Exons and Protein Modules

Abstract

Modules are versatile protein domains that are frequently used as building blocks in the construction of diverse multidomain proteins. The degree of versatility or promiscuity of protein modules is usually defined as the number of distinct domain architectures in which they are present or the number of domain types with which they are associated in diverse multidomain proteins. The assembly of multidomain proteins from modules is facilitated by recombination in introns flanking the exons that encode the modules, but it may also occur by recombination in exons or through cotranscription and fusion of tandem genes. Protein modules that frequently participate in domain‐shuffling events (that is, moved from one genomic location to the other) are usually referred to as mobile domains.

Key Concepts:

  • Domain types that are frequently used as building blocks of multidomain proteins are usually referred to as protein modules.

  • The degree of versatility or promiscuity of protein modules may be defined as the number of distinct domain architectures in which it is present or the number of domain types with which it is associated in diverse proteins.

  • Protein modules that frequently participate in domain‐shuffling events (that is, moved from one genomic location to the other) are usually referred to as mobile domains.

  • Protein modules flanked by introns of identical phase are exceptionally mobile because their shuffling is facilitated by intronic recombination.

  • Although assembly of multidomain proteins from modules is facilitated by recombination in introns it may also occur by recombination in exons.

Keywords: domain; module; multidomain protein; intronic recombination; exonic recombination; chimeric gene

Figure 1.

Modular structure and building blocks of some proteases of blood coagulation and fibrinolysis. The hatched bars represent the trypsin homologue serine protease domain. The box shows the schemes of vitamin K‐dependent calcium‐binding module (C), kringle module (K), growth factor module (G) and finger module (F). Reprinted from Patthy . with permission of Elsevier.

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Further Reading

Finn RD, Mistry J, Schuster‐Bockler B et al. (2006) Pfam: clans, web tools and services. Nucleic Acids Research 34(Database issue): D247–D251.

Letunic I, Copley RR, Pils B et al. (2006) SMART 5: domains in the context of genomes and networks. Nucleic Acids Research 34(Database issue): D257–D260.

Mulder NJ, Apweiler R, Attwood TK et al. (2007) New developments in the InterPro database. Nucleic Acids Research 35(Database issue): D224–D228.

Nagy A and Patthy L (2011) Reassessing domain architecture evolution of metazoan proteins: the contribution of different evolutionary mechanisms. Genes 2: 578–598.

Patthy L (2007) Protein Evolution. Oxford: Blackwell Science.

Web Links

EMBL‐EBI European Bioinformatics Database: Interpro database. http://www.ebi.ac.uk/interpro/

Pfam: Protein families database of alignments and HMMs. http://www.sanger.ac.uk/Software/Pfam/

SMART: simple modular architecture research tool. http://smart.embl‐heidelberg.de/

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How to Cite close
Patthy, László(Feb 2013) Exons and Protein Modules. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005086.pub3]