Dockerin Explained

Symbol:	Dockerin_1
Dockerin domain
Pfam:	PF00404
Interpro:	IPR018242
Prosite:	PDOC00416
Scop:	1daq
Cdd:	cd14253

Dockerin is a protein domain found in the cellulosome cellular structure of anaerobic bacteria. It is found on many endoglucanase enzymes. The dockerin's binding partner is the cohesin domain, located on the scaffoldin protein. This interaction between the dockerin domains of the enzyme constituents of the cellulosome and the cohesin domains of the scaffoldin protein is essential to the construction of the cellulosome complex.^[1] The Dockerin domain has two in-tandem repeats of a non-EF hand calcium binding motif. Each motif is characterized by a loop-helix structure. The three-dimensional structure of dockerin has been determined in solution,^[2] as well as in complex with Cohesin.^[3]

There are three types of Dockerin domains: I, II and III which bind to Cohesin Type I, Cohesin Type II and Cohesin Type III respectively. A type I dockerin domain is 65-70 residues long.^[4] The binding specificity of Type I interaction was well studied by structural and mutagenesis studies. Type II interaction is less well characterized.^[5]

See also

• EF hand
• cellulosome

External links

Protein Structure:

• Lytle BL, Volkman BF, Westler WM, Heckman MP, Wu JH. Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain. J Mol Biol. 307. 745–753. 2001 . 11273698 . 10.1006/jmbi.2001.4522 . 3 .
• Bayer EA, Shimon LJ, Shoham Y, Lamed R. Cellulosomes-structure and ultrastructure. J Struct Biol. 124. 2–3. 221–234. 1998. 10049808 . 10.1006/jsbi.1998.4065.

Specificity Characterization:

• Haimovitz R, Barak Y, Morag E, Voronov-Goldman M, Shoham Y, Lamed R, Bayer EA. Cohesin-dockerin microarray: Diverse specificities between two complementary families of interacting protein modules. Proteomics. 8. 5. 968–979. 2008 . 18219699 . 10.1002/pmic.200700486. 206360888.
• Adams JJ, Webb BA, Spencer HL, Smith SP. Structural characterization of type II dockerin module from the cellulosome of Clostridium thermocellum: calcium-induced effects on conformation and target recognition. Biochemistry. 44. 6. 2173–2182 . 2005 . 15697243 . 10.1021/bi048039u.
• Jindou S, Soda A, Karita S, Kajino T, Béguin P, Wu JH, Inagaki M, Kimura T, Sakka K, Ohmiya K. Cohesin-dockerin interactions within and between Clostridium josui and Clostridium thermocellum: binding selectivity between cognate dockerin and cohesin domains and species specificity. J Biol Chem. 279. 11. 9867–9874. 2004 . 14688277 . 10.1074/jbc.M308673200. free.

Notes and References

1. Ding SY, Rincon MT, Lamed R, Martin JC, McCrae SI, Aurilia V. Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens. . J Bacteriol . 2001 . 183 . 6 . 1945–53 . 11222592 . 10.1128/JB.183.6.1945-1953.2001 . 95089 . etal.

2. Lytle BL, Volkman BF, Westler WM, Heckman MP, Wu JH . Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain . J. Mol. Biol. . 307 . 3 . 745–53 . March 2001 . 11273698 . 10.1006/jmbi.2001.4522 .

3. Carvalho. A. L.. Dias. F. M. V.. Prates. J. A. M.. Nagy. T.. Gilbert. H. J.. Harry J. Gilbert. Davies. G. J.. Gideon Davies. Ferreira. L. M. A.. Romao. M. J.. Fontes. C. M. G. A.. Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex. Proceedings of the National Academy of Sciences. 100. 24. 2003. 13809–13814. 10.1073/pnas.1936124100. 14623971 . 283503. free.

4. [InterPro]
5. Adams JJ, Webb BA, Spencer HL, Smith SP . Structural characterization of type II dockerin module from the cellulosome of Clostridium thermocellum: calcium-induced effects on conformation and target recognition . Biochemistry . 44 . 6 . 2173–82 . February 2005 . 15697243 . 10.1021/bi048039u .