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4  structures 29  species 0  interactions 40  sequences 1  architecture

Family: Apo-CII (PF05355)

Summary: Apolipoprotein C-II

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Apolipoprotein C2". More...

Apolipoprotein C2 Edit Wikipedia article

Apolipoprotein C-II

PDB rendering based on 1by6.
Available structures
PDB Ortholog search: PDBe, RCSB
Identifiers
Symbols APOC2; APO-CII; APOC-II
External IDs OMIM608083 MGI88054 HomoloGene47928 GeneCards: APOC2 Gene
Orthologs
Species Human Mouse
Entrez 344 11813
Ensembl ENSG00000224916 ENSMUSG00000002992
UniProt P02655 Q05020
RefSeq (mRNA) NM_000483 NM_009695
RefSeq (protein) NP_000474 NP_033825
Location (UCSC) Chr 19:
45.45 – 45.45 Mb
Chr 7:
19.67 – 19.68 Mb
PubMed search [1] [2]
Apo-CII
PDB 1i5j EBI.jpg
nmr structure of human apolipoprotein c-ii in the presence of sds
Identifiers
Symbol Apo-CII
Pfam PF05355
InterPro IPR008019
SCOP 1by6
SUPERFAMILY 1by6

Apolipoprotein C2 or Apolipoprotein C-II is a protein that in humans is encoded by the APOC2 gene.

The protein encoded by this gene is secreted in plasma where it is a component of very low density lipoproteins and chylomicrons. This protein activates the enzyme lipoprotein lipase in capillaries,[1] which hydrolyzes triglycerides and thus provides free fatty acids for cells. Mutations in this gene cause hyperlipoproteinemia type IB, characterized by xanthomas, pancreatitis, and hepatosplenomegaly, but no increased risk for atherosclerosis. Lab tests will show elevated blood levels of triglycerides, cholesterol, and chylomicrons[2]

[edit] Interactive pathway map

Click on genes, proteins and metabolites below to link to respective articles. [§ 1]

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Statin Pathway edit
  1. ^ The interactive pathway map can be edited at WikiPathways: "Statin_Pathway_WP430". http://www.wikipathways.org/index.php/Pathway:WP430.

[edit] See also

[edit] References

  1. ^ Kim SY, Park SM, Lee ST (2006). "Apolipoprotein C-II is a novel substrate for matrix metalloproteinases". Biochem. Biophys. Res. Commun. 339 (1): 47–54. doi:10.1016/j.bbrc.2005.10.182. PMID 16314153.
  2. ^ "Entrez Gene: APOC2 apolipoprotein C-II". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=344.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Apolipoprotein C-II Provide feedback

Apolipoprotein C-II (ApoC-II) is the major activator of lipoprotein lipase, a key enzyme in the regulation of triglyceride levels in human serum [1].

Literature references

  1. Storjohann R, Rozek A, Sparrow JT, Cushley RJ; , Biochim Biophys Acta 2000;1486:253-264.: Structure of a biologically active fragment of human serum apolipoprotein C-II in the presence of sodium dodecyl sulfate and dodecylphosphocholine. PUBMED:10903476 EPMC:10903476


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008019

Apolipoprotein CII (apoC-II) is a surface constituent of plasma lipoproteins and the activator for lipoprotein lipase (LPL). It is therefore central for lipid transport in blood. Lipoprotein lipase is a key enzyme in the regulation of triglyceride levels in human serum [PUBMED:10903476]. It is the C-terminal helix of apoC-II that is responsible for the activation of LPL [PUBMED:12590574]. The active peptide of apoC-II occurs at residues 44-79 and has been shown to reverse the symptoms of genetic apoC-II deficiency in a human subject [PUBMED:10903476].

Micellar SDS, a commonly used mimetic of the lipoprotein surface, inhibits the aggregation of apoC-II and induces a stable structure containing approximately 60% alpha-helix. The first 12 residues of apoC-II are structurally heterogeneous but the rest of the protein forms a predominantly helical structure [PUBMED:11331005].

Gene Ontology

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

Domain organisation

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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...

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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.

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(6)
Full
(40)
Representative proteomes NCBI
(42)
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(1)
RP35
(2)
RP55
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RP75
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  Seed
(6)
Full
(40)
Representative proteomes NCBI
(42)
Meta
(0)
RP15
(1)
RP35
(2)
RP55
(6)
RP75
(19)
Alignment:
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Sequence:
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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
(6)
Full
(40)
Representative proteomes NCBI
(42)
Meta
(0)
RP15
(1)
RP35
(2)
RP55
(6)
RP75
(19)
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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.

Pfam alignments:

HMM logo

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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 View help on the curation process

Seed source: Pfam-B_6456 (release 7.8)
Previous IDs: none
Type: Family
Author: Finn RD
Number in seed: 6
Number in full: 40
Average length of the domain: 73.00 aa
Average identity of full alignment: 46 %
Average coverage of the sequence by the domain: 75.96 %

HMM information View help on HMM parameters

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 22.1 22.1
Trusted cut-off 22.1 24.5
Noise cut-off 18.8 21.9
Model length: 78
Family (HMM) version: 6
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 Apo-CII domain has been found. There are 4 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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