus, through measurement of serum concentration of pancreatic lipase, acute pancreatitis can be diagnosed.
One peptide selected by phage display was found to inhibit pancreatic lipase.
- Chapus C, Rovery M, Sarda L, Verger R (1988). "Minireview on pancreatic lipase and colipase". Biochimie 70 (9): 1223–1234. doi:10.1016/0300-9084(88)90188-5. PMID 3147715.
- Persson B, Bengtsson-Olivecrona G, Enerback S, Olivecrona T, Jornvall H (1989). "Structural features of lipoprotein lipase. Lipase family relationships, binding interactions, non-equivalence of lipase cofactors, vitellogenin similarities and functional subdivision of lipoprotein lipase". Eur. J. Biochem. 179 (1): 39–45. doi:10.1111/j.1432-1033.1989.tb14518.x. PMID 2917565.
- Blow D (1990). "Enzymology. More of the catalytic triad". Nature 343 (6260): 694–695. doi:10.1038/343694a0. PMID 2304545.
- McLean J, Fielding C, Drayna D, Dieplinger H, Baer B, Kohr W, Henzel W, Lawn R (1986). "Cloning and expression of human lecithin-cholesterol acyltransferase cDNA". Proc. Natl. Acad. Sci. U.S.A. 83 (8): 2335–2339. doi:10.1073/pnas.83.8.2335. PMC 323291. PMID 3458198.
- Davis RC, Diep A, Hunziker W, Klisak I, Mohandas T, Schotz MC, Sparkes RS, Lusis AJ (December 1991). "Assignment of human pancreatic lipase gene (PNLIP) to chromosome 10q24-q26". Genomics 11 (4): 1164–6. doi:10.1016/0888-7543(91)90048-J. PMID 1783385.
- "Entrez Gene: pancreatic lipase".
- Koop H (September 1984). "Serum levels of pancreatic enzymes and their clinical significance". Clin Gastroenterol 13 (3): 739–61. PMID 6207965.
- Lunder, M., Bratkovič, T., Kreft, S., Štrukelj, B. (2005). Peptide inhibitor of pancreatic lipase selected by phage display using different elution strategies. Journal of Lipid Research, 46:1512-1516 http://www.jlr.org/content/46/7/1512.long
- Roussel A, Yang Y, Ferrato F, Verger R, Cambillau C, Lowe M (November 1998). "Structure and activity of rat pancreatic lipase-related protein 2". J. Biol. Chem. 273 (48): 32121–8. doi:10.1074/jbc.273.48.32121. PMID 9822688.
- Crandall WV, Lowe ME (2001). "Colipase residues Glu64 and Arg65 are essential for normal lipase-mediated fat digestion in the presence of bile salt micelles". J. Biol. Chem. 276 (16): 12505–12. doi:10.1074/jbc.M009986200. PMID 11278590.
- Freie AB, Ferrato F, Carrière F, Lowe ME (2006). "Val-407 and Ile-408 in the beta5'-loop of pancreatic lipase mediate lipase-colipase interactions in the presence of bile salt micelles". J. Biol. Chem. 281 (12): 7793–800. doi:10.1074/jbc.M512984200. PMC 3695395. PMID 16431912.
- Hegele RA, Ramdath DD, Ban MR, Carruthers MN, Carrington CV, Cao H (2001). "Polymorphisms in PNLIP, encoding pancreatic lipase, and associations with metabolic traits". J. Hum. Genet. 46 (6): 320–4. doi:10.1007/s100380170066. PMID 11393534.
- Chahinian H, Sias B, Carrière F (2000). "The C-terminal domain of pancreatic lipase: functional and structural analogies with c2 domains". Curr. Protein Pept. Sci. 1 (1): 91–103. PMID 12369922.
- Ranaldi S, Belle V, Woudstra M, Rodriguez J, Guigliarelli B, Sturgis J, Carriere F, Fournel A (2009). "Lid opening and unfolding in human pancreatic lipase at low pH revealed by site-directed spin labeling EPR and FTIR spectroscopy". Biochemistry 48 (3): 630–8. doi:10.1021/bi801250s. PMID 19113953.
- Grupe A, Li Y, Rowland C, Nowotny P, Hinrichs AL, Smemo S, Kauwe JS, Maxwell TJ, Cherny S, Doil L, Tacey K, van Luchene R, Myers A, Wavrant-De Vrièze F, Kaleem M, Hollingworth P, Jehu L, Foy C, Archer N, Hamilton G, Holmans P, Morris CM, Catanese J, Sninsky J, White TJ, Powell J, Hardy J, O'Donovan M, Lovestone S, Jones L, Morris JC, Thal L, Owen M, Williams J, Goate A (2006). "A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease". Am. J. Hum. Genet. 78 (1): 78–88. doi:10.1086/498851. PMC 1380225. PMID 16385451.
- Thomas A, Allouche M, Basyn F, Brasseur R, Kerfelec B (2005). "Role of the lid hydrophobicity pattern in pancreatic lipase activity". J. Biol. Chem. 280 (48): 40074–83. doi:10.1074/jbc.M502123200. PMID 16179352.
- van Tilbeurgh H, Egloff MP, Martinez C, Rugani N, Verger R, Cambillau C (1993). "Interfacial activation of the lipase-procolipase complex by mixed micelles revealed by X-ray crystallography". Nature 362 (6423): 814–20. doi:10.1038/362814a0. PMID 8479519.
- Lessinger JM, Arzoglou P, Ramos P, Visvikis A, Parashou S, Calam D, Profilis C, Férard G (2003). "Preparation and characterization of reference materials for human pancreatic lipase: BCR 693 (from human pancreatic juice) and BCR 694 (recombinant)". Clin. Chem. Lab. Med. 41 (2): 169–76. doi:10.1515/CCLM.2003.028. PMID 12667003.
- Colin DY, Deprez-Beauclair P, Allouche M, Brasseur R, Kerfelec B (2008). "Exploring the active site cavity of human pancreatic lipase". Biochem. Biophys. Res. Commun. 370 (3): 394–8. doi:10.1016/j.bbrc.2008.03.043. PMID 18353248.
- Ramos P, Coste T, Piémont E, Lessinger JM, Bousquet JA, Chapus C, Kerfelec B, Férard G, Mély Y (2003). "Time-resolved fluorescence allows selective monitoring of Trp30 environmental changes in the seven-Trp-containing human pancreatic lipase". Biochemistry 42 (43): 12488–96. doi:10.1021/bi034900e. PMID 14580194.
- Yang Y, Lowe ME (1998). "Human pancreatic triglyceride lipase expressed in yeast cells: purification and characterization". Protein Expr. Purif. 13 (1): 36–40. doi:10.1006/prep.1998.0874. PMID 9631512.
- Sims HF, Jennens ML, Lowe ME (1993). "The human pancreatic lipase-encoding gene: structure and conservation of an Alu sequence in the lipase gene family". Gene 131 (2): 281–5. doi:10.1016/0378-1119(93)90307-O. PMID 8406023.
- Grandval P, De Caro A, De Caro J, Sias B, Carrière F, Verger R, Laugier R (2004). "Critical evaluation of a specific ELISA and two enzymatic assays of pancreatic lipases in human sera". Pancreatology 4 (6): 495–503; discussion 503–4. doi:10.1159/000080246. PMID 15316225.
- Belle V, Fournel A, Woudstra M, Ranaldi S, Prieri F, Thomé V, Currault J, Verger R, Guigliarelli B, Carrière F (2007). "Probing the opening of the pancreatic lipase lid using site-directed spin labeling and EPR spectroscopy". Biochemistry 46 (8): 2205–14. doi:10.1021/bi0616089. PMID 17269661.
- Lowe ME (1997). "Structure and function of pancreatic lipase and colipase". Annu. Rev. Nutr. 17: 141–58. doi:10.1146/annurev.nutr.17.1.141. PMID 9240923.
- Bourbon-Freie A, Dub RE, Xiao X, Lowe ME (2009). "Trp-107 and trp-253 account for the increased steady state fluorescence that accompanies the conformational change in human pancreatic triglyceride lipase induced by tetrahydrolipstatin and bile salt". J. Biol. Chem. 284 (21): 14157–64. doi:10.1074/jbc.M901154200. PMC 2682864. PMID 19346257.
- Ranaldi S, Belle V, Woudstra M, Bourgeas R, Guigliarelli B, Roche P, Vezin H, Carrière F, Fournel A (2010). "Amplitude of pancreatic lipase lid opening in solution and identification of spin label conformational subensembles by combining continuous wave and pulsed EPR spectroscopy and molecular dynamics". Biochemistry 49 (10): 2140–9. doi:10.1021/bi901918f. PMID 20136147.
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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.
Lipase Provide feedback
No Pfam abstract.
Internal database links
|SCOOP:||Lipase_3 DUF726 DUF900 VirJ LIDHydrolase Abhydrolase_6|
|Similarity to PfamA using HHSearch:||Abhydrolase_1 Abhydrolase_6|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR013818
This entry represents a domain usually found in the N-terminal of the lipase family members.
Triglyceride lipases (EC) are lipolytic enzymes that hydrolyse ester linkages of triglycerides [PUBMED:3147715]. Lipases are widely distributed in animals, plants and prokaryotes. At least three tissue-specific isozymes exist in higher vertebrates, pancreatic, hepatic and gastric/lingual. These lipases are closely related to each other and to lipoprotein lipase (EC), which hydrolyses triglycerides of chylomicrons and very low density lipoproteins (VLDL) [PUBMED:2917565]. The most conserved region in all these proteins is centred around a serine residue which has been shown [PUBMED:2304545] to participate, with an histidine and an aspartic acid residue, in a charge relay system. Such a region is also present in lipases of prokaryotic origin and in lecithin-cholesterol acyltransferase (EC) (LCAT) [PUBMED:3458198], which catalyzes fatty acid transfer between phosphatidylcholine and cholesterol.
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 66 members:Abhydro_lipase Abhydrolase_1 Abhydrolase_2 Abhydrolase_3 Abhydrolase_4 Abhydrolase_5 Abhydrolase_6 Abhydrolase_7 Abhydrolase_8 Acyl_transf_2 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 Lipase_2 Lipase_3 Ndr 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:
- the curated alignment from which the HMM for the family is built
- 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:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
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...
If you find these logos useful in your own work, please consider citing the following article:
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.
Note: You can also download the data file for the tree.
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:||Sonnhammer ELL, Griffiths-Jones SR|
|Number in seed:||12|
|Number in full:||1995|
|Average length of the domain:||266.70 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||69.45 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 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.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
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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 are 5 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 Lipase domain has been found. There are 16 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 seqence.
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