Online citations, reference lists, and bibliographies.
← Back to Search

A Conserved 3′→5′ Exonuclease Active Site In Prokaryotic And Eukaryotic DNA Polymerases

A. Bernad, L. Blanco, J. Lázaro, Gil Martín, M. Salas
Published 1989 · Biology, Medicine

Cite This
Download PDF
Analyze on Scholarcy
Share
The 3'----5' exonuclease active site of E. coli DNA polymerase I is predicted to be conserved for both prokaryotic and eukaryotic DNA polymerases based on amino acid sequence homology. Three amino acid regions containing the critical residues in the E. coli DNA polymerase I involved in metal binding, single-stranded DNA binding, and catalysis of the exonuclease reaction are located in the amino-terminal half and in the same linear arrangement in several prokaryotic and eukaryotic DNA polymerases. Site-directed mutagenesis at the predicted exonuclease active site of the phi 29 DNA polymerase, a model enzyme for prokaryotic and eukaryotic alpha-like DNA polymerases, specifically inactivated the 3'----5' exonuclease activity of the enzyme. These results reflect a high evolutionary conservation of this catalytic domain. Based on structural and functional data, a modular organization of enzymatic activities in prokaryotic and eukaryotic DNA polymerases is also proposed.
This paper references
10.1016/0022-2836(85)90105-6
Genetic mapping and DNA sequence analysis of mutations in the polA gene of Escherichia coli.
C. Joyce (1985)
10.1128/JVI.61.1.125-133.1987
Sequence and transcription analysis of the human cytomegalovirus DNA polymerase gene.
T. Kouzarides (1987)
10.1021/BI00431A004
DNA substrate structural requirements for the exonuclease and polymerase activities of procaryotic and phage DNA polymerases.
M. Cowart (1989)
10.1016/0378-1119(82)90149-4
Nucleotide sequence of the major early region of bacteriophage phi 29.
H. Yoshikawa (1982)
10.1093/NAR/14.24.9679
Inhibition of restriction endonuclease Nci I cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis.
K. Nakamaye (1986)
Enzymatic Synthesis of Deoxyribonucleic Acid XXXVI. A PROOFREADING FUNCTION FOR THE 3' → 5' EXONUCLEASE ACTIVITY IN DEOXYRIBONUCLEIC ACID POLYMERASES
D. Brutlag (1972)
10.1016/S0022-2836(83)80282-4
Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements.
J. Dunn (1983)
10.1002/j.1460-2075.1987.tb02770.x
Structural and functional relationships between prokaryotic and eukaryotic DNA polymerases.
A. Bernad (1987)
10.1128/JB.169.12.5735-5744.1987
Sequence analysis of the Escherichia coli dnaE gene.
H. G. Tomasiewicz (1991)
10.1002/j.1460-2075.1987.tb04735.x
Related functional domains in virus DNA polymerases.
B. Larder (1987)
10.1073/PNAS.85.23.8924
Cocrystal structure of an editing complex of Klenow fragment with DNA.
P. Freemont (1988)
DNA sequence analysis of the region encoding the terminal protein and the hypothetical N-gene product of adenovirus type 2.
P. Aleström (1982)
10.1073/PNAS.83.11.3659
Homology between DNA polymerases of poxviruses, herpesviruses, and adenoviruses: nucleotide sequence of the vaccinia virus DNA polymerase gene.
P. Earl (1986)
10.1126/SCIENCE.2832946
Genetic and crystallographic studies of the 3',5'-exonucleolytic site of DNA polymerase I.
V. Derbyshire (1988)
10.1073/PNAS.81.6.1639
Purification in a functional form of the terminal protein of Bacillus subtilis phage phi 29.
I. Priéto (1984)
10.1073/PNAS.85.11.3772
DNA polymerase I gene of Saccharomyces cerevisiae: nucleotide sequence, mapping of a temperature-sensitive mutation, and protein homology with other DNA polymerases.
A. Pizzagalli (1988)
10.1038/313818A0
Domain of E. coli DNA polymerase I showing sequence homology to T7 DNA polymerase
D. Ollis (1985)
10.1016/0022-2836(88)90552-9
Amino acid changes coded by bacteriophage T4 DNA polymerase mutator mutants. Relating structure to function.
L. Reha-Krantz (1988)
10.1099/0022-1317-67-9-1759
The complete DNA sequence of varicella-zoster virus.
A. Davison (1986)
10.1016/0378-1119(87)90183-1
The complete nucleotide sequence of the left very early region of Escherichia coli bacteriophage PRD1 coding for the terminal protein and the DNA polymerase.
H. Savilahti (1987)
10.1128/JVI.52.1.9-15.1984
Nucleotide sequence of the temperate Bacillus subtilis bacteriophage SPO2 DNA polymerase gene L.
B. Raden (1984)
Primary structure of T4 DNA polymerase. Evolutionary relatedness to eucaryotic and other procaryotic DNA polymerases.
E. Spicer (1988)
10.1073/PNAS.84.23.8287
Bacteriophage PRD1 DNA polymerase: evolution of DNA polymerases.
G. Jung (1987)
10.1073/PNAS.82.4.1074
A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes.
S. Tabor (1985)
10.1093/nar/12.1Part1.387
A comprehensive set of sequence analysis programs for the VAX
J. Devereux (1984)
Selective inactivation of the exonuclease activity of bacteriophage T7 DNA polymerase by in vitro mutagenesis.
S. Tabor (1989)
10.1093/NAR/13.22.8143
DNA sequence of the region in the genome of herpes simplex virus type 1 containing the genes for DNA polymerase and the major DNA binding protein.
J. Quinn (1985)
10.1016/0003-2697(83)90689-9
Improved conditions for activity gel analysis of DNA polymerase catalytic polypeptides.
E. Karawya (1983)
10.1016/0042-6822(86)90021-8
Effect of aphidicolin and nucleotide analogs on the phage phi 29 DNA polymerase.
L. Blanco (1986)
10.1016/0042-6822(88)90122-5
The location, sequence, transcription, and regulation of a baculovirus DNA polymerase gene.
M. Tomalski (1988)
10.1016/0968-0004(87)90143-5
DNA polymerase I: from crystal structure to function via genetics
C. Joyce (1987)
10.1038/313762A0
Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP
D. Ollis (1985)
10.1093/NAR/13.4.1239
Characterization of a 3'----5' exonuclease activity in the phage phi 29-encoded DNA polymerase.
L. Blanco (1985)
10.1093/NAR/12.15.6011
Nucleotide sequence and transcription analysis of a linear DNA plasmid associated with the killer character of the yeast Khuyveromyces lactis
M. Stark (1984)
10.1073/PNAS.79.18.5522
Initiation of phage phi 29 DNA replication in vitro: formation of a covalent complex between the terminal protein, p3, and 5'-dAMP.
M. A. Peñalva (1982)
10.1002/PROT.340010111
A domain of the klenow fragment of Escherichia coli DNA polymerase I has polymerase but no exonuclease activity
P. Freemont (1986)
10.1038/310207A0
DNA sequence and expression of the B95-8 Epstein—Barr virus genome
R. Baer (1984)
10.1016/0022-2836(86)90385-2
Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes.
F. W. Studier (1986)
10.1002/j.1460-2075.1985.tb03749.x
Nucleotide sequence of the S‐1 mitochondrial DNA from the S cytoplasm of maize
M. Paillard (1985)
10.1002/j.1460-2075.1988.tb02781.x
Human DNA polymerase alpha gene expression is cell proliferation dependent and its primary structure is similar to both prokaryotic and eukaryotic replicative DNA polymerases.
S. W. Wong (1988)
10.1073/PNAS.81.17.5325
Characterization and purification of a phage phi 29-encoded DNA polymerase required for the initiation of replication.
L. Blanco (1984)
10.1073/PNAS.86.12.4421
DNA polymerase III gene of Bacillus subtilis.
B. Sanjanwala (1989)
10.1073/PNAS.82.19.6404
Replication of phage phi 29 DNA with purified terminal protein and DNA polymerase: synthesis of full-length phi 29 DNA.
L. Blanco (1985)
10.1073/PNAS.84.16.5635
A cryptic proofreading 3'----5' exonuclease associated with the polymerase subunit of the DNA polymerase-primase from Drosophila melanogaster.
S. M. Cotterill (1987)
Isolation, characterization, and expression in Escherichia coli of the DNA polymerase gene from Thermus aquaticus.
F. C. Lawyer (1989)
10.1016/s0022-2836(64)80089-9
Enzymatic synthesis of deoxyribonucleic acid.
A. Kornberg (1957)
Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I.
C. Joyce (1982)
10.1111/J.1432-1033.1976.TB11091.X
Transcription in vitro of phi29 DNA and EcoRI fragments by Bacillus subtilis RNA polymerase.
M. R. Inciarte (1976)
10.13039/501100003339
Characterization of the polA gene of Streptococcus pneumoniae and comparison of the DNA polymerase I it encodes to homologous enzymes from Escherichia coli and phage T7.
P. López (1989)



This paper is referenced by
10.1007/BF00712969
A DNA-polymerase-related reading frame (pol-r) in the mtDNA ofSecale cereale
G. Dohmen (2004)
10.1074/jbc.271.15.8509
Relating Structure to Function in 29 DNA Polymerase (*)
L. Blanco (1996)
10.1007/978-1-4615-4707-5_8
Mechanisms of initiation of linear DNA replication in prokaryotes.
M. Salas (1999)
10.1007/PL00006461
Phylogeny of Organisms Investigated by the Base-Pair Changes in the Stem Regions of Small and Large Ribosomal Subunit RNAs
J. Otsuka (1999)
10.1016/J.JMB.2004.02.018
phi29 DNA polymerase-terminal protein interaction. Involvement of residues specifically conserved among protein-primed DNA polymerases.
I. Rodríguez (2004)
10.1073/PNAS.0600833103
Self-synthesizing DNA transposons in eukaryotes.
V. Kapitonov (2006)
10.1016/0042-6822(91)90685-5
Characterization of 3'-to 5'-exonuclease activity associated with Epstein-Barr virus DNA polymerase.
T. Tsurumi (1991)
10.1007/978-3-642-85004-2_6
Herpes Simplex Virus Type 1 DNA Polymerase: Eukaryotic Model Enzyme and Principal Target of Antiviral Therapy
C. W. Knopf (1994)
10.1016/0378-1119(95)00215-R
Isolation and characterization of ten mutator alleles of the mitochondrial DNA polymerase-encoding MIP1 gene from Saccharomyces cerevisiae.
J. Hu (1995)
10.1002/(SICI)1097-0061(19970615)13:7<613::AID-YEA116>3.0.CO;2-B
The Linear Plasmid pDHL1 from Debaryomyces hansenii Encodes a Protein Highly Homologous to the pGKL1‐Plasmid DNA Polymerase
K. Fukuda (1997)
10.1073/pnas.1718787115
Noncatalytic aspartate at the exonuclease domain of proofreading DNA polymerases regulates both degradative and synthetic activities
Alicia del Prado (2018)
10.1016/j.molcel.2013.09.025
PrimPol, an Archaic Primase/Polymerase Operating in Human Cells
Sara García-Gómez (2013)
5 Mechanisms for Priming DNA Synthesis
M. Salas (2005)
10.1074/jbc.274.42.30094
Exonuclease X of Escherichia coli
M. Viswanathan (1999)
Cellular factors involved with, and fidelity of herpes simplex virus replication
R. O. Baker (1999)
10.1038/ni788
Distinct and opposite diversifying activities of terminal transferase splice variants
T. Thai (2002)
10.1021/CR040463D
DNA polymerase gamma in mitochondrial DNA replication and repair.
M. A. Graziewicz (2006)
10.1371/journal.pgen.1008271
Viral quasispecies
E. Domingo (2019)
10.1371/journal.pone.0048257
The Essential Role of the 3′ Terminal Template Base in the First Steps of Protein-Primed DNA Replication
I. Rodríguez (2012)
10.3390/biom9110648
The Loop of the TPR1 Subdomain of Phi29 DNA Polymerase Plays a Pivotal Role in Primer-Terminus Stabilization at the Polymerization Active Site
Alicia del Prado (2019)
10.1111/J.1574-6976.1995.TB00189.X
Protein-nucleic acid interactions in bacteriophage phi 29 DNA replication.
M. Salas (1995)
10.1016/0167-4781(94)90048-5
Purification and characterization of PRD1 DNA polymerase.
W. Zhu (1994)
10.1101/087969459.31.131
Mechanisms for Priming DNA Synthesis
M. Salas (1996)
10.1074/jbc.X112.433458
My Life with Bacteriophage φ29
M. Salas (2012)
10.1128/AAC.00633-06
Multidrug Resistance Conferred by Novel DNA Polymerase Mutations in Human Cytomegalovirus Isolates
G. Scott (2006)
10.1074/jbc.273.37.24075
Impaired Mismatch Extension by a Herpes Simplex DNA Polymerase Mutant with an Editing Nuclease Defect*
R. O. Baker (1998)
10.1093/NAR/29.5.1017
Exoribonuclease superfamilies: structural analysis and phylogenetic distribution.
Y. Zuo (2001)
10.1007/BF02451783
Structural and functional studies on ø29 DNA polymerase
M. Blasco (2006)
Probing the base stacking contributions during translesion DNA synthesis.
Babho Devadoss (2008)
10.1371/journal.pone.0072765
Dual Role of φ29 DNA Polymerase Lys529 in Stabilisation of the DNA Priming-Terminus and the Terminal Protein-Priming Residue at the Polymerisation Site
Alicia del Prado (2013)
10.1073/pnas.1501715112
Clonality and intracellular polyploidy in virus evolution and pathogenesis
C. Perales (2015)
10.1007/BF00260660
Genetic structure and domains of DNA polymerase III of Bacillus subtilis
B. Sanjanwala (2004)
See more
Semantic Scholar Logo Some data provided by SemanticScholar