Protein Family Models

This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices [4]. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site. [1]. 1631169. Identification of a family of bacteriophage T4 genes encoding proteins similar to those present in group I introns of fungi and phage. Sharma M, Ellis RL, Hinton DM;. Proc Natl Acad Sci U S A 1992;89:6658-6662. [2]. 9973609. Conserved domains in DNA repair proteins and evolution of repair systems. Aravind L, Walker DR, Koonin EV;. Nucleic Acids Res 1999;27:1223-1242. [3]. 10219084. Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings. Kowalski JC, Belfort M, Stapleton MA, Holpert M, Dansereau JT, Pietrokovski S, Baxter SM, Derbyshire V;. Nucleic Acids Res 1999;27:2115-2125. [4]. 12379841. Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. Van Roey P, Meehan L, Kowalski JC, Belfort M, Derbyshire V;. Nat Struct Biol 2002;9:806-811. [5]. 16646971. Phylogenomic analysis of the GIY-YIG nuclease superfamily. Dunin-Horkawicz S, Feder M, Bujnicki JM;. BMC Genomics. 2006;7:98. (from Pfam)

Date:

2024-10-16

This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.; [1]. 8506149. RNase T shares conserved sequence motifs with DNA proofreading exonucleases. Koonin EV, Deutscher MP;. Nucleic Acids Res 1993;21:2521-2522. (from Pfam)

Date:

2024-10-16

All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

Date:

2024-05-14