PROSITE documentation PDOC00499
Avidin-like domain signature and profile


Avidin [1] is a minor constituent of egg white in several groups of oviparous vertebrates. Avidin, which was discovered in the 1920's, takes its name from the avidity with which it binds biotin. These two molecules bind so strongly that is highly difficult to separate them. Streptavidin is a protein produced by Streptomyces avidinii which also binds biotin and whose sequence is evolutionary related to that of avidin.

Avidin and streptavidin both form homotetrameric complexes of noncovalently associated chains. Each chain forms a very strong and specific non-covalent complex with one molecule of biotin.

Fibropellins I and III [2] are proteins that form the apical lamina of the sea urchin embryo, a component of the extracellular matrix. These two proteins have a modular structure composed of a CUB domain (see <PDOC00908>), followed by a variable number of EGF repeats (see <PDOC00021>) and a C-terminal avidin-like domain. The fibropellin avidin-like domain forms a homotetramer incapable of binding biotin [3].

The three-dimensional structures of both streptavidin [4,5] and avidin [6] have been determined and revealed them to share a common fold: an eight stranded anti-parallel β-barrel with a repeated +1 topology enclosing an internal ligand binding site (see <PDB:1AVD>).

As a signature sequence for the avidin-like domain we selected a conserved motif located in its C-terminal section. We also developed a profile that covers the entire avidin-like domain.


It is suggested, on the basis of similarities of structure, function, and sequence, that this family forms an overall superfamily, called the calycins, with the lipocalin <PDOC00187> and the cytosolic fatty-acid binding proteins <PDOC00188> families [7,8].

Expert(s) to contact by email:

Flower D.R.

Last update:

August 2007 / Text revised; profile added.


Technical section

PROSITE methods (with tools and information) covered by this documentation:

AVIDIN_2, PS51326; Avidin-like domain profile  (MATRIX)

AVIDIN_1, PS00577; Avidin-like domain signature  (PATTERN)


1AuthorsGreen N.M.
TitleAvidin and streptavidin.
SourceMethods Enzymol. 184:51-67(1990).
PubMed ID2388586

2AuthorsBisgrove B.W. Raff R.A.
TitleThe SpEGF III gene encodes a member of the fibropellins: EGF repeat-containing proteins that form the apical lamina of the sea urchin embryo.
SourceDev. Biol. 157:526-538(1993).
PubMed ID8500658

3AuthorsYanai I. Yu Y. Zhu X. Cantor C.R. Weng Z.
TitleAn avidin-like domain that does not bind biotin is adopted for oligomerization by the extracellular mosaic protein fibropellin.
SourceProtein. Sci. 14:417-423(2005).
PubMed ID15659374

4AuthorsHendrickson W.A. Pahler A. Smith J.L. Satow Y. Merritt E.A. Phizackerley R.P.
TitleCrystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation.
SourceProc. Natl. Acad. Sci. U.S.A. 86:2190-2194(1989).
PubMed ID2928324

5AuthorsPugliese L. Coda A. Malcovati M. Bolognesi M.
TitleThree-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 A resolution.
SourceJ. Mol. Biol. 231:698-710(1993).
PubMed ID8515446

6AuthorsHunt L.T. Barker W.C.
TitleAvidin-like domain in an epidermal growth factor homolog from a sea urchin.
SourceFASEB J. 3:1760-1764(1989).
PubMed ID2784773

7AuthorsFlower D.R.
TitleStructural relationship of streptavidin to the calycin protein superfamily.
SourceFEBS Lett. 333:99-102(1993).
PubMed ID8224179

8AuthorsHolm L. Sander C.
TitleSearching protein structure databases has come of age.
SourceProteins 19:165-173(1994).
PubMed ID7937731

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