Dockerin

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.[2] The three-dimensional structure of dockerin has been determined in solution,[3] as well as in complex with Cohesin.[4]

Dockerin domain
Structure of the Dockerin type I domain from C. thermocellum cellulosome.
Identifiers
Symbol	Dockerin_1
Pfam	PF00404
InterPro	IPR018242
PROSITE	PDOC00416
SCOPe	1daq / SUPFAM
CDD	cd14253
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

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.[5] The binding specificity of Type I interaction was well studied by structural and mutagenesis studies. Type II interaction is less well characterized.[6]

See also

• EF hand
• cellulosome

References

1. Ding SY, Rincon MT, Lamed R, Martin JC, McCrae SI, Aurilia V, et al. (2001). "Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens". J Bacteriol. 183 (6): 1945–53. doi:10.1128/JB.183.6.1945-1953.2001. PMC 95089. PMID 11222592.
2. SCOP 63447
3. PDB: 1DAQ​; Lytle BL, Volkman BF, Westler WM, Heckman MP, Wu JH (March 2001). "Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain". J. Mol. Biol. 307 (3): 745–53. doi:10.1006/jmbi.2001.4522. PMID 11273698.
4. PDB: 1OHZ​; Carvalho, A. L.; Dias, F. M. V.; Prates, J. A. M.; Nagy, T.; Gilbert, H. J.; Davies, G. J.; Ferreira, L. M. A.; Romao, M. J.; Fontes, C. M. G. A. (2003). "Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex". Proceedings of the National Academy of Sciences. 100 (24): 13809–13814. doi:10.1073/pnas.1936124100. PMC 283503. PMID 14623971.
5. InterPro: InterPro: IPR016134
6. Adams JJ, Webb BA, Spencer HL, Smith SP (February 2005). "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. doi:10.1021/bi048039u. PMID 15697243.

External links

Protein Structure:

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

Specificity Characterization:

• Haimovitz R, Barak Y, Morag E, Voronov-Goldman M, Shoham Y, Lamed R, Bayer EA (2008). "Cohesin-dockerin microarray: Diverse specificities between two complementary families of interacting protein modules". Proteomics. 8 (5): 968–979. doi:10.1002/pmic.200700486. PMID 18219699.
• Adams JJ, Webb BA, Spencer HL, Smith SP (2005). "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. doi:10.1021/bi048039u. PMID 15697243.
• Jindou S, Soda A, Karita S, Kajino T, Béguin P, Wu JH, Inagaki M, Kimura T, Sakka K, Ohmiya K (2004). "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. doi:10.1074/jbc.M308673200. PMID 14688277.