Summary: Apolipoprotein A-II (ApoA-II)

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Wikipedia: APOA2
Pfam
InterPro

This is the Wikipedia entry entitled "APOA2". More...

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APOA2 Edit Wikipedia article

Apolipoprotein A-II

Rendering of 1L6L

Available structures

PDB

Ortholog search: PDBe, RCSB

List of PDB id codes
1L6L, 2OU1

Identifiers

Symbols

APOA2; Apo-AII; ApoA-II; apoAII

External IDs

OMIM: 107670 MGI: 88050 HomoloGene: 1242 GeneCards: APOA2 Gene

Gene Ontology
Molecular function	• lipid transporter activity • protein binding • phospholipid binding • high-density lipoprotein particle binding • lipid binding • cholesterol binding • cholesterol transporter activity • phosphatidylcholine binding • apolipoprotein receptor binding • protein homodimerization activity • protein heterodimerization activity • lipase inhibitor activity • phosphatidylcholine-sterol O-acyltransferase activator activity • high-density lipoprotein particle receptor binding
Cellular component	• extracellular region • endoplasmic reticulum lumen • very-low-density lipoprotein particle • high-density lipoprotein particle • spherical high-density lipoprotein particle • chylomicron
Biological process	• acute inflammatory response • negative regulation of cytokine secretion involved in immune response • protein folding • lipid metabolic process • triglyceride metabolic process • phosphatidylcholine biosynthetic process • cholesterol metabolic process • phospholipid catabolic process • response to glucose stimulus • positive regulation of cholesterol esterification • negative regulation of very-low-density lipoprotein particle remodeling • protein oxidation • peptidyl-methionine modification • virus-host interaction • regulation of intestinal cholesterol absorption • organ regeneration • regulation of protein stability • negative regulation of cholesterol transport • cholesterol efflux • phospholipid efflux • triglyceride-rich lipoprotein particle remodeling • low-density lipoprotein particle remodeling • high-density lipoprotein particle remodeling • high-density lipoprotein particle assembly • high-density lipoprotein particle clearance • lipoprotein metabolic process • response to drug • cholesterol homeostasis • response to estrogen stimulus • reverse cholesterol transport • cellular lipid metabolic process • small molecule metabolic process • positive regulation of interleukin-8 biosynthetic process • diacylglycerol catabolic process • negative regulation of lipid catabolic process • positive regulation of lipid catabolic process • response to glucocorticoid stimulus • negative regulation of lipase activity • negative regulation of cholesterol import • negative regulation of cholesterol transporter activity
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 1:
161.19 – 161.19 Mb

Chr 1:
171.23 – 171.23 Mb

PubMed search

[1]

[2]

ApoA-II

structures of apolipoprotein a-ii and a lipid surrogate complex provide insights into apolipoprotein-lipid interactions

Identifiers

Symbol

ApoA-II

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

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

[edit] Function

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]

[edit] Interactions

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

[edit] Interactive pathway map

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

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Statin Pathway edit

^ The interactive pathway map can be edited at WikiPathways: "Statin_Pathway_WP430".

[edit] References

^ 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.
^ "Entrez Gene: APOA2 apolipoprotein A-II".
^ 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.

[edit] Further reading

Blanco-Vaca F, Escolà-Gil JC, Martín-Campos JM, Julve J (2002). "Role of apoA-II in lipid metabolism and atherosclerosis: advances in the study of an enigmatic protein.". J. Lipid Res. 42 (11): 1727–39. PMID 11714842.
Kalopissis AD, Pastier D, Chambaz J (2003). "Apolipoprotein A-II: beyond genetic associations with lipid disorders and insulin resistance.". Curr. Opin. Lipidol. 14 (2): 165–72. doi:10.1097/01.mol.0000064047.08840.50. PMID 12642785.
Vollmer E, Brust J, Roessner A, et al. (1991). "Distribution patterns of apolipoproteins A1, A2, and B in the wall of atherosclerotic vessels.". Virchows Archiv. A, Pathological anatomy and histopathology 419 (2): 79–88. doi:10.1007/BF01600220. PMID 1908160.
Deeb SS, Takata K, Peng RL, et al. (1990). "A splice-junction mutation responsible for familial apolipoprotein A-II deficiency.". Am. J. Hum. Genet. 46 (4): 822–7. PMC 1683675. PMID 2107739.
Gordon JI, Sims HF, Edelstein C, et al. (1985). "Extracellular processing of proapolipoprotein A-II in Hep G2 cell cultures is mediated by a 54-kDa protease immunologically related to cathepsin B.". J. Biol. Chem. 260 (27): 14824–31. PMID 2414299.
Lackner KJ, Law SW, Brewer HB (1985). "The human apolipoprotein A-II gene: complete nucleic acid sequence and genomic organization.". Nucleic Acids Res. 13 (12): 4597–608. doi:10.1093/nar/13.12.4597. PMC 321808. PMID 2989800.
Knott TJ, Wallis SC, Robertson ME, et al. (1985). "The human apolipoprotein AII gene: structural organization and sites of expression.". Nucleic Acids Res. 13 (17): 6387–98. doi:10.1093/nar/13.17.6387. PMC 321960. PMID 2995928.
Chan L, Moore MN, Tsao YK (1986). [43] Molecular cloning and sequence analysis of human apolipoprotein A-II cDNA. "Molecular cloning and sequence analysis of human apolipoprotein A-II cDNA.". Meth. Enzymol. Methods in Enzymology 128: 745–52. doi:10.1016/0076-6879(86)28103-3. ISBN 978-0-12-182028-2. PMID 3088392.
Middleton-Price HR, van den Berghe JA, Scott J, et al. (1988). "Regional chromosomal localisation of APOA2 to 1q21-1q23". Hum. Genet. 79 (3): 283–5. doi:10.1007/BF00366253. PMID 3136074.
Shelley CS, Sharpe CR, Baralle FE, Shoulders CC (1986). "Comparison of the human apolipoprotein genes. Apo AII presents a unique functional intron-exon junction". J. Mol. Biol. 186 (1): 43–51. doi:10.1016/0022-2836(85)90255-4. PMID 3935800.
Brewer HB, Lux SE, Ronan R, John KM (1972). "Amino acid sequence of human apoLp-Gln-II (apoA-II), an apolipoprotein isolated from the high-density lipoprotein complex". Proc. Natl. Acad. Sci. U.S.A. 69 (5): 1304–8. doi:10.1073/pnas.69.5.1304. PMC 426687. PMID 4338591.
Lux SE, John KM, Ronan R, Brewer HB (1973). "Isolation and characterization of the tryptic and cyanogen bromide peptides of apoLp-Gln-II (apoA-II), plasma high density apolipoprotein". J. Biol. Chem. 247 (23): 7519–27. PMID 4344225.
Moore MN, Kao FT, Tsao YK, Chan L (1984). "Human apolipoprotein A-II: nucleotide sequence of a cloned cDNA, and localization of its structural gene on human chromosome 1". Biochem. Biophys. Res. Commun. 123 (1): 1–7. doi:10.1016/0006-291X(84)90371-1. PMID 6089788.
Lackner KJ, Law SW, Brewer HB (1984). "Human apolipoprotein A-II: complete nucleic acid sequence of preproapo A-II". FEBS Lett. 175 (1): 159–64. doi:10.1016/0014-5793(84)80590-6. PMID 6090207.
Gordon JI, Budelier KA, Sims HF, et al. (1984). "Biosynthesis of human preproapolipoprotein A-II". J. Biol. Chem. 258 (22): 14054–9. PMID 6315718.
Sharpe CR, Sidoli A, Shelley CS, et al. (1984). "Human apolipoproteins AI, AII, CII and CIII. cDNA sequences and mRNA abundance". Nucleic Acids Res. 12 (9): 3917–32. doi:10.1093/nar/12.9.3917. PMC 318799. PMID 6328445.
Stoffel W, Krüger E, Deutzmann R (1983). "Cell-free translation of human liver apolipoprotein AI and AII mRNA. Processing of primary translation products". Hoppe-Seyler's Z. Physiol. Chem. 364 (3): 227–37. PMID 6407957.
Knott TJ, Priestley LM, Urdea M, Scott J (1984). "Isolation and characterisation of a cDNA encoding the precursor for human apolipoprotein AII". Biochem. Biophys. Res. Commun. 120 (3): 734–40. doi:10.1016/S0006-291X(84)80168-0. PMID 6428397.
Lackner KJ, Law SW, Brewer HB, et al. (1984). "The human apolipoprotein A-II gene is located on chromosome 1". Biochem. Biophys. Res. Commun. 122 (3): 877–83. doi:10.1016/0006-291X(84)91172-0. PMID 6433912.

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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

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

PANDIT:	PF04711
Pseudofam:	PF04711
SCOP:	1l6k
SYSTERS:	ApoA-II

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.

Cellular component	extracellular region (GO:0005576)
Molecular function	lipid binding (GO:0008289)
Biological process	lipid transport (GO:0006869)
Biological process	lipoprotein metabolic process (GO:0042157)

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:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: 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
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:

Selex
Stockholm
FASTA
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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.

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 (5)	Full (38)	Representative proteomes				NCBI (41)	Meta (0)
	Seed (5)	Full (38)	RP15 (1)	RP35 (1)	RP55 (1)	RP75 (15)	NCBI (41)	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 (5)	Full (38)	Representative proteomes				NCBI (41)	Meta (0)
	Seed (5)	Full (38)	RP15 (1)	RP35 (1)	RP55 (1)	RP75 (15)	NCBI (41)	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 (5)	Full (38)	Representative proteomes				NCBI (41)	Meta (0)
	Seed (5)	Full (38)	RP15 (1)	RP35 (1)	RP55 (1)	RP75 (15)	NCBI (41)	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:

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

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

Sunburst
Tree

Sunburst controls

Show

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.

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".

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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The tree shows the occurrence of this domain across different species. More...

Species trees

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.

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.

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
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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.

Loading structure mapping...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: ApoA-II (PF04711)

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Summary: Apolipoprotein A-II (ApoA-II)

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Editing Wikipedia articles

Before you edit for the first time

How your contribution will be recorded

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APOA2 Edit Wikipedia article

Contents

[edit] Function

[edit] Interactions

[edit] Interactive pathway map

[edit] References

[edit] Further reading

Apolipoprotein A-II (ApoA-II) Provide feedback

Literature references

External database links

InterPro entry IPR006801

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