Difference between revisions of "Protein Domain"

Revision as of 20:45, 1 June 2015

Most domains can be computationally profiled by Hidden Markov Model (HMM), which can be found in Pfam, SMART, NCBI CDD, Gene3D, Superfamily and similar databases.

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Description

FERM

FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus in the majority of proteins in which it is found.

PTB

The PTB domain is a structural domain of ~130 aa (Pfam model). It usually binds to phosphorylated tyrosine. However, PTB domain of SHC can bind to NPLH sequence found in the carboxyl terminus of murine PTPN12/PTP-PEST [2]. PTB domain is found at least in 27 genes in human genome.

PDZ

The PDZ domain is a common structural domain of 80-90 amino-acids found in the signaling proteins of all three kingdoms of life. PDZ is an acronym combining the first letters of three proteins — post synaptic density protein (PSD95), Drosophila disc large tumor suppressor (Dlg1), and zonula occludens-1 protein (zo-1) — which were first discovered to share the domain. It has previously been referred to as DHR (Dlg homologous region) or GLGF (glycine-leucine-glycine-phenylalanine) domains.

Proteins with these domains help hold together and organize signaling complexes at cellular membranes. In general PDZ domains bind to a short region of the C-terminus of other specific proteins. These short regions bind to the PDZ domain by beta sheet augmentation. This means that the beta sheet in the PDZ domain is extended by the addition of a further beta strand from the tail of the binding partner protein. About 260 PDZ domains within 180 proteins in human have been found.

PEST sequence

A PEST sequence is a peptide sequence that is rich in proline (P), glutamic acid (E), serine (S), and threonine (T). This sequence is associated with proteins that are rapidly degraded, possibly via the proteasome or calpain.

The computational tool ePESTfind is used to predict PEST sequence.

SH2

The SH2 (Src Homology 2) domain is a structurally conserved protein domain of ~100 aa long. SH2 typically binds to pTyr (phosphorylated tyrosine) which usually locates in peptide linear motif of 3-6 aa long. About 120 SH2 domains within 115 proteins in human have been found.

SH3: binding to proline-rich peptide

The SRC Homology 3 Domain (or SH3 domain) is a small protein domain of about 60 aa long. SH3 typically via binding to proline-rich peptides in their respective binding partner. Approximately 300 SH3 domains are found in proteins in human genome.

References

1. Frame MC, Patel H, Serrels B, Lietha D, and Eck MJ. The FERM domain: organizing the structure and function of FAK. Nat Rev Mol Cell Biol. 2010 Nov;11(11):802-14. DOI:10.1038/nrm2996 | PubMed ID:20966971 | HubMed [Frame10]
3. Charest A, Wagner J, Jacob S, McGlade CJ, and Tremblay ML. Phosphotyrosine-independent binding of SHC to the NPLH sequence of murine protein-tyrosine phosphatase-PEST. Evidence for extended phosphotyrosine binding/phosphotyrosine interaction domain recognition specificity. J Biol Chem. 1996 Apr 5;271(14):8424-9. DOI:10.1074/jbc.271.14.8424 | PubMed ID:8626541 | HubMed [Charest96]