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Escherichia coli K-12 substr. MG1655 Polypeptide: DNA polymerase III, γ subunit



Gene: dnaX Accession Numbers: EG10245 (EcoCyc), b0470, ECK0464

Synonyms: dnaZ

Regulation Summary Diagram: ?

Summary:
The gamma subunit of polymerase III is generated by a programmed frameshift that occurs about half the time and leads to early termination of translation and a protein that lacks the final two domains found in tau. The frameshift occurs in a poly(A) tract and yields a new stop codon immediately following the frameshift signal [Tsuchihashi90, Flower90, Blinkowa90]. Frameshift depends on base pairing between the 3' end of the 16S rRNA and a sequence upstream from the poly(A) tract, as well as the presence of a stable stem loop 3' from the shift point [Larsen94, Larsen97].

The third domain of gamma, which is shared with the tau subunit, is required for oligomerization of both gamma and tau, and also includes the binding sites for delta, delta', chi and psi [Glover01, Gao01b].

Crystal structures of the amino-terminal half of gamma in ATP-bound and unbound states show that ATP binding induces a conformational change that should disrupt dimerization of gamma [Podobnik03].
As described in the gamma subunit description, DnaX undergoes a programmed -1 frameshift roughly half of the time that yields a new stop codon just after the frameshift point [Tsuchihashi90, Flower90, Blinkowa90].

The "Spliced Nucleotide Sequence" link above refers to this frameshifted variant, but note that no splicing occurs.

Citations: [Hubscher80]

Gene Citations: [Chen93]

Locations: cytosol

Map Position: [491,316 -> 493,247] (10.59 centisomes)
Length: 1932 bp / 431 aa

Molecular Weight of Polypeptide: 47.545 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001633 , CGSC:838 , EchoBASE:EB0241 , EcoGene:EG10245 , OU-Microarray:b0470 , PortEco:dnaX , RegulonDB:EG10245

Relationship Links: EcoliWiki:RELATED-TO:b0470 , Pfam:IN-FAMILY:PF00004 , UniProt:RELATED-TO:P06710

In Paralogous Gene Group: 134 (5 members)

Gene-Reaction Schematic: ?

GO Terms:

Cellular Component: GO:0005737 - cytoplasm
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer DNA related DNA replication

Essentiality data for dnaX knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[UniProt12b]
UniProt: Removed.
Nucleotide-Phosphate-Binding-Region 45 -> 52
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: potential;
Intrinsic-Sequence-Variant 431
[UniProt12b]
Alternate sequence: E → E; UniProt: (in isoform gamma).


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

Exons/Introns:

History:
10/20/97 Gene b0470 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10245; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Blinkowa90: Blinkowa AL, Walker JR (1990). "Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III gamma subunit from within the tau subunit reading frame." Nucleic Acids Res 18(7);1725-9. PMID: 2186364

Chen93: Chen KS, Saxena P, Walker JR (1993). "Expression of the Escherichia coli dnaX gene." J Bacteriol 175(20);6663-70. PMID: 7691799

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Flower90: Flower AM, McHenry CS (1990). "The gamma subunit of DNA polymerase III holoenzyme of Escherichia coli is produced by ribosomal frameshifting." Proc Natl Acad Sci U S A 87(10);3713-7. PMID: 2187190

Gao01b: Gao D, McHenry CS (2001). "Tau binds and organizes Escherichia coli replication proteins through distinct domains. Domain III, shared by gamma and tau, binds delta delta ' and chi psi." J Biol Chem 276(6);4447-53. PMID: 11078742

Glover01: Glover BP, Pritchard AE, McHenry CS (2001). "tau binds and organizes Escherichia coli replication proteins through distinct domains: domain III, shared by gamma and tau, oligomerizes DnaX." J Biol Chem 276(38);35842-6. PMID: 11463787

Hubscher80: Hubscher U, Kornberg A (1980). "The dnaZ protein, the gamma subunit of DNA polymerase III holoenzyme of Escherichia coli." J Biol Chem 255(24);11698-703. PMID: 6254978

Larsen94: Larsen B, Wills NM, Gesteland RF, Atkins JF (1994). "rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift." J Bacteriol 176(22);6842-51. PMID: 7961443

Larsen97: Larsen B, Gesteland RF, Atkins JF (1997). "Structural probing and mutagenic analysis of the stem-loop required for Escherichia coli dnaX ribosomal frameshifting: programmed efficiency of 50%." J Mol Biol 271(1);47-60. PMID: 9300054

Podobnik03: Podobnik M, Weitze TF, O'Donnell M, Kuriyan J (2003). "Nucleotide-induced conformational changes in an isolated Escherichia coli DNA polymerase III clamp loader subunit." Structure 11(3);253-63. PMID: 12623013

Tsuchihashi90: Tsuchihashi Z, Kornberg A (1990). "Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme." Proc Natl Acad Sci U S A 87(7);2516-20. PMID: 2181440

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12b: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

Other References Related to Gene Regulation

Flower86: Flower AM, McHenry CS (1986). "The adjacent dnaZ and dnaX genes of Escherichia coli are contained within one continuous open reading frame." Nucleic Acids Res 14(20);8091-101. PMID: 3534795


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sat Dec 20, 2014, biocyc14.