User:Cboursnell/Sandbox/5 3 exonuc
| 5_3_exonuc | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 divalent metal ions (zinc) bound to t5 5'-exonuclease | |||||||||
| Identifiers | |||||||||
| Symbol | 5_3_exonuc | ||||||||
| Pfam | PF01367 | ||||||||
| Pfam clan | CL0464 | ||||||||
| InterPro | IPR020047 | ||||||||
| SCOP2 | 1taq / SCOPe / SUPFAM | ||||||||
| |||||||||
The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (<a class="ext" href="http://expasy.org/prosite/PDOC00658">PROSITEDOC</a>) are never found outside the '53EXO' domains. The latter are found in more diverse proteins.[1][2][3] The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families.
In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures.
This entry represents the SAM-fold domain found in 5'-3' exonucleases. This domain consists of 4-5 helices in a bundle of two orthogonally packed alpha-hairpins.[4][5]
References
[edit]- ^ Harrington JJ, Lieber MR (June 1994). "Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair". Genes Dev. 8 (11): 1344–1355. doi:10.1101/gad.8.11.1344. PMID 7926735.
{{cite journal}}: CS1 maint: date and year (link) - ^ Smith TF, Gaitatzes C, Saxena K, Neer EJ (May 1999). "The WD repeat: a common architecture for diverse functions". Trends Biochem. Sci. 24 (5): 181–185. doi:10.1016/s0968-0004(99)01384-5. PMID 10322433.
{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link) - ^ Carr AM, Sheldrick KS, Murray JM, al-Harithy R, Watts FZ, Lehmann AR (March 1993). "Evolutionary conservation of excision repair in Schizosaccharomyces pombe: evidence for a family of sequences related to the Saccharomyces cerevisiae RAD2 gene". Nucleic Acids Res. 21 (6): 1345–1349. doi:10.1093/nar/21.6.1345. PMC 309318. PMID 8464724.
{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link) - ^ Eom SH, Wang J, Steitz TA (July 1996). "Structure of Taq polymerase with DNA at the polymerase active site". Nature. 382 (6588): 278–281. doi:10.1038/382278a0. PMID 8717047.
{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link) - ^ Ceska TA, Sayers JR, Stier G, Suck D (July 1996). "A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease". Nature. 382 (6586): 90–93. doi:10.1038/382090a0. PMID 8657312.
{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)