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DNA binding

Last modified March 28, 2017

This subsection of the ‘Function’ section specifies the position and type of each DNA-binding domain present within the protein.

We annotate experimentally defined DNA-binding domains and conserved DNA-binding domains defined by the InterPro resources PROSITE, Pfam and SMART; examples include the AP2/ERF domain, the ETS domain, the Fork-Head domain, the HMG box and the Myb domain.

1. Predicted DNA-binding domains

Examples: P10103, P46200, Q9SGJ6, P14921, P55317, P30658

Special types of DNA-binding domain

a. bHLH and bZIP proteins

In the case of basic helix-loop-helix (bHLH) and basic leucine-zipper (bZIP) domains, we describe the C-terminal HLH and leucine zipper motifs separately in the ‘Domain’ subsection of the ‘Family and Domains’ section. The N-terminal basic region of these domains is described in the ‘DNA-binding’ subsection.

For bHLH proteins, the basic region is usually directly followed by the HLH domain in the sequence.
Example: P35869

In bZIP proteins, the basic region is followed by the leucine-zipper domain, characterized by an LXXXXXXL motif, and begins with the first Leu/Ile and stops with the last Leu/Ile residues.
Examples: P18289, P15407

b. Homeobox proteins

Homeobox proteins constitute a large family which contains several subtypes. When a homeobox belongs to a subtype, it is indicated in the ‘Description’ field after ‘Homeobox’ preceded by a semicolon.
Examples: Q9H2P0, O81788, Q90655, P20823

When a particular homeobox is incomplete or differs significantly from the consensus it may be annotated as either ‘partial’ or ‘atypical’.
Examples: Q6WRX8, Q8MJD5

2. Experimentally determined DNA-binding domains

When a DNA-binding domain has been identified experimentally but does not correspond to a domain modelled by an InterPro resource, then the simple fact of the existence of the domain is indicated but no particular description is provided.
Example: P13574

Such domains are transferred to close species using the ‘By similarity’ qualifier.
Example: Q08400

Related keywords: DNA-binding, Homeobox.