Summary: Lipocalin / cytosolic fatty-acid binding protein family
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Lipocalin Edit Wikipedia article
|Retinol-binding protein in a calculated membrane-bound state of the protein|
|Structure of the Escherichia coli lipocalin.|
The lipocalins are a family of proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids. They share limited regions of sequence homology and a common tertiary structure architecture. This is an eight stranded antiparallel beta-barrel with a repeated + 1 topology enclosing an internal ligand binding site.
These proteins are found in gram negative bacteria, vertebrate cells, and invertebrate cells, and in plants. Lipocalins have been associated with many biological processes, among them immune response, pheromone transport, biological prostaglandin synthesis, retinoid binding, and cancer cell interactions.
 Immune response
Lipocalin proteins are involved in inflammation and detoxification processes caused by immune system activation in mammals. They are known respiratory allergens of mice, cats, dogs, horses, and other animals. Examples of lipocalin proteins involved in immune system responses include alpha-1-microglobulin, alpha-1-acid glycoprotein, and c8gamma. Structural information for many immune system influencing lipocalin proteins is available, while their exact role in biological systems is still somewhat unclear. Human allergenic reactions to lipocalins have not been extensively investigated.
 Pheromone transport
The lipocalin family has been connected with the transport of mammalian pheromones due to easily observable protein-pheromone interactions. Lipocalins are comparatively small in size, and are thus less complicated to study as opposed to large, bulky proteins. They can also bind to various ligands for different biological purposes. Lipocalins have been detected as carrier proteins of important pheromones in the nasal mucus of rodents. Major urinary proteins, a lipocalin subfamily, are found in mouse and rat urine and may act as protein pheromones themselves.
 Prostaglandin synthesis
This family of proteins plays a part in the biological system of terminal prostaglandin synthesis.
 Retinoid binding
Retinol, (vitamin A), is an important micronutrient that affects eyesight, cell differentiation, immune system function, bone growth, and tumor suppression. Retinol absorption and metabolism depends on lipocalins that act as binding proteins. Retinyl esters (present in meats) and beta-carotene (present in plants) are the two main sources of retinoids in the diet. After intake, they are converted to retinol, successively metabolized, and finally bound to retinol binding proteins (lipocalins) in the blood plasma.
 Cancer cell interactions
Because lipocalins are extracellular proteins, their intracellular effects are not obvious, and demand further study. However, lipophilic ligands, present as substituents to the lipocalins, have the ability to enter the cell, where they can act as tumor protease inhibitors. This research suggests another possible route of protein-tumor investigations.
Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an Arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation.
The allergens in this family include allergens with the following designations: Bla g 4, Bos d 2, Bos d 5, Can f 1, Can f 2, Fel d 4, Equ c 1 and Equ c 2.
Although lipocalins are a broad family of greatly varied proteins, their three-dimensional structure is a unifying characteristic. Lipocalins have an eight-stranded, antiparallel, symmetrical Î²-barrel fold, which is in essence a beta sheet which has been rolled into a cylindrical shape. Inside this barrel is located a ligand binding site, which plays an important role in the lipocalin classification as a transport protein. If lipocalins are genetically engineered in the attempt to modify their binding properties, they are called anticalins.
 Family members
The name "lipocalin" has been proposed for this protein family, but cytosolic fatty acid binding proteins are also included. The sequences of most members of the family, the core or kernel lipocalins, are characterised by three short conserved stretches of residues, while others, the outlier lipocalin group, share only one or two of these. Proteins known to belong to this family include alpha-1-microglobulin (protein HC); major urinary proteins; alpha-1-acid glycoprotein (orosomucoid); aphrodisin; apolipoprotein D; beta-lactoglobulin; complement component C8 gamma chain; crustacyanin; epididymal-retinoic acid binding protein (E-RABP); insectacyanin; odorant binding protein (OBP); human pregnancy-associated endometrial alpha-2 globulin (PAEP); probasin (PB), a prostatic protein; prostaglandin D synthase; purpurin; Von Ebner's gland protein (VEGP); and lizard epididymal secretory protein IV (LESP IV).
Human proteins that contain lipocalin domain include:
- AMBP, APOD
- C8G, CRABP1, CRABP2
- FABP1, FABP2, FABP3, FABP4, FABP5, FABP6, FABP7
- LCN1, LCN2, LCN8, LCN9, LCN10, LCN12
- OBP2A, OBP2B
- ORM1, ORM2
- PAEP, PERF15, PMP2, PTGDS
- RBP1, RBP2, RBP4, RBP5, RBP7
 See also
- Campanacci V, Nurizzo D, Spinelli S, Valencia C, Tegoni M, Cambillau C (March 2004). "The crystal structure of the Escherichia coli lipocalin Blc suggests a possible role in phospholipid binding". FEBS Lett. 562 (1-3): 183â8. doi:10.1016/S0014-5793(04)00199-1. PMID 15044022.
- Pervaiz S, Brew K (1987). "Homology and structure-function correlations between alpha 1-acid glycoprotein and serum retinol-binding protein and its relatives". FASEB J. 1 (3): 209â214. PMID 3622999.
- Nagata A, Igarashi M, Toh H, Urade Y, Hayaishi O (1992). "Structural organization of the gene for prostaglandin D synthase in the rat brain". Proc. Natl. Acad. Sci. U.S.A. 89 (12): 5376â5380. doi:10.1073/pnas.89.12.5376. PMC 49294. PMID 1608945. //www.ncbi.nlm.nih.gov/pmc/articles/PMC49294/.
- Cowan SW, Jones TA, Newcomer ME (1990). "Crystallographic refinement of human serum retinol binding protein at 2A resolution". Proteins 8 (1): 44â61. doi:10.1002/prot.340080108. PMID 2217163.
- Flower DR, Attwood TK, North AC (1993). "Structure and sequence relationships in the lipocalins and related proteins". Protein Sci. 2 (5): 753â761. doi:10.1002/pro.5560020507. PMC 2142497. PMID 7684291. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2142497/.
- Godovac-Zimmermann J (1988). "The structural motif of beta-lactoglobulin and retinol-binding protein: a basic framework for binding and transport of small hydrophobic molecules?". Trends Biochem. Sci. 13 (2): 64â66. doi:10.1016/0968-0004(88)90031-X. PMID 3238752.
- Chamero P, Marton TF, Logan DW, Flanagan K, Cruz JR, Saghatelian A, Cravatt BF, Stowers L (December 2007). "Identification of protein pheromones that promote aggressive behaviour". Nature 450 (7171): 899â902. doi:10.1038/nature05997. PMID 18064011. Lay summary â BBC News.
- [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]
- Flower DR, Attwood TK, North AC (1991). "Mouse oncogene protein 24p3 is a member of the lipocalin protein family". Biochem. Biophys. Res. Commun. 180 (1): 69â74. doi:10.1016/S0006-291X(05)81256-2. PMID 1834059.
- Wilting J, Kremer JM, Janssen LH (1988). "Drug binding to human alpha-1-acid glycoprotein in health and disease". Pharmacol. Rev. 40 (1): 1â47. PMID 3064105.
- Peitsch MC, Tschopp J, Jenne DE, Haefliger JA (1991). "Structural and functional characterization of complement C8 gamma, a member of the lipocalin protein family". Mol. Immunol. 28 (1): 123â131. doi:10.1016/0161-5890(91)90095-2. PMID 1707134.
- Keen JN, Caceres I, Eliopoulos EE, Zagalsky PF, Findlay JB (1991). "Complete sequence and model for the A2 subunit of the carotenoid pigment complex, crustacyanin". Eur. J. Biochem. 197 (2): 407â417. doi:10.1111/j.1432-1033.1991.tb15925.x. PMID 2026162.
- Newcomer ME (1993). "Structure of the epididymal retinoic acid binding protein at 2.1 A resolution". Structure 1 (1): 7â18. doi:10.1016/0969-2126(93)90004-Z. PMID 8069623.
- Boguski MS, Peitsch MC (1991). "The first lipocalin with enzymatic activity". Trends Biochem. Sci. 16 (10): 363â363. doi:10.1016/0968-0004(91)90149-P. PMID 1723819.
- Kock K, Ahlers C, Schmale H (1994). "Structural organization of the genes for rat von Ebner's gland proteins 1 and 2 reveals their close relationship to lipocalins". Eur. J. Biochem. 221 (3): 905â916. doi:10.1111/j.1432-1033.1994.tb18806.x. PMID 7514123.
- Morel L, Depeiges A, Dufaure JP (1993). "LESP, an androgen-regulated lizard epididymal secretory protein family identified as a new member of the lipocalin superfamily". J. Biol. Chem. 268 (14): 10274â10281. PMID 8486691.
 Further reading
- Paine K, Flower DR (October 2000). "The lipocalin website". Biochim. Biophys. Acta 1482 (1-2): 351â2. doi:10.1016/S0167-4838(00)00166-7. PMID 11058775.
- Virtanen T, Zeiler T, MÃ¤ntyjÃ¤rvi R (December 1999). "Important animal allergens are lipocalin proteins: why are they allergenic?". Int. Arch. Allergy Immunol. 120 (4): 247â58. doi:10.1159/000024277. PMID 10640908.
- Bratt T (October 2000). "Lipocalins and cancer". Biochim. Biophys. Acta 1482 (1-2): 318â26. doi:10.1016/S0167-4838(00)00154-0. PMID 11058772.
- Charron JB, Ouellet F, Pelletier M, Danyluk J, Chauve C, Sarhan F (December 2005). "Identification, expression, and evolutionary analyses of plant lipocalins". Plant Physiol. 139 (4): 2017â28. doi:10.1104/pp.105.070466. PMC 1310578. PMID 16306142. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1310578/.
- Novotny MV (February 2003). "Pheromones, binding proteins and receptor responses in rodents". Biochem. Soc. Trans. 31 (Pt 1): 117â22. doi:10.1042/BST0310117. PMID 12546667.
- Lipocalins in SCOP database
- UMich Orientation of Proteins in Membranes families/superfamily-52 - Calculated spatial positions of some Lipocalins in membranes
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Lipocalin / cytosolic fatty-acid binding protein family Provide feedback
Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase ( EC:220.127.116.11). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel.
Internal database links
|Similarity to PfamA using HHSearch:||Lipocalin_2 ApoM|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000566Proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids share limited regions of sequence homology and a common tertiary structure architecture [PUBMED:3622999, PUBMED:1608945, PUBMED:2217163, PUBMED:7684291, PUBMED:3238752]. This is an eight stranded antiparallel beta-barrel with a repeated + 1 topology enclosing a internal ligand binding site [PUBMED:7684291, PUBMED:2217163]. The name 'lipocalin' has been proposed [PUBMED:3622999] for this protein family, but cytosolic fatty-acid binding proteins are also included. The sequences of most members of the family, the core or kernal lipocalins, are characterised by three short conserved stretches of residues, while others, the outlier lipocalin group, share only one or two of these [PUBMED:1834059, PUBMED:7684291]. Proteins known to belong to this family include alpha-1-microglobulin (protein HC); alpha-1-acid glycoprotein (orosomucoid) [PUBMED:3064105]; aphrodisin; apolipoprotein D; beta-lactoglobulin; complement component C8 gamma chain [PUBMED:1707134]; crustacyanin [PUBMED:2026162]; epididymal-retinoic acid binding protein (E-RABP) [PUBMED:8069623]; insectacyanin; odorant-binding protein (OBP); human pregnancy-associated endometrial alpha-2 globulin; probasin (PB), a rat prostatic protein; prostaglandin D synthase (EC) [PUBMED:1723819]; purpurin; Von Ebner's gland protein (VEGP) [PUBMED:7514123]; and lizard epididymal secretory protein IV (LESP IV) [PUBMED:8486691].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Key: available, not generated, — not available.
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|Seed source:||Prosite and HMM_iterative_training|
|Number in seed:||156|
|Number in full:||2221|
|Average length of the domain:||128.60 aa|
|Average identity of full alignment:||17 %|
|Average coverage of the sequence by the domain:||76.93 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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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.
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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.
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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.
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The tree shows the occurrence of this domain across different species. More...
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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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There is 1 interaction 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 Lipocalin domain has been found. There are 489 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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