Primary structure of T4 DNA polymerase. Evolutionary relatedness to eucaryotic and other procaryotic DNA polymerases.

Spicer, Eleanor K.; Rush, A. John; Fung, Celia; Reha-Krantz, Linda J.; Karam, J.D.; Konigsberg, William H.

doi:10.1016/s0021-9258(18)68523-0

Cited by 132 publications

(23 citation statements)

References 83 publications

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“…However, there are additional interactions between the four nucleotides and residues of the polymerase thumb domain (S735, S784, N786, F828, and K829), resulting in the substrate being completely surrounded by the polymerase (Figure 6B). Also in contrast to the T4 gp43 fragment of other studies (Reha-Krantz, 1988;Sattar et al, 1996) Only two Asp residues (open circles) are conserved among the four that certain mutations in either the polymerase or the enzymes. Asp-186 in HIV RT is either a Ser (square) or Glu (closed exonuclease domains affect both the polymerase and circle) in the other enzymes.…”

Section: Structural Overviewmentioning

confidence: 74%

Crystal Structure of a pol α Family Replication DNA Polymerase from Bacteriophage RB69

Wang¹,

Sattar²,

Wang

et al. 1997

Cell

438

508

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The 2.8 A resolution crystal structure of the bacteriophage RB69 gp43, a member of the eukaryotic pol alpha family of replicative DNA polymerases, shares some similarities with other polymerases but shows many differences. Although its palm domain has the same topology as other polymerases, except rat DNA polymerase beta, one of the three carboxylates required for nucleotidyl transfer is located on a different beta strand. The structures of the fingers and thumb domains are unrelated to all other known polymerase structures. The editing 3'-5' exonuclease domain of gp43 is homologous to that of E. coli DNA polymerase I but lies on the opposite side of the polymerase active site. An extended structure-based alignment of eukaryotic DNA polymerase sequences provides structural insights that should be applicable to most eukaryotic DNA polymerases.

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Section: Structural Overviewmentioning

confidence: 74%

Crystal Structure of a pol α Family Replication DNA Polymerase from Bacteriophage RB69

Wang¹,

Sattar²,

Wang

et al. 1997

Cell

438

508

View full text Add to dashboard Cite

show abstract

“…This motif is highly conserved among B family DNA polymerases but absent in the pol I (A family). Because the Exo I′ motif in the polymerase B family closely resembles the Exo I motif of the pol I family, they were previously misaligned (Spicer et al, 1988).…”

Section: Resultsmentioning

confidence: 99%

“…The DNA polymerase of bacteriophage T4 is an essential component of the T4-encoded DNA replication complex. In addition to polymerase activity it has an editing 3′-5′ exonuclease activity located in a region proximal to the polymerase domain (Spicer et al, 1988), a situation similar to that observed in the Klenow fragment (KF) 1 of Escherichia coli DNA polymerase I. However, the exonuclease activity of the T4 enzyme is about 10 3 times greater than that of KF (Huang & Lehman, 1972;Capson et al, 1992;Lin et al, 1994;Bloom et al, 1994).…”

mentioning

confidence: 87%

Crystal Structures of an NH₂-Terminal Fragment of T4 DNA Polymerase and Its Complexes with Single-Stranded DNA and with Divalent Metal Ions

et al. 1996

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We report the crystal structure of an NH2-terminal 388-residue fragment of T4 DNA polymerase (protein N388) refined at 2.2 A resolution. This fragment contains both the 3'-5' exonuclease active site and part of the autologous mRNA binding site (J. D. Karam, personal communication). The structure of a complex between the apoprotein N388 and a substrate, p(dT)3, has been refined at 2.5 A resolution to a crystallographic R-factor of 18.7%. Two divalent metal ion cofactors, Zn(II) and Mn(II), have been located in crystals of protein N388 which had been soaked in solutions containing Zn(II), Mn(II), or both. The structure of the 3'-5' exonuclease domain of protein N388 closely resembles the corresponding region in the Klenow fragment despite minimal sequence identity. The side chains of four carboxylate residues that serve as ligands for the two metal ions required for catalysis are located in geometrically equivalent positions in both proteins with a rms deviation of 0.87 A. There are two main differences between the 3'-5' exonuclease active site regions of the two proteins: (I) the OH of Tyr-497 in the Klenow fragment interacts with the scissile phosphate in the active site whereas the OH of the equivalent tyrosine (Tyr-320) in protein N388 points away from the active center; (II) different residues form of the binding pocket for the 3'-terminal bases of the substrate. In the protein N388 complex the 3'-terminal base of p(dT)3 is rotated approximately 60 degrees relative to the position that the corresponding base occupies in the p(dT)3 complex with the Klenow fragment. Finally, a separate domain (residues 1-96) of protein N388 may be involved in mRNA binding that results in translational regulation of T4 DNA polymerase (Pavlov & Karam, 1994).

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“…Numbers below the HSV-1 sequence indicate the residue number which initiates each group of conserved residues. Also shown is an alignment between the HSV-1 (hsv) sequence ( 43) and other DNA polymerase sequences from Epstein Barr virus (ebv) (44), varicella zoster virus (vzv) (45), human cytomegalovirus (cmv) (46), vaccinia virus (47), baculovirus (48), human cells (DNA polymerase alpha) (17), yeast (DNA polymerase 1 (49) and DNA polymerase I (50)), yeast killer plasmid pGKL1 (51), maize mitochondria (52), adenovirus-2 (53), 429 bacteriophage (54), PRD1 bacteriophage (55,56) and T4 bacteriophage (57). Only regions which exhibit high similarity are shown in detail.…”

Section: Discussionmentioning

confidence: 99%

Aphidicolin resistance in Herpes simplex virus type I reveals features of the DNA polymerase dNTP binding site

et al. 1989

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We describe the mapping and sequencing of mutations within the DNA polymerase gene of herpes simplex virus type 1 which confer resistance to aphidicolin, a DNA polymerase inhibitor. The mutations occur near two regions which are highly conserved among DNA polymerases related to the herpes simplex enzyme. They also occur near other herpes simplex mutations which affect the interactions between the polymerase and deoxyribonucleoside triphosphate substrates. Consequently, we argue in favor of the idea that the aphidicolin binding site overlaps the substrate binding site and that the near-by conserved regions are functionally required for substrate binding. Our mutants also exhibit abnormal sensitivity to another DNA polymerase inhibitor, phosphonoacetic acid. This drug is thought to bind as an analogue of pyrophosphate. A second-site mutation which suppresses the hypersensitivity of one mutant to phosphonoacetic acid (but not its aphidicolin resistance) is described. This second mutation may represent a new class of mutations, which specifically affects pyrophosphate, but not substrate, binding.

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Primary structure of T4 DNA polymerase. Evolutionary relatedness to eucaryotic and other procaryotic DNA polymerases.

Cited by 132 publications

References 83 publications

Crystal Structure of a pol α Family Replication DNA Polymerase from Bacteriophage RB69

Crystal Structure of a pol α Family Replication DNA Polymerase from Bacteriophage RB69

Crystal Structures of an NH₂-Terminal Fragment of T4 DNA Polymerase and Its Complexes with Single-Stranded DNA and with Divalent Metal Ions

Aphidicolin resistance in Herpes simplex virus type I reveals features of the DNA polymerase dNTP binding site

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Primary structure of T4 DNA polymerase. Evolutionary relatedness to eucaryotic and other procaryotic DNA polymerases.

Cited by 132 publications

References 83 publications

Crystal Structure of a pol α Family Replication DNA Polymerase from Bacteriophage RB69

Crystal Structure of a pol α Family Replication DNA Polymerase from Bacteriophage RB69

Crystal Structures of an NH2-Terminal Fragment of T4 DNA Polymerase and Its Complexes with Single-Stranded DNA and with Divalent Metal Ions

Aphidicolin resistance in Herpes simplex virus type I reveals features of the DNA polymerase dNTP binding site

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Crystal Structures of an NH₂-Terminal Fragment of T4 DNA Polymerase and Its Complexes with Single-Stranded DNA and with Divalent Metal Ions