PROSITE documentation PDOC50171

Zinc finger matrin-type profile

This C2H2 zinc finger was first identified in the protein Matrin 3 [1]. It is also found in several spliceosome RNA-binding proteins, suggesting a possible role in pre-mRNA binding.

The matrin zinc finger follows the general pattern C-x2-C-x(12,16)-H-x5-H. The spacings are different from the 'classical' DNA-binding C2H2 zinc finger (see <PDOC00028>), nevertheless these two domains are too closely related to be fully separated by a pattern.

Some of the proteins containing this domain are listed below:

• Matrin 3. May interact with other nuclear matrix proteins to form the internal fibrogranular network.
• Eukaryotic splicing factor 3A subunits 2 (SAP62/PRP11) and 3 (SAP60/PRP9). These are subunits of the SF3A complex required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. May anchor U2 snRNP to pre-mRNA.
• U1 small nuclear ribonucleoprotein C. Directly bind pre-mRNA [2].
• Mammalian nuclear protein NP220. Related to matrin 3.
• Formin binding protein 21, a spliceosome-associated protein.

We have developed a profile that covers the whole zinc finger with 2 positions upstream, usually aromatic, and 5 positions downstream which could form a positively charge tail important for RNA binding activity.