MG_001_MONOMER – DNA polymerase III, beta subunit

Name
WID	MG_001_MONOMER
Name	DNA polymerase III, beta subunit
Cross references	PDB: 1OK7, PDB: 3BEP

Genetics
Gene	MG_001

Structure
Sequence	1 51 101 151 201 251 301 351 MKILINKSELNKILKKMNNVIISNNKIKPHHSYFLIEAKEKEINFYANNE YFSVKCNLNKNIDILEQGSLIVKGKIFNDLINGIKEEIITIQEKDQTLLV KTKKTSINLNTINVNEFPRIRFNEKNDLSEFNQFKINYSLLVKGIKKIFH SVSNNREISSKFNGVNFNGSNGKEIFLEASDTYKLSVFEIKQETEPFDFI LESNLLSFINSFNPEEDKSIVFYYRKDNKDSFSTEMLISMDNFMISYTSV NEKFPEVNYFFEFEPETKIVVQKNELKDALQRIQTLAQNERTFLCDMQIN SSELKIRAIVNNIGNSLEEISCLKFEGYKLNISFNPSSLLDHIESFESNE INFDFQGNSKYFLITSKSEPELKQILVPSR 50 100 150 200 250 300 350 380
Is N‑terminal methionine cleaved	No
DNA footprint	Length: 25 (nt), Binding: ssDNA, Region: xsDNA
Empirical formula (pH 7.5)	H₃₁₃₆C₂₀₀₂N₅₁₀O₆₀₅S₉
Molecular weight (pH 7.5; Da)	44317.83
Extinction coefficient (260 nm, 25C, pH 7.0)	16765
Instability index	38.61
Is stable	True
Aliphatic index	91.79
GRAVY (25C, pH 7.0)	-0.417
Half life (OD (600 nm) = 0.3, M9 media, 36C; min)	1200

Synthesis
Localization	c

Function
Enzyme	DNA polymerization (dATP) [c]: DAMP + DATP ⇒ dApdAp + PPI DNA polymerization (dACP) [c]: DCMP + DCTP ⇒ dCpdCp + PPI DNA polymerization (dGTP) [c]: DGMP + DGTP ⇒ dGpdGp + PPI DNA polymerization (dGTP) [c]: DTMP + DTTP ⇒ dTpdTp + PPI deoxyribose 5'-phosphate lyase [c]: dRibose5P_dRibose5P + H2O ⇒ (2) DR5P + H
Reaction participant	DNA bound protein release (DNA polymerase III, beta subunit releases DnaA 6mer-(5)ATP-(1)ADP) MG_001_MONOMER[c] + MG_469_6MER_5ATP_ADP[d] ⇒ MG_001_MONOMER[d] + MG_469_6MER_5ATP_ADP[c] DNA bound protein release (DNA polymerase III, beta subunit releases DnaA-ATP 7mer) MG_001_MONOMER[c] + MG_469_7MER_ATP[d] ⇒ MG_001_MONOMER[d] + MG_469_7MER_ATP[c] DNA bound protein release (DNA polymerase III, beta subunit releases single-strand binding protein family, octamer) MG_001_MONOMER[c] + MG_091_OCTAMER[d] ⇒ MG_001_MONOMER[d] + MG_091_OCTAMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases LuxR bacterial regulatory protein, putative) MG_001_MONOMER[c] + MG_428_DIMER[d] ⇒ MG_001_MONOMER[d] + MG_428_DIMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases recombination protein, strand exchange) MG_001_MONOMER[c] + MG_339_MONOMER[d] ⇒ MG_001_MONOMER[d] + MG_339_MONOMER[c] ... 31 more DNA bound protein release (DNA polymerase III, beta subunit releases DnaA 4mer-(3)ATP-(1)ADP) MG_001_MONOMER[c] + MG_469_4MER_3ATP_ADP[d] ⇒ MG_001_MONOMER[d] + MG_469_4MER_3ATP_ADP[c] DNA bound protein release (DNA polymerase III, beta subunit releases Uncharacterized HTH-type transcriptional regulator) MG_001_MONOMER[c] + MG_101_MONOMER[d] ⇒ MG_001_MONOMER[d] + MG_101_MONOMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases DNA polymerase (2) core, β-clamp, γ-complex, and primase) DNA_POLYMERASE_2CORE_BETA_CLAMP_GAMMA_COMPLEX_PRIMASE[d] + MG_001_MONOMER[c] ⇒ DNA_POLYMERASE_2CORE_BETA_CLAMP_GAMMA_COMPLEX_PRIMASE[c] + MG_001_MONOMER[d] DNA bound protein release (DNA polymerase III, beta subunit releases DNA polymerase core, β-clamp, and γ-complex) DNA_POLYMERASE_CORE_BETA_CLAMP_GAMMA_COMPLEX[d] + MG_001_MONOMER[c] ⇒ DNA_POLYMERASE_CORE_BETA_CLAMP_GAMMA_COMPLEX[c] + MG_001_MONOMER[d] DNA bound protein release (DNA polymerase III, beta subunit releases DnaA 3mer-(2)ATP-(1)ADP) MG_001_MONOMER[c] + MG_469_3MER_2ATP_ADP[d] ⇒ MG_001_MONOMER[d] + MG_469_3MER_2ATP_ADP[c] DNA bound protein release (DNA polymerase III, beta subunit releases DnaA 5mer-(4)ATP-(1)ADP) MG_001_MONOMER[c] + MG_469_5MER_4ATP_ADP[d] ⇒ MG_001_MONOMER[d] + MG_469_5MER_4ATP_ADP[c] DNA bound protein release (DNA polymerase III, beta subunit releases DnaA-ATP 5mer) MG_001_MONOMER[c] + MG_469_5MER_ATP[d] ⇒ MG_001_MONOMER[d] + MG_469_5MER_ATP[c] DNA bound protein release (DNA polymerase III, beta subunit releases DNA-directed RNA polymerase) MG_001_MONOMER[c] + RNA_POLYMERASE[d] ⇒ MG_001_MONOMER[d] + RNA_POLYMERASE[c] DNA bound protein release (DNA polymerase III, beta subunit releases Spx subfamily protein) MG_001_MONOMER[c] + MG_127_MONOMER[d] ⇒ MG_001_MONOMER[d] + MG_127_MONOMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases DNA ligase, NAD-dependent) MG_001_MONOMER[c] + MG_254_MONOMER[d] ⇒ MG_001_MONOMER[d] + MG_254_MONOMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases DnaA-ATP 4mer) MG_001_MONOMER[c] + MG_469_4MER_ATP[d] ⇒ MG_001_MONOMER[d] + MG_469_4MER_ATP[c] DNA bound protein release (DNA polymerase III, beta subunit releases type I restriction modification DNA specificity domain protein) MG_001_MONOMER[c] + MG_438_MONOMER[d] ⇒ MG_001_MONOMER[d] + MG_438_MONOMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases DnaA 2mer-(1)ATP-(1)ADP) MG_001_MONOMER[c] + MG_469_2MER_1ATP_ADP[d] ⇒ MG_001_MONOMER[d] + MG_469_2MER_1ATP_ADP[c] DNA bound protein release (DNA polymerase III, beta subunit releases Chromosome Segregation Protein SMC with SCP Proteins-ADP) MG_001_MONOMER[c] + MG_213_214_298_6MER_ADP[d] ⇒ MG_001_MONOMER[d] + MG_213_214_298_6MER_ADP[c] DNA bound protein release (DNA polymerase III, beta subunit releases DnaA-ATP 2mer) MG_001_MONOMER[c] + MG_469_2MER_ATP[d] ⇒ MG_001_MONOMER[d] + MG_469_2MER_ATP[c] DNA bound protein release (DNA polymerase III, beta subunit releases DNA polymerase core, β-clamp, and primase) DNA_POLYMERASE_CORE_BETA_CLAMP_PRIMASE[d] + MG_001_MONOMER[c] ⇒ DNA_POLYMERASE_CORE_BETA_CLAMP_PRIMASE[c] + MG_001_MONOMER[d] DNA bound protein release (DNA polymerase III, beta subunit releases adenine-specific DNA modification methylase) MG_001_MONOMER[c] + MG_184_DIMER[d] ⇒ MG_001_MONOMER[d] + MG_184_DIMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases topoisomerase IV) MG_001_MONOMER[c] + MG_203_204_TETRAMER[d] ⇒ MG_001_MONOMER[d] + MG_203_204_TETRAMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases DNA topoisomerase I) MG_001_MONOMER[c] + MG_122_MONOMER[d] ⇒ MG_001_MONOMER[d] + MG_122_MONOMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases putative DNA integrity scanning protein) MG_001_MONOMER[c] + MG_105_OCTAMER[d] ⇒ MG_001_MONOMER[d] + MG_105_OCTAMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases DnaA 7mer-(6)ATP-(1)ADP) MG_001_MONOMER[c] + MG_469_7MER_6ATP_ADP[d] ⇒ MG_001_MONOMER[d] + MG_469_7MER_6ATP_ADP[c] DNA bound protein release (DNA polymerase III, beta subunit releases heat-inducible transcription repressor HrcA, putative) MG_001_MONOMER[c] + MG_205_DIMER[d] ⇒ MG_001_MONOMER[d] + MG_205_DIMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases DNA-directed RNA polymerase holoenzyme) MG_001_MONOMER[c] + RNA_POLYMERASE_HOLOENZYME[d] ⇒ MG_001_MONOMER[d] + RNA_POLYMERASE_HOLOENZYME[c] DNA bound protein release (DNA polymerase III, beta subunit releases DnaA-ATP 6mer) MG_001_MONOMER[c] + MG_469_6MER_ATP[d] ⇒ MG_001_MONOMER[d] + MG_469_6MER_ATP[c] DNA bound protein release (DNA polymerase III, beta subunit releases DNA polymerase III, beta clamp) MG_001_DIMER[d] + MG_001_MONOMER[c] ⇒ MG_001_DIMER[c] + MG_001_MONOMER[d] DNA bound protein release (DNA polymerase III, beta subunit releases ferric uptake repressor) MG_001_MONOMER[c] + MG_236_MONOMER[d] ⇒ MG_001_MONOMER[d] + MG_236_MONOMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases DnaA-ADP) MG_001_MONOMER[c] + MG_469_1MER_ADP[d] ⇒ MG_001_MONOMER[d] + MG_469_1MER_ADP[c] DNA bound protein release (DNA polymerase III, beta subunit releases DNA gyrase) DNA_GYRASE[d] + MG_001_MONOMER[c] ⇒ DNA_GYRASE[c] + MG_001_MONOMER[d] DNA bound protein release (DNA polymerase III, beta subunit releases DnaA-ATP 3mer) MG_001_MONOMER[c] + MG_469_3MER_ATP[d] ⇒ MG_001_MONOMER[d] + MG_469_3MER_ATP[c] DNA bound protein release (DNA polymerase III, beta subunit releases replicative DNA helicase) MG_001_MONOMER[c] + MG_094_HEXAMER[d] ⇒ MG_001_MONOMER[d] + MG_094_HEXAMER[c] DNA bound protein release (DNA polymerase III, beta subunit releases DnaA-ATP) MG_001_MONOMER[c] + MG_469_1MER_ATP[d] ⇒ MG_001_MONOMER[d] + MG_469_1MER_ATP[c]
Complex subunit	DNA polymerase (2) core, β-clamp, γ-complex, and primase [c]: (2) DNA_POLYMERASE_CORE + DNA_POLYMERASE_GAMMA_COMPLEX + (2) MG_001_MONOMER + MG_250_MONOMER ⇒ DNA_POLYMERASE_2CORE_BETA_CLAMP_GAMMA_COMPLEX_PRIMASE DNA polymerase core, β-clamp, and γ-complex [c]: DNA_POLYMERASE_CORE + DNA_POLYMERASE_GAMMA_COMPLEX + (2) MG_001_MONOMER ⇒ DNA_POLYMERASE_CORE_BETA_CLAMP_GAMMA_COMPLEX DNA polymerase core, β-clamp, and primase [c]: DNA_POLYMERASE_CORE + (2) MG_001_MONOMER + MG_250_MONOMER ⇒ DNA_POLYMERASE_CORE_BETA_CLAMP_PRIMASE DNA-directed DNA polymerase holoenzyme [c]: (2) DNA_POLYMERASE_CORE + DNA_POLYMERASE_GAMMA_COMPLEX + (2) MG_001_MONOMER ⇒ DNA_POLYMERASE_HOLOENZYME DNA polymerase III, beta clamp [c]: (2) MG_001_MONOMER ⇒ MG_001_DIMER Replisome [c]: (2) DNA_POLYMERASE_CORE + DNA_POLYMERASE_GAMMA_COMPLEX + (4) MG_001_MONOMER + MG_094_HEXAMER + MG_250_MONOMER ⇒ REPLISOME

Comments
Comments	Functional Macromolecule Functional as monomer [PUB_0312, PUB_0313, PUB_0314]. 2 copies assemble into DNA polymerase III holoenzyme [PUB_0312, PUB_0313, PUB_0314]. DNA-binding DNA polymerase III preinitiation complex (γ-complex and β-subunit) has 51 nt footprint [PUB_0743]. Assuming the γ-complex and β-subunit contribute equally to the footprint, we conclude that each has a footprint 25-26 nt.
References	Bruck I, O'Donnell M. The DNA replication machine of a gram-positive organism. J Biol Chem 275, 28971-83 (2000). WholeCell: PUB_0314, PubMed: 10878011 Kelman Z, O'Donnell M. DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annu Rev Biochem 64, 171-200 (1995). WholeCell: PUB_0312, PubMed: 7574479 Razin S, Yogev D, Naot Y. Molecular biology and pathogenicity of mycoplasmas. Microbiol Mol Biol Rev 62, 1094-156 (1998). WholeCell: PUB_0313, PubMed: 9841667 Reems JA, McHenry CS. Escherichia coli DNA polymerase III holoenzyme footprints three helical turns of its primer. J Biol Chem 269, 33091-6 (1994). WholeCell: PUB_0743, PubMed: 7806536

Metadata
Created	2012-10-01 15:07:43
Last updated	2012-10-01 15:14:20