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

Gene: holD Accession Numbers: EG11414 (EcoCyc), b4372, ECK4363

Regulation Summary Diagram

Regulation summary diagram for holD

Component of:
DNA polymerase III, ψ-χ subunit (extended summary available)
DNA polymerase III, holoenzyme (extended summary available)

Citations: [Xiao93, Carter93]

Locations: cytosol

Map Position: [4,605,826 -> 4,606,239] (99.27 centisomes, 357°)
Length: 414 bp / 137 aa

Molecular Weight of Polypeptide: 15.174 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0014340, CGSC:31460, DIP:DIP-9934N, EchoBASE:EB1386, EcoGene:EG11414, EcoliWiki:b4372, Mint:MINT-1224283, ModBase:P28632, OU-Microarray:b4372, PortEco:holD, PR:PRO_000022919, Protein Model Portal:P28632, RefSeq:NP_418789, RegulonDB:EG11414, SMR:P28632, String:511145.b4372, UniProt:P28632

Relationship Links: InterPro:IN-FAMILY:IPR004615, InterPro:IN-FAMILY:IPR018382, PDB:Structure:1EM8, PDB:Structure:3GLI, PDB:Structure:3SXU, Pfam:IN-FAMILY:PF03603, ProDom:IN-FAMILY:PD032475

Gene-Reaction Schematic

Gene-Reaction Schematic

GO Terms:
Biological Process:
Inferred by computational analysisGO:0006260 - DNA replication [UniProtGOA11, GOA01]
Inferred by computational analysisGO:0071897 - DNA biosynthetic process [UniProtGOA11, GOA01a, GOA01]
Inferred by computational analysisGO:0090305 - nucleic acid phosphodiester bond hydrolysis [GOA01]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Rajagopala14, Marceau11, Kelman98, Xiao93a, Naktinis95, Olson95, Rajagopala12, Simonetta09, Song01, Glover01, Gao01, Butland05, Gulbis04]
Inferred by computational analysisGO:0003887 - DNA-directed DNA polymerase activity [UniProtGOA11, GOA01a, GOA01]
Inferred by computational analysisGO:0008408 - 3'-5' exonuclease activity [GOA01]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11]
Inferred by computational analysisGO:0016779 - nucleotidyltransferase activity [UniProtGOA11]
Cellular Component:
GO:0005737 - cytoplasm []
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: information transferDNA relatedDNA replication

Essentiality data for holD knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Subunit of: DNA polymerase III, ψ-χ subunit

Subunit composition of DNA polymerase III, ψ-χ subunit = [HolC][HolD]
         DNA polymerase III, χ subunit = HolC
         DNA polymerase III, ψ subunit = HolD

Component of: DNA polymerase III, holoenzyme (extended summary available)

The ψ-χ dimer is an accessory protein that significantly enhances the ability of the DNA polymerase III preiniation complex to bind template DNA and initiate replication.

ψ-χ acts in multiple ways to improve polymerase binding and subsequent activity. The dimer interacts directly with single-strand binding protein (SSB) via binding to the carboxy-terminus of SSB [Glover98, Witte03, Kelman98]. This increases the overall affinity of the preinitiation complex for SSB-bound template [Glover98]. The interaction between the ψ subunit of ψ-χ and the preinitation complex also stabilizes the high-DNA-affinity, post-ATP state of the preinitiation complex, helping maintain the complex's affinity for template DNA [Anderson07]. Finally, the binding of the χ subunit to SSB disrupts the SSB-primase interaction, aiding release of primase from the primer, thus paving the way for the initiation of replication [Yuzhakov99].

ψ-χ interacts with the preinitiation complex via binding of the ψ amino-terminus to the complex. A 3.5 Å structure of the isolated ψ amino-terminus bound to this complex suggests tight binding [Simonetta09].

The structure of the ψ-χ dimer has been crystallized to 2.1 Å resolution [Olson95, Gulbis04, Xiao93a].

Created 04-Nov-2010 by Shearer A, SRI International

Subunit of: DNA polymerase III, holoenzyme

Subunit composition of DNA polymerase III, holoenzyme = [(DnaE)(DnaQ)(HolE)]3[(DnaX)3(HolB)(HolA)][(DnaN)2]2[(DnaX)2][(HolC)(HolD)]4
         DNA polymerase III, core enzyme = (DnaE)(DnaQ)(HolE) (summary available)
                 DNA polymerase III, α subunit = DnaE (extended summary available)
                 DNA polymerase III, ε subunit = DnaQ (extended summary available)
                 DNA polymerase III, θ subunit = HolE (extended summary available)
         DNA polymerase III, preinitiation complex = (DnaX)3(HolB)(HolA) (extended summary available)
                 DNA polymerase III, τ subunit = DnaX
                 DNA polymerase III, δ prime subunit = HolB (summary available)
                 DNA polymerase III, δ subunit = HolA (summary available)
         DNA polymerase III, β subunit = (DnaN)2 (extended summary available)
         DNA polymerase III, τ subunit dimer = (DnaX)2 (extended summary available)
                 DNA polymerase III, τ subunit = DnaX
         DNA polymerase III, ψ-χ subunit = (HolC)(HolD) (extended summary available)
                 DNA polymerase III, χ subunit = HolC
                 DNA polymerase III, ψ subunit = HolD

DNA polymerase III holoenzyme is the enzyme primarily responsible for replicative DNA synthesis in E. coli. It carries out primer-initiated 5' to 3' polymerization of DNA on a single-stranded DNA template, as well as 3' to 5' exonucleolytic editing of mispaired nucleotides.

Replicative DNA polymerization begins when the preinitiation complex binds single-stranded DNA near an RNA primer. The preinitiation complex then loads the beta processivity clamp onto the DNA at this site, after which three core polymerases, chaperoned into place by the tau subunit, bind to the processivity clamp, with one polymerase on the leading strand and two on the lagging. DNA is synthesized 5' to 3' from primers on both the leading and lagging strands, covalently attaching the newly synthesized DNA to the primer. Tau displaces beta in the presence of duplex DNA, dissociating the polymerase from the template when it reaches a temporary stop on the lagging strand or when synthesis is complete on either strand [Maki88, Maki88a, Onrust95, Maki88b, Nusslein76, ReyesLamothe10].

For more detailed discussion of the stages of polymerase binding and DNA synthesis, see the individual entries for DNA polymerase III, preinitiation complex, DNA polymerase III, β subunit, DNA polymerase III, τ subunit dimer, DNA polymerase III, core enzyme and their constituent parts.

DNA polymerase III binds a region about 30 nucleotides long upstream of the RNA primer, with the alpha subunit making contact 9 nucleotides upstream and the beta clamp making contact 22 nucleotides upstream [Reems95, Reems94]. The preinitiation complex binds an area larger than this prior to being displaced by the core polymerase [Reems94]. In the presence of DNA polymerase III, RNA primer length is limited to 10 nucleotides, a limitation that is independent of the epsilon-mediated 3' to 5' exonuclease activity [Zechner92].

During polymerization, DNA polymerase III pauses at sites of potential secondary structure [LaDuca83]. The holoenzyme can traverse distances as long as 400 base pairs of duplex DNA to reach the next available 3' end and restart synthesis [ODonnell85]. Such jumps within the same template take 2 to 5 seconds, whereas transfer to a new template takes 30 seconds [Burgers83].

DNA polymerase III is required for several kinds of DNA repair, including some forms of double-strand break repair, fixing hydrogen-peroxide-induced damage and methyl-directed mismatch repair [Motamedi99, Hagensee89, Cooper93]. Mutations that inhibit polymerase III stimulate repeat expansion and lead to lower levels of unsaturation in fatty acids [Morag99, Suzuki98].

UV mutagenesis and gap repair following UV damage to DNA both involve DNA polymerase III [CohenFix94, Tomer96]. The polymerase stalls at pyrimidine photodimers in vitro, but is capable of bypassing such lesions to continue synthesis [Shwartz87, Livneh86]. This bypass activity is stimulated by single-strand binding protein (SSB) but inhibited by the polymerase III beta subunit, which explains the relatively low rate of bypass in vivo [Shwartz87, Shavitt89].

Citations: [Cull95]

Last-Curated 09-Jan-2006 by Shearer A, SRI International

Sequence Features

Protein sequence of DNA polymerase III, psi subunit with features indicated

Feature Class Location Citations Comment
Pfam PF03603 3 -> 127
Inferred by computational analysis[Finn14]
DNA_III_psi : DNA polymerase III psi subunit

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram


10/20/97 Gene b4372 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11414; confirmed by SwissProt match.


Anderson07: Anderson SG, Williams CR, O'donnell M, Bloom LB (2007). "A function for the psi subunit in loading the Escherichia coli DNA polymerase sliding clamp." J Biol Chem 282(10);7035-45. PMID: 17210572

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

Burgers83: Burgers PM, Kornberg A (1983). "The cycling of Escherichia coli DNA polymerase III holoenzyme in replication." J Biol Chem 258(12);7669-75. PMID: 6345527

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Carter93: Carter JR, Franden MA, Aebersold R, McHenry CS (1993). "Identification, isolation, and overexpression of the gene encoding the psi subunit of DNA polymerase III holoenzyme." J Bacteriol 175(17);5604-10. PMID: 8366044

CohenFix94: Cohen-Fix O, Livneh Z (1994). "In vitro UV mutagenesis associated with nucleotide excision-repair gaps in Escherichia coli." J Biol Chem 269(7);4953-8. PMID: 8106470

Cooper93: Cooper DL, Lahue RS, Modrich P (1993). "Methyl-directed mismatch repair is bidirectional." J Biol Chem 268(16);11823-9. PMID: 8389365

Cull95: Cull MG, McHenry CS (1995). "Purification of Escherichia coli DNA polymerase III holoenzyme." Methods Enzymol 262;22-35. PMID: 8594350

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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

Gao01: 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

Glover98: Glover BP, McHenry CS (1998). "The chi psi subunits of DNA polymerase III holoenzyme bind to single-stranded DNA-binding protein (SSB) and facilitate replication of an SSB-coated template." J Biol Chem 273(36);23476-84. PMID: 9722585

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Gulbis04: Gulbis JM, Kazmirski SL, Finkelstein J, Kelman Z, O'Donnell M, Kuriyan J (2004). "Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex." Eur J Biochem 271(2);439-49. PMID: 14717711

Hagensee89: Hagensee ME, Moses RE (1989). "Multiple pathways for repair of hydrogen peroxide-induced DNA damage in Escherichia coli." J Bacteriol 171(2);991-5. PMID: 2644241

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kelman98: Kelman Z, Yuzhakov A, Andjelkovic J, O'Donnell M (1998). "Devoted to the lagging strand-the subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly." EMBO J 17(8);2436-49. PMID: 9545254

LaDuca83: LaDuca RJ, Fay PJ, Chuang C, McHenry CS, Bambara RA (1983). "Site-specific pausing of deoxyribonucleic acid synthesis catalyzed by four forms of Escherichia coli DNA polymerase III." Biochemistry 22(22);5177-88. PMID: 6360204

Livneh86: Livneh Z (1986). "Mechanism of replication of ultraviolet-irradiated single-stranded DNA by DNA polymerase III holoenzyme of Escherichia coli. Implications for SOS mutagenesis." J Biol Chem 261(20);9526-33. PMID: 2941423

Maki88: Maki S, Kornberg A (1988). "DNA polymerase III holoenzyme of Escherichia coli. III. Distinctive processive polymerases reconstituted from purified subunits." J Biol Chem 263(14);6561-9. PMID: 3283127

Maki88a: Maki S, Kornberg A (1988). "DNA polymerase III holoenzyme of Escherichia coli. II. A novel complex including the gamma subunit essential for processive synthesis." J Biol Chem 263(14);6555-60. PMID: 3283126

Maki88b: Maki H, Maki S, Kornberg A (1988). "DNA Polymerase III holoenzyme of Escherichia coli. IV. The holoenzyme is an asymmetric dimer with twin active sites." J Biol Chem 263(14);6570-8. PMID: 3283128

Marceau11: Marceau AH, Bahng S, Massoni SC, George NP, Sandler SJ, Marians KJ, Keck JL (2011). "Structure of the SSB-DNA polymerase III interface and its role in DNA replication." EMBO J 30(20);4236-47. PMID: 21857649

Morag99: Morag AS, Saveson CJ, Lovett ST (1999). "Expansion of DNA repeats in Escherichia coli: effects of recombination and replication functions." J Mol Biol 289(1);21-7. PMID: 10339402

Motamedi99: Motamedi MR, Szigety SK, Rosenberg SM (1999). "Double-strand-break repair recombination in Escherichia coli: physical evidence for a DNA replication mechanism in vivo." Genes Dev 13(21);2889-903. PMID: 10557215

Naktinis95: Naktinis V, Onrust R, Fang L, O'Donnell M (1995). "Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. II. Intermediate complex between the clamp loader and its clamp." J Biol Chem 270(22);13358-65. PMID: 7768937

Nusslein76: Nusslein V, Henke S, Johnston LH (1976). "Replication of E. coli duplex DNA in vitro. The separation of the DNA containing fractions of a lysate from the soluble enzymes and their complementation properties." Mol Gen Genet 145(2);183-90. PMID: 778584

ODonnell85: O'Donnell ME, Kornberg A (1985). "Dynamics of DNA polymerase III holoenzyme of Escherichia coli in replication of a multiprimed template." J Biol Chem 260(23);12875-83. PMID: 2413035

Olson95: Olson MW, Dallmann HG, McHenry CS (1995). "DnaX complex of Escherichia coli DNA polymerase III holoenzyme. The chi psi complex functions by increasing the affinity of tau and gamma for' to a physiologically relevant range." J Biol Chem 270(49);29570-7. PMID: 7494000

Onrust95: Onrust R, Finkelstein J, Turner J, Naktinis V, O'Donnell M (1995). "Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. III. Interface between two polymerases and the clamp loader." J Biol Chem 270(22);13366-77. PMID: 7768938

Rajagopala12: Rajagopala SV, Sikorski P, Caufield JH, Tovchigrechko A, Uetz P (2012). "Studying protein complexes by the yeast two-hybrid system." Methods 58(4);392-9. PMID: 22841565

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Reems94: Reems JA, McHenry CS (1994). "Escherichia coli DNA polymerase III holoenzyme footprints three helical turns of its primer." J Biol Chem 269(52);33091-6. PMID: 7806536

Reems95: Reems JA, Wood S, McHenry CS (1995). "Escherichia coli DNA polymerase III holoenzyme subunits alpha, beta, and gamma directly contact the primer-template." J Biol Chem 270(10);5606-13. PMID: 7890680

ReyesLamothe10: Reyes-Lamothe R, Sherratt DJ, Leake MC (2010). "Stoichiometry and architecture of active DNA replication machinery in Escherichia coli." Science 328(5977);498-501. PMID: 20413500

Shavitt89: Shavitt O, Livneh Z (1989). "The beta subunit modulates bypass and termination at UV lesions during in vitro replication with DNA polymerase III holoenzyme of Escherichia coli." J Biol Chem 264(19);11275-81. PMID: 2661556

Shwartz87: Shwartz H, Livneh Z (1987). "Dynamics of termination during in vitro replication of ultraviolet-irradiated DNA with DNA polymerase III holoenzyme of Escherichia coli." J Biol Chem 262(22);10518-23. PMID: 2956258

Simonetta09: Simonetta KR, Kazmirski SL, Goedken ER, Cantor AJ, Kelch BA, McNally R, Seyedin SN, Makino DL, O'Donnell M, Kuriyan J (2009). "The mechanism of ATP-dependent primer-template recognition by a clamp loader complex." Cell 137(4);659-71. PMID: 19450514

Song01: Song MS, McHenry CS (2001). "Carboxyl-terminal domain III of the delta' subunit of DNA polymerase III holoenzyme binds DnaX and supports cooperative DnaX complex assembly." J Biol Chem 276(52);48709-15. PMID: 11606586

Suzuki98: Suzuki E, Kondo T, Makise M, Mima S, Sakamoto K, Tsuchiya T, Mizushima T (1998). "Alteration in levels of unsaturated fatty acids in mutants of Escherichia coli defective in DNA replication." Biol Pharm Bull 21(7);657-61. PMID: 9703244

Tomer96: Tomer G, Cohen-Fix O, O'Donnell M, Goodman M, Livneh Z (1996). "Reconstitution of repair-gap UV mutagenesis with purified proteins from Escherichia coli: a role for DNA polymerases III and II." Proc Natl Acad Sci U S A 93(4);1376-80. PMID: 8643639

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Witte03: Witte G, Urbanke C, Curth U (2003). "DNA polymerase III chi subunit ties single-stranded DNA binding protein to the bacterial replication machinery." Nucleic Acids Res 31(15);4434-40. PMID: 12888503

Xiao93: Xiao H, Crombie R, Dong Z, Onrust R, O'Donnell M (1993). "DNA polymerase III accessory proteins. III. holC and holD encoding chi and psi." J Biol Chem 268(16);11773-8. PMID: 8389364

Xiao93a: Xiao H, Dong Z, O'Donnell M (1993). "DNA polymerase III accessory proteins. IV. Characterization of chi and psi." J Biol Chem 268(16);11779-84. PMID: 8505305

Yuzhakov99: Yuzhakov A, Kelman Z, O'Donnell M (1999). "Trading places on DNA--a three-point switch underlies primer handoff from primase to the replicative DNA polymerase." Cell 96(1);153-63. PMID: 9989506

Zechner92: Zechner EL, Wu CA, Marians KJ (1992). "Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. III. A polymerase-primase interaction governs primer size." J Biol Chem 267(6);4054-63. PMID: 1531480

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

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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 19.5 on Sun Nov 29, 2015, BIOCYC14B.