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43 DNA polymerase [ Escherichia phage RB69 ]

Gene ID: 1494172, updated on 31-May-2023

Summary

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Gene symbol
43
Gene description
DNA polymerase
Locus tag
RB69p056
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Escherichia phage RB69 (nat-host: Escherichia coli)
Lineage
Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Straboviridae; Tevenvirinae; Mosigvirus
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Genomic context

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Sequence:
NC_004928.1 (30639..33350, complement)

NC_004928.1Genomic Context describing neighboring genes Neighboring gene RB69ORF054c hypothetical protein Neighboring gene arabinose 5-phosphate isomerase Neighboring gene translation repressor Neighboring gene clamp loader small subunit Neighboring gene clamp loader of DNA polymerase

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_004928.1

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Modular organization of T4 DNA polymerase. Evidence from phylogenetics. Wang CC, et al. J Biol Chem, 1995 Nov 3. PMID 7592876

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The control of the discrimination between dNTP and rNTP in DNA and RNA polymerases has been described.
    Title: The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase.
  2. Co(2+) and Mn(2+) enhanced ground-state binding of both correct and incorrect dNTPs to RB69pol:dideoxy-terminated primer-template complexes.
    Title: Effect of Different Divalent Cations on the Kinetics and Fidelity of RB69 DNA Polymerase.
  3. Data indicate that alanine replacement of residues distant from the active site of the replicative RB69 DNA polymerase renders the enzyme incapable of sustaining phage replication in vivo.
    Title: A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site.
  4. structures of the various RB69pol ternary complexes can be used to rationalize the results obtained from pre-steady-state kinetic assays[review]
    Title: RB69 DNA polymerase structure, kinetics, and fidelity.
  5. Determined is the crystal structure of the dATP/tC(o)-containing ternary complex of the RB69 DNA polymerase Y567A mutant at 1.9 A resolution; the incoming dATP formed two hydrogen bonds with an imino-tautomerized form of tC(o).
    Title: Using a fluorescent cytosine analogue tC(o) to probe the effect of the Y567 to Ala substitution on the preinsertion steps of dNMP incorporation by RB69 DNA polymerase.
  6. evaluated the contribution of minor groove hydrogen bonding interactions with RB69pol
    Title: Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA.
  7. The miscoding potential of 5-hydroxycytosine arises due to template instability in the DNA polymerase active site.
    Title: The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site.
  8. The authors show that the S565G/Y567A mutant generally had greater base selectivity than the Y567A mutant and that the kinetic parameters for dNMP insertion, excision of the 3'-terminal nucleotide residue, and primer extension beyond a mispair differed.
    Title: Variation in mutation rates caused by RB69pol fidelity mutants can be rationalized on the basis of their kinetic behavior and crystal structures.
  9. The structure of an RB69 pol ternary complex at 1.8 A is reported. A network of five highly ordered, buried water molecules can be seen to interact with the N3 and O2 atoms in the minor groove of the DNA duplex.
    Title: Insights into base selectivity from the 1.8 Å resolution structure of an RB69 DNA polymerase ternary complex.
  10. When Y567A and S565G replacements were combined, mutator activity was strongly decreased compared to that with Y567A replacement alone.
    Title: Reversal of a mutator activity by a nearby fidelity-neutral substitution in the RB69 DNA polymerase binding pocket.
Submit: New GeneRIF Correction See all GeneRIFs (17)

General gene information

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Homology

General protein information

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Preferred Names
DNA polymerase
NP_861746.1
  • possesses DNA synthesis, 3' to 5' exonuclease (ssDNA), dNTP binding, and DNA binding activities; belongs to the DNA polymerase type-B family

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_004928.1 Reference assembly

    Range
    30639..33350 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_861746.1 DNA polymerase [Escherichia phage RB69]

    See identical proteins and their annotated locations for NP_861746.1

    Status: PROVISIONAL

    UniProtKB/Swiss-Prot
    Q38087, Q76XX8
    Conserved Domains (1) summary
    PHA02528
    Location:1 → 902
    43; DNA polymerase; Provisional
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
1CLQ_A.1
1IH7_A.1
1WAF_A.1
1WAF_B.1
1WAJ_A.1
3UIQ_A.1
Q38087.1

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