Protein domain

A protein domain is a portion of a protein with a stable, usually compact folded structure, which is functionally and structurally ( quasi-) independent of adjacent sections.

  • 4.1 2ZIP
  • 4.2 3Dee
  • 4.3 DALI Domain Dictionary

Properties

A protein can consist of a single domain or multiple. A domain usually corresponds to a contiguous portion of the amino acid sequence. Exceptions are the two - and multi-part protein domains (English bi -and multipartite domains) such as the POU domain. Not the entire protein chain consists of domains. A domain is often made ​​up of bundles of secondary structures such as α - helices and β -sheet structures, with connecting curves (English turn) between the secondary structures. Small domains are often stabilized by a complex binding of metal ions or by disulfide bridges.

The length of domains varies between 30 and more than 400 amino acids, typically it is approximately from 100 to 200 amino acids. The length of domains is probably limited by constraints in protein folding upwards because the difficulty of the correct folding increases greatly with the length of the chain. The modular structure of proteins from different domains is partly explicable.

Based on the results from the primary and secondary structure tertiary structure remain protein domains generally also functional if they are from the larger protein, of which they form, cut out. The tertiary structure is made up of the successive protein domains. Protein domains are either immobile bonded or connected by flexible sections (English left ) with variable folding structure with each other, where they, like on a hinge or hinge ( engl. hinge), movement in opposite directions. Frequently, these regions between the domains of a constriction or groove of the outer contour of the corresponding protein. In many cases, these are like an arm from one domain to another rich, partially fixed by other sections. Within the same protein, a domain can repeatedly occur or different domains may be combined with each other. Often, for a particular function, e.g. Substrate binding, multiple domains necessary. In some cases domains correspond in their exact delimitation exons of DNA, for example, immunoglobulins, that can also be defined as genetic units. This is not true in every case.

Many proteins are modular from a combination of different protein domains that can perform the specific function of the protein only in their combination. So there are transcription factors usually of at least one DNA binding domain and a transactivation domain, which is involved in the initiation of transcription. As another example, cell-cell and cell - matrix interaction proteins can be cited: Here bring different binding domains in some cases of variable formation with a particular substrate specificity.

A protein domain can be found in over a hundred different proteins use, which, however, differ from one another in the combination of their respective functional domains. This allows an increased evolutionary rate in the emergence of new proteins, as already existing blocks can be put together quickly. Owing primarily to two mechanisms: non- allelic homologous recombination and transposon - mediated insertion of a DNA segment to another position in the genome.

Domains of unknown function ( DUFs )

Many protein domains have no known function. They are called domains of unknown function (german domain of unknown function, DUF ). Such domains are surprisingly common. For example, about 2700 different DUFs have been identified in bacteria. In eukaryotes, there are about 1500 DUFs of which about 800 occur also in bacteria (as of 2013). Goodacre et al. (2013 ) have also 238 essential DUFs ( eDUFs ) identified in bacteria, the deletion was found to be lethal for the cells.

Databases of protein domains

Pfam

Pfam contains the families of protein domains. With the aid of known domains the user can similarly close to a function or evolutionary relationship over a sequence comparison in an unknown protein.

ProDom

ProDom protein contains domains that are derived from sequences from SWISS-PROT and TrEMBL. Furthermore, the domain structure of a protein can be represented graphically.

SMART

SMART is an acronym for Simple Modular Architecture Research Tool and is a database of families of protein domains. Among these, the user can obtain information on function, important amino acids, phylogenetic development and tertiary structure.

CDD

CDD Conserved Domain Database represents and is a database that you can query domains and the corresponding sequence alignment. The entries are derived here from Pfam, SMART and COG.

HITS

With the HITS database can be queried protein domains.

InterPro

About the InterPro description of the function of the protein family, literature references and cross-references are available. Information is thus collected by integrating various databases such as PROSITE, PRINTS, Pfam and ProDom.

Identification of domains

2ZIP

With the help of 2ZIP to predict leucine zipper domains can be made.

3Dee

This database contains definitions of protein domains.

DALI Domain Dictionary

Domains of the DALI dictionary makes an automatic classification of protein domains based on sequence similarities. With this dictionary, the user can compare 3 - D protein structures and identify structural domains that are similar in two different proteins, although the sequences differ.

Protein domains

  • FERM domain
  • Protein transduction domain
Enzyme substrate (biology) DNA-binding protein Lubert Stryer Digital Object Identifier
415213
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