Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
1086  structures 436  species 0  interactions 7532  sequences 91  architectures

Family: Lipocalin (PF00061)

Summary: Lipocalin / cytosolic fatty-acid binding protein family

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 "Lipocalin". More...

Lipocalin Edit Wikipedia article

1kt6 opm.png
Retinol-binding protein in a calculated membrane-bound state of the protein 1kt6
Pfam clanCL0116
OPM superfamily50
OPM protein1kt6
Lipocalin-like domain
PDB 1qwd EBI.jpg
Structure of the Escherichia coli lipocalin.[1]
Pfam clanCL0116

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.[2][3][4][5][6] This is an eight stranded antiparallel beta barrel with a repeated + 1 topology enclosing an internal ligand binding site.[4][5]

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. Lipocalin allergens have been shown to evoke a Th2-deviated immune response, important for allergic sensitization, when applied in their apo-form (with an empty calyx devoid of ligands), whereas the holo-form seemed to exert immune-suppressive properties in vitro.[7]

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.[8]

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.[9] 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.


LCN2 (Lipocalin 2) acts as bone-derived hormone which crosses the BBB and acts on PVN paraventricular nucleus of hypothalamus in the brain.


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 β-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[2] 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.[5][10] Proteins known to belong to this family include alpha-1-microglobulin (protein HC); major urinary proteins; alpha-1-acid glycoprotein (orosomucoid);[11] aphrodisin; apolipoprotein D; beta-lactoglobulin; complement component C8 gamma chain;[12] crustacyanin;[13] epididymal-retinoic acid binding protein (E-RABP);[14] insectacyanin; odorant binding protein (OBP); human pregnancy-associated endometrial alpha-2 globulin (PAEP); probasin (PB), a prostatic protein; prostaglandin D synthase;[15] purpurin; Von Ebner's gland protein (VEGP);[16] and lizard epididymal secretory protein IV (LESP IV).[17]

Human proteins that contain lipocalin domain include:

See also


  1. ^ 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): 183–8. doi:10.1016/S0014-5793(04)00199-1. PMID 15044022.
  2. ^ a b 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): 209–214. doi:10.1096/fasebj.1.3.3622999. PMID 3622999.
  3. ^ 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): 5376–5380. doi:10.1073/pnas.89.12.5376. PMC 49294. PMID 1608945.
  4. ^ a b Cowan SW, Jones TA, Newcomer ME (1990). "Crystallographic refinement of human serum retinol binding protein at 2A resolution". Proteins. 8 (1): 44–61. doi:10.1002/prot.340080108. PMID 2217163.
  5. ^ a b c Flower DR, Attwood TK, North AC (1993). "Structure and sequence relationships in the lipocalins and related proteins". Protein Sci. 2 (5): 753–761. doi:10.1002/pro.5560020507. PMC 2142497. PMID 7684291.
  6. ^ 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): 64–66. doi:10.1016/0968-0004(88)90031-X. PMID 3238752.
  7. ^ Roth-Walter, Franziska; Pacios, Luis F.; Gomez-Casado, Cristina; Hofstetter, Gerlinde; Roth, Georg A.; Singer, Josef; Diaz-Perales, Araceli; Jensen-Jarolim, Erika (2014-08-12). "The Major Cow Milk Allergen Bos d 5 Manipulates T-Helper Cells Depending on Its Load with Siderophore-Bound Iron". PLoS ONE. 9 (8): e104803. doi:10.1371/journal.pone.0104803. PMC 4130594. PMID 25117976.
  8. ^ 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): 899–902. doi:10.1038/nature05997. PMID 18064011. Lay summary – BBC News.
  9. ^ [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)]
  10. ^ 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): 69–74. doi:10.1016/S0006-291X(05)81256-2. PMID 1834059.
  11. ^ Wilting J, Kremer JM, Janssen LH (1988). "Drug binding to human alpha-1-acid glycoprotein in health and disease". Pharmacol. Rev. 40 (1): 1–47. PMID 3064105.
  12. ^ 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): 123–131. doi:10.1016/0161-5890(91)90095-2. PMID 1707134.
  13. ^ 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): 407–417. doi:10.1111/j.1432-1033.1991.tb15925.x. PMID 2026162.
  14. ^ Newcomer ME (1993). "Structure of the epididymal retinoic acid binding protein at 2.1 A resolution". Structure. 1 (1): 7–18. doi:10.1016/0969-2126(93)90004-Z. PMID 8069623.
  15. ^ Boguski MS, Peitsch MC (1991). "The first lipocalin with enzymatic activity". Trends Biochem. Sci. 16 (10): 363. doi:10.1016/0968-0004(91)90149-P. PMID 1723819.
  16. ^ 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): 905–916. doi:10.1111/j.1432-1033.1994.tb18806.x. PMID 7514123.
  17. ^ 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): 10274–10281. PMID 8486691.

Further reading

External links

This article incorporates text from the public domain Pfam and InterPro: IPR000566

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.

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: 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

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000566

Proteins 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 ].

Domain organisation

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

Loading domain graphics...

Pfam Clan


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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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.

Representative proteomes UniProt
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

Key: ✓ available, x not generated, not available.

Format an alignment

Representative proteomes UniProt

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.

Representative proteomes UniProt
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.

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...


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: Prosite and HMM_iterative_training
Previous IDs: lipocalin;
Type: Domain
Sequence Ontology: SO:0000417
Author: Eddy SR
Number in seed: 155
Number in full: 7532
Average length of the domain: 128.20 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 69.81 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 144
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls


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


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


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 1086 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 sequence.

Loading structure mapping...