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44  structures 26  species 1  interaction 38  sequences 1  architecture

Family: ApoA-II (PF04711)

Summary: Apolipoprotein A-II (ApoA-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 "APOA2". More...

APOA2 Edit Wikipedia article

Apolipoprotein A-II

Rendering of 1L6L
Available structures
PDB Ortholog search: PDBe, RCSB
Identifiers
Symbols APOA2; Apo-AII; ApoA-II; apoAII
External IDs OMIM107670 MGI88050 HomoloGene1242 GeneCards: APOA2 Gene
RNA expression pattern
PBB GE APOA2 219466 s at tn.png
PBB GE APOA2 219465 at tn.png
More reference expression data
Orthologs
Species Human Mouse
Entrez 336 11807
Ensembl ENSG00000158874 ENSMUSG00000005681
UniProt P02652 P09813
RefSeq (mRNA) NM_001643 NM_013474
RefSeq (protein) NP_001634 NP_038502
Location (UCSC) Chr 1:
161.19 – 161.19 Mb
Chr 1:
171.23 – 171.23 Mb
PubMed search [1] [2]
ApoA-II
PDB 1l6l EBI.jpg
structures of apolipoprotein a-ii and a lipid surrogate complex provide insights into apolipoprotein-lipid interactions
Identifiers
Symbol ApoA-II
Pfam PF04711
InterPro IPR006801
SCOP 1l6k
SUPERFAMILY 1l6k

Apolipoprotein A-II is a protein that in humans is encoded by the APOA2 gene.[1]

Function[edit]

This gene encodes apolipoprotein (apo-) A-II, which is the second most abundant protein of the high density lipoprotein particles. The protein is found in plasma as a monomer, homodimer, or heterodimer with apolipoprotein D. Defects in this gene may result in apolipoprotein A-II deficiency or hypercholesterolemia.[2]

Interactions[edit]

APOA2 has been shown to interact with PLTP.[3]

Interactive pathway map[edit]

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

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Statin_Pathway_WP430 go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article
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Statin Pathway edit
  1. ^ The interactive pathway map can be edited at WikiPathways: "Statin_Pathway_WP430". 

References[edit]

  1. ^ Tsao YK, Wei CF, Robberson DL, Gotto AM Jr, Chan L (Jan 1986). "Isolation and characterization of the human apolipoprotein A-II gene. Electron microscopic analysis of RNA:DNA hybrids, nucleotide sequence, identification of a polymorphic MspI site, and general structural organization of apolipoprotein genes". J Biol Chem 260 (28): 15222–31. PMID 2415515. 
  2. ^ "Entrez Gene: APOA2 apolipoprotein A-II". 
  3. ^ Pussinen PJ, Jauhiainen M, Metso J, Pyle LE, Marcel YL, Fidge NH, Ehnholm C (January 1998). "Binding of phospholipid transfer protein (PLTP) to apolipoproteins A-I and A-II: location of a PLTP binding domain in the amino terminal region of apoA-I". J. Lipid Res. 39 (1): 152–61. PMID 9469594. 

Further reading[edit]

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 A-II (ApoA-II) Provide feedback

Apolipoprotein A-II (ApoA-II) is the second major apolipoprotein of high density lipoprotein in human plasma. Mature ApoA-II is present as a dimer of two 77-amino acid chains joined by a disulphide bridge [1]. ApoA-II regulates many steps in HDL metabolism, and its role in coronary heart disease is unclear [1]. In bovine serum, the ApoA-II homologue is present in almost free form. Bovine ApoA-II shows antimicrobial activity against Escherichia coli and yeasts in phosphate buffered saline (PBS) [2].

Literature references

  1. Tailleux A, Duriez P, Fruchart JC, Clavey V; , Atherosclerosis 2002;164:1-13.: Apolipoprotein A-II, HDL metabolism and atherosclerosis. PUBMED:12119188 EPMC:12119188

  2. Motizuki M, Itoh T, Yamada M, Shimamura S, Tsurugi K; , J Biochem (Tokyo) 1998;123:675-679.: Purification, primary structure, and antimicrobial activities of bovine apolipoprotein A-II. PUBMED:9538260 EPMC:9538260


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006801

Apolipoprotein A-II (ApoA-II) is the second major apolipoprotein of high density lipoprotein in human plasma. Mature ApoA-II is present as a dimer of two 77-amino acid chains joined by a disulphide bridge [PUBMED:12119188]. ApoA-II regulates many steps in HDL metabolism, and its role in coronary heart disease is unclear [PUBMED:12119188]. In bovine serum, the ApoA-II homologue is present in almost free form. Bovine ApoA-II shows antimicrobial activity against Escherichia coli and yeasts in phosphate buffered saline (PBS) [PUBMED:9538260].

Gene Ontology

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

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...

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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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(5)
Full
(38)
Representative proteomes NCBI
(41)
Meta
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(1)
RP35
(1)
RP55
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RP75
(15)
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Key: ✓ available, x not generated, not available.

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  Seed
(5)
Full
(38)
Representative proteomes NCBI
(41)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(1)
RP75
(15)
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
(5)
Full
(38)
Representative proteomes NCBI
(41)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(1)
RP75
(15)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
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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.

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 View help on the curation process

Seed source: DOMO:DM04862;
Previous IDs: none
Type: Family
Author: Kerrison ND
Number in seed: 5
Number in full: 38
Average length of the domain: 73.20 aa
Average identity of full alignment: 61 %
Average coverage of the sequence by the domain: 73.18 %

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 24.3 24.3
Trusted cut-off 24.7 24.7
Noise cut-off 23.8 24.0
Model length: 76
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

ApoA-II

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 ApoA-II domain has been found. There are 44 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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