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PMID: 9396823 Published · ppublish English Comparative Study Journal Article Research Support, U.S. Gov't, Non-P.H.S.

The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains.

Nucleic acids research ·Vol. 25 ·No. 24 ·1997-12-15 ·Pages 5110-8

Moser MJ, Holley WR, Chatterjee A, Mian IS

Abstract

Prior sequence analysis studies have suggested that bacterial ribonuclease (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 domain was predicted to have a structure and mechanism of action similar to the 3'-->5' exodeoxyibonuclease (proofreading) domain of DNA polymerases. Here, hidden Markov model (HMM) and phylogenetic studies have been used to identify and characterise other sequences that may possess this exonuclease domain. Results indicate that it is also present in the RNase T family; Borrelia burgdorferi P93 protein, an immunodominant antigen in Lyme disease; bacteriophage T4 dexA and Escherichia coli exonuclease I, processive 3'-->5' exodeoxyribonucleases that degrade single-stranded DNA; Bacillus subtilis dinG, a probable helicase involved in DNA repair and possibly replication, and peptide synthase 1; Saccharomyces cerevisiae Pab1p-dependent poly(A) nuclease PAN2 subunit, required for shortening mRNA poly(A) tails; Caenorhabditis elegans and Mus musculus CAF1, transcription factor CCR4-associated factor 1; Xenopus laevis XPMC2, prevention of mitotic catastrophe in fission yeast; Drosophila melanogaster egalitarian, oocyte specification and axis determination, and exuperantia, establishment of oocyte polarity; H.sapiens HEM45, expressed in tumour cell lines and uterus and regulated by oestrogen; and 31 open reading frames including one in Methanococcus jannaschii . Examination of a multiple sequence alignment and two three-dimensional structures of proofreading domains has allowed definition of the core sequence, structural and functional elements of this exonuclease domain.

Keywords
Non-programmatic
MeSH Terms
Amino Acid Sequence Animals Bacteria/enzymology Bacterial Proteins/chemistry,metabolism Caenorhabditis elegans/enzymology DNA Polymerase I/chemistry,metabolism DNA, Bacterial/metabolism Drosophila melanogaster/enzymology Escherichia coli/enzymology Exonucleases/chemistry Fungal Proteins/chemistry Helminth Proteins/chemistry Insect Proteins/chemistry Markov Chains Mice Models, Molecular Molecular Sequence Data Phylogeny Protein Structure, Tertiary RNA, Bacterial/metabolism Saccharomyces cerevisiae/enzymology Sequence Alignment Sequence Homology, Amino Acid Species Specificity Xenopus laevis/metabolism
Chemicals
Bacterial Proteins DNA, Bacterial Fungal Proteins Helminth Proteins Insect Proteins RNA, Bacterial DNA Polymerase I Exonucleases
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Moser M J
Life Sciences Division (Mail Stop 29-100), Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Holley W R
Chatterjee A
Mian I S
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/25.24.5110
Published
1997-12-15
Pages
5110-8
Language
English
Region
England
NLM ID
0411011
PMCID
PMC147149
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/25.24.5110 PMC Full Text View journal details
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