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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
Identifiers
SymbolLipocalin
PfamPF00061
Pfam clanCL0116
InterProIPR000566
PROSITEPDOC00187
SCOPe1hms / SUPFAM
OPM superfamily50
OPM protein1kt6
Lipocalin-like domain
PDB 1qwd EBI.jpg
Structure of the Escherichia coli lipocalin.[1]
Identifiers
SymbolLipocalin_2
PfamPF08212
Pfam clanCL0116
InterProIPR013208

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.

Function

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.

Allergens

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.

Hormone

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

Structure

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

References

  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:5.3.99.2). 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...

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Pfam Clan

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

  Seed
(155)
Full
(7532)
Representative proteomes UniProt
(12583)
RP15
(936)
RP35
(2490)
RP55
(6285)
RP75
(8367)
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  Seed
(155)
Full
(7532)
Representative proteomes UniProt
(12583)
RP15
(936)
RP35
(2490)
RP55
(6285)
RP75
(8367)
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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
(155)
Full
(7532)
Representative proteomes UniProt
(12583)
RP15
(936)
RP35
(2490)
RP55
(6285)
RP75
(8367)
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...

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.

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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

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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 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.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A096MK41 View 3D Structure Click here
A0A096MKC6 View 3D Structure Click here
A0A0G2JV11 View 3D Structure Click here
A0A0G2JZ62 View 3D Structure Click here
A0A1B0GSM6 View 3D Structure Click here
A0A1B0GUV8 View 3D Structure Click here
A0A2R8PW45 View 3D Structure Click here
A0A2R8PX25 View 3D Structure Click here
A0A2R8QHL7 View 3D Structure Click here
A0A2R8QRB3 View 3D Structure Click here
A1Z991 View 3D Structure Click here
A2AEN9 View 3D Structure Click here
A2AEP0 View 3D Structure Click here
A2AJB7 View 3D Structure Click here
A2AJB9 View 3D Structure Click here
A2AV72 View 3D Structure Click here
A2BHD2 View 3D Structure Click here
A2BHR0 View 3D Structure Click here
A2BHR2 View 3D Structure Click here
A2BIM8 View 3D Structure Click here
A2BIN1 View 3D Structure Click here
A2CEK7 View 3D Structure Click here
A6NFH5 View 3D Structure Click here
A8MUU1 View 3D Structure Click here
A9JR93 View 3D Structure Click here
A9R9W0 View 3D Structure Click here
B0R174 View 3D Structure Click here
B1AVU4 View 3D Structure Click here
B3DHK5 View 3D Structure Click here
B3EY82 View 3D Structure Click here
B3EY83 View 3D Structure Click here
B3EY84 View 3D Structure Click here
B3EY86 View 3D Structure Click here
B3EY87 View 3D Structure Click here
B5X0G2 View 3D Structure Click here
B7SUM8 View 3D Structure Click here
D3ZAA7 View 3D Structure Click here
D3ZFG5 View 3D Structure Click here
D3ZFU1 View 3D Structure Click here
D3ZJV7 View 3D Structure Click here
D3ZK46 View 3D Structure Click here
D3ZPI8 View 3D Structure Click here
D4ABD9 View 3D Structure Click here
E9PTR6 View 3D Structure Click here
E9PVW0 View 3D Structure Click here
E9QA79 View 3D Structure Click here
E9QD41 View 3D Structure Click here
E9QGL3 View 3D Structure Click here
F1LQM1 View 3D Structure Click here
F1M6Y6 View 3D Structure Click here
F1R6B8 View 3D Structure Click here
F6PDB9 View 3D Structure Click here
F7ET54 View 3D Structure Click here
F8WFF8 View 3D Structure Click here
L7N222 View 3D Structure Click here
M0R460 View 3D Structure Click here
M0RBS2 View 3D Structure Click here
O01812 View 3D Structure Click here
O01814 View 3D Structure Click here
O02323 View 3D Structure Click here
O02324 View 3D Structure Click here
O08716 View 3D Structure Click here
O08976 View 3D Structure Click here
O09114 View 3D Structure Click here
O15540 View 3D Structure Click here
P02689 View 3D Structure Click here
P02693 View 3D Structure Click here
P02696 View 3D Structure Click here
P02753 View 3D Structure Click here
P02760 View 3D Structure Click here
P02761 View 3D Structure Click here
P02762 View 3D Structure Click here
P02763 View 3D Structure Click here
P02764 View 3D Structure Click here
P04117 View 3D Structure Click here
P04916 View 3D Structure Click here
P04938 View 3D Structure Click here
P04939 View 3D Structure Click here
P05090 View 3D Structure Click here
P05413 View 3D Structure Click here
P06768 View 3D Structure Click here
P06911 View 3D Structure Click here
P07360 View 3D Structure Click here
P07361 View 3D Structure Click here
P07483 View 3D Structure Click here
P08937 View 3D Structure Click here
P09455 View 3D Structure Click here
P09466 View 3D Structure Click here
P11404 View 3D Structure Click here
P11588 View 3D Structure Click here
P11589 View 3D Structure Click here
P11590 View 3D Structure Click here
P11591 View 3D Structure Click here
P11672 View 3D Structure Click here
P12104 View 3D Structure Click here
P12710 View 3D Structure Click here
P15090 View 3D Structure Click here
P15399 View 3D Structure Click here
P19652 View 3D Structure Click here
P20289 View 3D Structure Click here
P22057 View 3D Structure Click here
P22935 View 3D Structure Click here
P23593 View 3D Structure Click here
P24526 View 3D Structure Click here
P29373 View 3D Structure Click here
P29762 View 3D Structure Click here
P30152 View 3D Structure Click here
P31025 View 3D Structure Click here
P41222 View 3D Structure Click here
P41244 View 3D Structure Click here
P50120 View 3D Structure Click here
P51673 View 3D Structure Click here
P51880 View 3D Structure Click here
P55050 View 3D Structure Click here
P55051 View 3D Structure Click here
P55053 View 3D Structure Click here
P55054 View 3D Structure Click here
P62502 View 3D Structure Click here
P62965 View 3D Structure Click here
P62966 View 3D Structure Click here
P70623 View 3D Structure Click here
P80188 View 3D Structure Click here
P82980 View 3D Structure Click here
Q00724 View 3D Structure Click here
Q00915 View 3D Structure Click here
Q01469 View 3D Structure Click here
Q05816 View 3D Structure Click here
Q07456 View 3D Structure Click here
Q08652 View 3D Structure Click here
Q0P3U6 View 3D Structure Click here
Q0Z7S8 View 3D Structure Click here
Q4FZE8 View 3D Structure Click here
Q503X5 View 3D Structure Click here
Q5FW60 View 3D Structure Click here
Q5G9L7 View 3D Structure Click here
Q5VSP4 View 3D Structure Click here
Q60590 View 3D Structure Click here
Q62471 View 3D Structure Click here
Q62472 View 3D Structure Click here
Q63805 View 3D Structure Click here
Q64240 View 3D Structure Click here
Q66I80 View 3D Structure Click here
Q6IVM1 View 3D Structure Click here
Q6IWJ1 View 3D Structure Click here
Q6JVE5 View 3D Structure Click here
Q6JVE9 View 3D Structure Click here
Q6JVL5 View 3D Structure Click here
Q6KGV4 View 3D Structure Click here
Q6P5J2 View 3D Structure Click here
Q6PC07 View 3D Structure Click here
Q6U1J7 View 3D Structure Click here
Q6UWW0 View 3D Structure Click here
Q6ZST4 View 3D Structure Click here
Q801Y4 View 3D Structure Click here
Q80YX8 View 3D Structure Click here
Q810Z1 View 3D Structure Click here
Q8INK3 View 3D Structure Click here
Q8K1H9 View 3D Structure Click here
Q8QGV5 View 3D Structure Click here
Q8UVG6 View 3D Structure Click here
Q8UVG7 View 3D Structure Click here
Q8VCG4 View 3D Structure Click here
Q8WX39 View 3D Structure Click here
Q924P3 View 3D Structure Click here
Q965W1 View 3D Structure Click here
Q96R05 View 3D Structure Click here
Q9D267 View 3D Structure Click here
Q9D3H2 View 3D Structure Click here
Q9D3N5 View 3D Structure Click here
Q9DAK4 View 3D Structure Click here
Q9EPC5 View 3D Structure Click here
Q9I8N9 View 3D Structure Click here
Q9NPH6 View 3D Structure Click here
Q9NY56 View 3D Structure Click here
Q9PRH9 View 3D Structure Click here
Q9PT95 View 3D Structure Click here
Q9QYU9 View 3D Structure Click here