THE PROOFREADING DOMAIN OF ESCHERICHIA-COLI DNA-POLYMERASE-I AND OTHER DNA AND OR RNA EXONUCLEASE DOMAINS/

Prior sequence analysis studies have suggested that bacterial ribonucl ease (RNase) Ds comprise a complete domain that is found also in Homo sapiens polymyositis-scleroderma overlap syndrome 100 kDa autoantigen and Werner syndrome protein. This RNase D 3'-->5' exoribonuclease doma in was predicted to have a structure and mechanism of action similar t o the 3'-->5' exodeoxyibonuclease (proofreading) domain of DNA polymer ases. Here, hidden Markov model (HMM) and phylogenetic studies have be en used to identify and characterise other sequences that may possess this exonuclease domain. Results indicate that it is also present in t he RNase T family; Borrelia burgdorferi P93 protein, an immunodominant antigen in Lyme disease; bacteriophage T4 dexA and Escherichia coli e xonuclease I, processive 3'-->5' exodeoxyribonucleases that degrade si ngle-stranded DNA; Bacillus subtilis dinG, a probable helicase involve d in DNA repair and possibly replication, and peptide synthase 1; Sacc haromyces cerevisiae Pab1p-dependent poly(A) nuclease PAN2 subunit, re quired for shortening mRNA poly(A) tails; Caenorhabditis elegans and M us musculus CAF1, transcription factor CCR4-associated factor 1; Xenop us laevis XPMC2, prevention of mitotic catastrophe in fission yeast; D rosophila melanogaster egalitarian, oocyte specification and axis dete rmination, and exuperantia, establishment of oocyte polarity; H.sapien s HEM45, expressed in tumour cell lines and uterus and regulated by oe strogen; and 31 open reading frames including one in Methanococcus jan naschii. Examination of a multiple sequence alignment and two three-di mensional structures of proofreading domains has allowed definition of the core sequence, structural and functional elements of this exonucl ease domain.