Summary: Colipase, N-terminal domain

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Wikipedia: Colipase
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Colipase Edit Wikipedia article

Colipase, pancreatic

Cartoon diagram of pig colipase (blue) in complex with human pancreatic lipase and a small molecule inhibitor. From PDB 1LPB.

Identifiers

Symbol

CLPS

External IDs

OMIM: 120105 MGI: 88421 HomoloGene: 1383 GeneCards: CLPS Gene

Gene Ontology
Molecular function	• enzyme activator activity
Cellular component	• extracellular region
Biological process	• retinoid metabolic process • lipid metabolic process • steroid metabolic process • post-embryonic development • lipid catabolic process • response to food • lipid digestion • small molecule metabolic process
Sources: Amigo / QuickGO

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 6:
35.76 – 35.77 Mb

Chr 17:
28.56 – 28.56 Mb

PubMed search

[1]

[2]

Colipase is a protein co-enzyme required for optimal enzyme activity of pancreatic lipase. It is secreted by the pancreas in an inactive form, procolipase, which is activated in the intestinal lumen by trypsin. Its function is to prevent the inhibitory effect of bile salts on the lipase-catalyzed intraduodenal hydrolysis of dietary long-chain triglycerides.

In humans, the colipase protein is encoded by the CLPS gene.^[1]

[edit] Protein domain

Colipase is also a family of evolutionarily related proteins.

Colipase is a small protein cofactor needed by pancreatic lipase for efficient dietary lipid hydrolyisis. Efficient absorption of dietary fats is dependent on the action of pancreatic triglyceride lipase. Colipase binds to the C-terminal, non-catalytic domain of lipase, thereby stabilising an active conformation and considerably increasing the hydrophobicity binding site. Structural studies of the complex and of colipase alone have revealed the functionality of its architecture.^[2]^[3]

Colipase is a small protein with five conserved disulphide bonds. Structural analogies have been recognised between a developmental protein (Dickkopf), the pancreatic lipase C-terminal domain, the N-terminal domains of lipoxygenases and the C-terminal domain of alpha-toxin. These non-catalytic domains in the latter enzymes are important for interaction with membrane. It has not been established if these domains are also involved in eventual protein cofactor binding as is the case for pancreatic lipase.^[3]

Colipase N-terminal domain

Structure of the pancreatic lipase-colipase complex inhibited by a C11 alkyl phosphonate.^[4]

Identifiers

Symbol

Colipase

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Colipase C-terminal domain

solution structure of porcine pancreatic procolipase as determined from 1h homonuclear two-and three-dimensional nmr

Identifiers

Symbol

Colipase_C

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

[edit] See also

Enterostatin

[edit] References

^ Davis RC, Xia YR, Mohandas T, Schotz MC, Lusis AJ (May 1991). "Assignment of the human pancreatic colipase gene to chromosome 6p21.1 to pter". Genomics 10 (1): 262–5. doi:10.1016/0888-7543(91)90509-D. PMID 2045105.
^ Lowe ME (1997). "Structure and function of pancreatic lipase and colipase". Annu. Rev. Nutr. 17: 141–158. doi:10.1146/annurev.nutr.17.1.141. PMID 9240923.
^ ^a ^b Verger R, van Tilbeurgh H, Cambillau C, Bezzine S, Carriere F (1999). "Colipase: structure and interaction with pancreatic lipase". Biochim. Biophys. Acta 1441 (2–3): 173–184. PMID 10570245.
^ Egloff MP, Marguet F, Buono G, Verger R, Cambillau C, van Tilbeurgh H (March 1995). "The 2.46 A resolution structure of the pancreatic lipase-colipase complex inhibited by a C11 alkyl phosphonate". Biochemistry 34 (9): 2751–62. doi:10.1021/bi00009a003. PMID 7893686.

[edit] Further reading

Weyrich P, Albet S, Lammers R, et al. (2009). "Genetic variability of procolipase associates with altered insulin secretion in non-diabetic Caucasians". Exp. Clin. Endocrinol. Diabetes 117 (2): 83–7. doi:10.1055/s-2008-1078733. PMID 18726866.
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.
Miled N, Canaan S, Dupuis L, et al. (2000). "Digestive lipases: from three-dimensional structure to physiology". Biochimie 82 (11): 973–86. doi:10.1016/S0300-9084(00)01179-2. PMID 11099794.
van Tilbeurgh H, Egloff MP, Martinez C, et al. (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.
Wermter AK, Scherag A, Holter K, et al. (2009). "Procolipase gene: no association with early-onset obesity or fat intake". Obes Facts 2 (1): 40–4. doi:10.1159/000196379. PMID 20054203.
Lindner I, Helwig U, Rubin D, et al. (2005). "Putative association between a new polymorphism in exon 3 (Arg109Cys) of the pancreatic colipase gene and type 2 diabetes mellitus in two independent Caucasian study populations". Mol Nutr Food Res 49 (10): 972–6. doi:10.1002/mnfr.200500087. PMID 16189801.
Sims HF, Lowe ME (1992). "The human colipase gene: isolation, chromosomal location, and tissue-specific expression". Biochemistry 31 (31): 7120–5. doi:10.1021/bi00146a013. PMID 1643046.
Lowe ME, Rosenblum JL, McEwen P, Strauss AW (1990). "Cloning and characterization of the human colipase cDNA". Biochemistry 29 (3): 823–8. doi:10.1021/bi00455a032. PMID 2337598.
van Tilbeurgh H, Bezzine S, Cambillau C, et al. (1999). "Colipase: structure and interaction with pancreatic lipase". Biochim. Biophys. Acta 1441 (2–3): 173–84. PMID 10570245.
D'Silva S, Xiao X, Lowe ME (2007). "A polymorphism in the gene encoding procolipase produces a colipase, Arg92Cys, with decreased function against long-chain triglycerides". J. Lipid Res. 48 (11): 2478–84. doi:10.1194/jlr.M700371-JLR200. PMID 17715423.
Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121–7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334. //www.ncbi.nlm.nih.gov/pmc/articles/PMC528928/.
Sternby B, Engström A, Hellman U, et al. (1984). "The primary sequence of human pancreatic colipase". Biochim. Biophys. Acta 784 (1): 75–80. doi:10.1016/0167-4838(84)90175-4. PMID 6691986.
Sias B, Ferrato F, Grandval P, et al. (2004). "Human pancreatic lipase-related protein 2 is a galactolipase". Biochemistry 43 (31): 10138–48. doi:10.1021/bi049818d. PMID 15287741.
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.
Strausberg RL, Feingold EA, Grouse LH, et al. (2002). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932. //www.ncbi.nlm.nih.gov/pmc/articles/PMC139241/.
Sugar IP, Mizuno NK, Momsen MM, et al. (2003). "Regulation of lipases by lipid-lipid interactions: implications for lipid-mediated signaling in cells". Chem. Phys. Lipids 122 (1–2): 53–64. doi:10.1016/S0009-3084(02)00178-0. PMID 12598038.
van Tilbeurgh H, Sarda L, Verger R, Cambillau C (1992). "Structure of the pancreatic lipase-procolipase complex". Nature 359 (6391): 159–62. doi:10.1038/359159a0. PMID 1522902.
Davis RC, Xia YR, Mohandas T, et al. (1991). "Assignment of the human pancreatic colipase gene to chromosome 6p21.1 to pter". Genomics 10 (1): 262–5. doi:10.1016/0888-7543(91)90509-D. PMID 2045105.

[edit] External links

Colipases at the US National Library of Medicine Medical Subject Headings (MeSH)

This article incorporates text from the public domain Pfam and InterPro IPR001981

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Colipase, N-terminal domain Provide feedback

SCOP reports duplication of common fold with Colipase C-terminal domain.

External database links

PANDIT:	PF01114
PROSITE:	PDOC00111
Pseudofam:	PF01114
SCOP:	1lpb
SYSTERS:	Colipase

This tab holds annotation information from the InterPro database.

InterPro entry IPR017913

This entry represents the N-terminal domain of colipase proteins. Colipase [PUBMED:1567900, PUBMED:3147715] is a small protein cofactor needed by pancreatic lipase for efficient dietary lipid hydrolyisis. It also binds to the bile-salt covered triacylglycerol interface, thus allowing the enzyme to anchor itself to the water-lipid interface. Efficient absorption of dietary fats is dependent on the action of pancreatic triglyceride lipase. Colipase binds to the C-terminal, non-catalytic domain of lipase, thereby stabilising as active conformation and considerably increasing the overall hydrophobic binding site. Structural studies of the complex and of colipase alone have revealed the functionality of its architecture [PUBMED:9240923, PUBMED:10570245].

Colipase is a small protein with five conserved disulphide bonds. Structural analogies have been recognised between a developmental protein (Dickkopf), the pancreatic lipase C-terminal domain, the N-terminal domains of lipoxygenases and the C-terminal domain of alpha-toxin. These non-catalytic domains in the latter enzymes are important for interaction with membrane. It has not been established if these domains are also involved in eventual protein cofactor binding as is the case for pancreatic lipase [PUBMED:10570245].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Cellular component	extracellular region (GO:0005576)
Molecular function	enzyme activator activity (GO:0008047)
Biological process	lipid catabolic process (GO:0016042)
Biological process	digestion (GO:0007586)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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PP/Heatmap: 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.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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Downloading

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.

View options

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.

	Seed (9)	Full (50)	Representative proteomes				NCBI (47)	Meta (0)
	Seed (9)	Full (50)	RP15 (3)	RP35 (3)	RP55 (7)	RP75 (28)	NCBI (47)	Meta (0)
Jalview	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (9)	Full (50)	Representative proteomes				NCBI (47)	Meta (0)
	Seed (9)	Full (50)	RP15 (3)	RP35 (3)	RP55 (7)	RP75 (28)	NCBI (47)	Meta (0)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

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.

	Seed (9)	Full (50)	Representative proteomes				NCBI (47)	Meta (0)
	Seed (9)	Full (50)	RP15 (3)	RP35 (3)	RP55 (7)	RP75 (28)	NCBI (47)	Meta (0)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

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...

Trees

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.

Curation

Seed source:

Prosite

Previous IDs:

none

Type:

Domain

Author:

Finn RD, Bateman A, Griffiths-Jones SR

Number in seed:

9

Number in full:

50

Average length of the domain:

39.20 aa

Average identity of full alignment:

63 %

Average coverage of the sequence by the domain:

37.13 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	19.4	19.4
Trusted cut-off	19.6	24.9
Noise cut-off	19.1	17.1

Model length:

40

Family (HMM) version:

13

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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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 adjacent tab. 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:

superkingdom
kingdom
phylum
class
order
family
genus
species

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.

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Missing taxonomic levels

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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".

Sub-species

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.

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Species trees

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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.

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Interactive tree

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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Interactions

There are 3 interactions for this family. More...

Lipase PLAT Colipase_C

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 Colipase domain has been found. There are 7 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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Colipase (PF01114)

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Summary: Colipase, N-terminal domain

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Colipase Edit Wikipedia article

Contents

[edit] Protein domain

[edit] See also

[edit] References

[edit] Further reading

[edit] External links

Colipase, N-terminal domain Provide feedback

External database links

InterPro entry IPR017913

Gene Ontology

Domain organisation

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures