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Gene |

Product(s) |

Expression|

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References |

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Standard Name	dnaN
Gene Synonym(s)	ECK3693, b3701, JW3678^[1], JW3678
Product Desc.	DnaN^[2]^[3]; Component of DNA polymerase III, β subunit^[3]; DNA polymerase III, holoenzyme^[3] DNA polymerase III sliding clamp beta subunit; required for high processivity; required for regulatory inactivation of DnaA^[4]
Product Synonyms(s)	DNA polymerase III, beta subunit^[1], B3701^[2]^[1], DnaN^[2]^[1] , ECK3693, JW3678, b3701
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): dnaN-recF^[2], dnaAN-recF^[2]
Regulation/Activity
Quick Links
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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	dnaN
Mnemonic	DNA
Synonyms	ECK3693, b3701, JW3678^[1], JW3678
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	83.61 minutes	MG1655: 3880344..3879244 <gbrowseImage> name=NC_000913:3879244..3880344 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3842682..3841582 <gbrowseImage> name=NC_012967:3841582..3842682 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3767577..3768677 <gbrowseImage> name=NC_012759:3767577..3768677 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3758094..3759194 <gbrowseImage> name=NC_007779:3758094..3759194 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3977928..3976828 <gbrowseImage> name=NC_010473:3976828..3977928 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	3879244	Edman degradation	PMID:9674428
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
dnaN59		Sensitivity to	Enhanced UV sensitivity	PMID:15466025	CGSC:27102	Other repair phenotypes also described in PMID:15466025
dnaN159(ts)	G66Q, G174A		temperature sensitive		CGSC:7438
dnaA(N346D)	N346D		Suppressor of redox defective multiple mutation	PMID:22247510
dnaN159(ts)	G66Q, G174A		temperature sensitive		CGSC:7438
dnaN(G157C)	G157C	replication	under initiation of DNA replication	PMID:16482221
dnaN159			requires PolI for viability	PMID:15466025
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW3678	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAATTTACCGTAGAACGTGA Primer 2:CCaAGTCTCATTGGCATGACAAC
3C10	Kohara Phage	Genobase	PMID:3038334
zid-501::Tn10	Linked marker	CAG18499 = CGSC7458^[5]	est. P1 cotransduction: 84% ^[6]
rbsD296::Tn10	Linked marker	CAG18501 = CGSC7460^[5]	est. P1 cotransduction: 9% ^[6] Synonyms:zie-296::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10242	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10242	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000236	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948218	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0238	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012098	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	DnaN
Synonyms	DNA polymerase III, beta subunit^[1], B3701^[2]^[1], DnaN^[2]^[1] , ECK3693, JW3678, b3701
Product description	DnaN^[2]^[3]; Component of DNA polymerase III, β subunit^[3]; DNA polymerase III, holoenzyme^[3] DNA polymerase III sliding clamp beta subunit; required for high processivity; required for regulatory inactivation of DnaA^[4]
EC number (for enzymes)	2.7.7.7^[1]
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001001	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003887	DNA-directed DNA polymerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001001	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030337	DNA polymerase processivity factor activity				F		Missing: evidence, reference
	GO:0003887	DNA-directed DNA polymerase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.7.7	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003887	DNA-directed DNA polymerase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0239	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	PMID:19703395	IPI: Inferred from Physical Interaction	UniProtKB:P05845	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	PMID:19703395	IPI: Inferred from Physical Interaction	UniProtKB:P06710	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0006260	DNA replication	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001001	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006260	DNA replication	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0235	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008408	3'-5' exonuclease activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001001	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016779	nucleotidyltransferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0548	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	Subunits of DNA polymerase III, β subunit	could be indirect
Protein	groL		PMID:16606699	Experiment(s):EBI-1146524
Protein	Subunits of DNA polymerase III, holoenzyme	could be indirect
Protein	Tn7 TnsE		PMID:19703395	Yeast 2-hybrid, protein EMSA, SPR
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MKFTVEREHL LKPLQQVSGP LGGRPTLPIL GNLLLQVADG TLSLTGTDLE MEMVARVALV QPHEPGATTV PARKFFDICR GLPEGAEIAV QLEGERMLVR SGRSRFSLST LPAADFPNLD DWQSEVEFTL PQATMKRLIE ATQFSMAHQD VRYYLNGMLF ETEGEELRTV ATDGHRLAVC SMPIGQSLPS HSVIVPRKGV IELMRMLDGG DNPLRVQIGS NNIRAHVGDF IFTSKLVDGR FPDYRRVLPK NPDKHLEAGC DLLKQAFARA AILSNEKFRG VRLYVSENQL KITANNPEQE EAEEILDVTY SGAEMEIGFN VSYVLDVLNA LKCENVRMML TDSVSSVQIE DAASQSAAYV VMPMRL
Length	366
Mol. Wt	40.586 kDa
pI	5.2 (calculated)
Extinction coefficient	15,930 - 16,430 (calc based on 7 Y, 1 W, and 4 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	References
Domain	1..120	PF00712 DNA polymerase III beta subunit, N-terminal domain	PMID:19920124
Domain	129..243	PF02767 DNA polymerase III beta subunit, central domain	PMID:19920124
Domain	245..365	PF02768 DNA polymerase III beta subunit, C-terminal domain	PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=dnaN taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

See Help:Jmol in EcoliWiki

Text label
<jmol> <jmolApplet> <color>white</color> <uploadedFileContents > 2POL.pdb </uploadedFileContents> <name></name> <script> wireframe off; spacefill off; trace off; rotate ON; cartoon; color chain; </script> </jmolApplet> </jmol>
<jmol> <jmolCheckbox > <scriptWhenChecked > rotate on; </scriptWhenChecked > <scriptWhenUnchecked > rotate off; </scriptWhenUnchecked > <checked>true</checked> <text>rotate</text> </jmolCheckbox > <jmolButton><script>reset; </script><text>reset</text></jmolButton> </jmol>

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16131569	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948218	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012098	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A988	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10242	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10242	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948218	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000236	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0238	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	1764	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	529	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	764	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
dnaN-recF
dnaAN-recF
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:3880324..3880364 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b3701 (EcoliWiki Page)	NCBI GEO profiles for dnaN
microarray	GenExpDB:b3701 (EcoliWiki Page)	Summary of data for dnaN from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to dnaN Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10242	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0238	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3701
EcoGene	EcoGene:EG10242	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000236	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012098	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000003308 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000023310 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	DNAN	From SHIGELLACYC
E. coli O157	DNAN	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF02768 DNA polymerase III beta subunit, C-terminal domain
Pfam (EcoliWiki Page)	PF02767 DNA polymerase III beta subunit, central domain
Pfam (EcoliWiki Page)	PF00712 DNA polymerase III beta subunit, N-terminal domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:55979
Superfamily (EcoliWiki Page)	SUPERFAMILY:55979
Superfamily (EcoliWiki Page)	SUPERFAMILY:55979
EcoCyc	EcoCyc:EG10242	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10242	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000236	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0238	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012098	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

dnaN:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to dnaN Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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