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Standard Name	holB
Gene Synonym(s)	ECK1085, b1099, JW1085^[1], JW1085
Product Desc.	DNA polymerase III, δ prime subunit^[2]^[3]; Component of DNA polymerase III, preinitiation complex^[3]; DNA polymerase III, holoenzyme^[3] DNA polymerase III, delta' subunit; part of the DnaX clamp loader complex, the stator protein^[4]
Product Synonyms(s)	DNA polymerase III, delta prime subunit^[1], B1099^[2]^[1], HolB^[2]^[1] , ECK1085, JW1085, b1099
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pabC^[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	holB
Mnemonic	Holoenzyme
Synonyms	ECK1085, b1099, JW1085^[1], JW1085
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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	24.89 minutes	MG1655: 1154985..1155989 <gbrowseImage> name=NC_000913:1154985..1155989 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1170331..1171335 <gbrowseImage> name=NC_012967:1170331..1171335 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1058910..1059914 <gbrowseImage> name=NC_012759:1058910..1059914 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1157339..1158343 <gbrowseImage> name=NC_007779:1157339..1158343 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1210430..1211434 <gbrowseImage> name=NC_010473:1210430..1211434 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	1154985	Edman degradation	PMID:8505303
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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	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
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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
JW1085	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGATGGTATCCATGGTTACG Primer 2:CCAAGATGAGGAACCGGTAGCAC
14C1	Kohara Phage	Genobase	PMID:3038334
E9G1	Kohara Phage	Genobase	PMID:3038334
zcc-282::Tn10	Linked marker	CAG18466 = CGSC7359^[5]	est. P1 cotransduction: % ^[6]
zce-726::Tn10	Linked marker	CAG12078 = CGSC7361^[5]	est. P1 cotransduction: 99% ^[6]
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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:EG11500	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11500	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001456	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945661	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1463	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003716	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	HolB
Synonyms	DNA polymerase III, delta prime subunit^[1], B1099^[2]^[1], HolB^[2]^[1] , ECK1085, JW1085, b1099
Product description	DNA polymerase III, δ prime subunit^[2]^[3]; Component of DNA polymerase III, preinitiation complex^[3]; DNA polymerase III, holoenzyme^[3] DNA polymerase III, delta' subunit; part of the DnaX clamp loader complex, the stator protein^[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:IPR008921	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015199	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:IPR004622	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:IPR015199	F	Seeded from EcoCyc (v14.0)	complete
	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:0006260	DNA replication	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004622	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006260	DNA replication	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008921	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006260	DNA replication	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015199	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:IPR004622	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009360	DNA polymerase III complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015199	C	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
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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, preinitiation complex	could be indirect
Protein	aceE		PMID:15690043	Experiment(s):EBI-880223
Protein	dnaX		PMID:15690043	Experiment(s):EBI-880223, EBI-885437
Protein	holA		PMID:15690043	Experiment(s):EBI-880223
Protein	rplA		PMID:15690043	Experiment(s):EBI-880223, EBI-885437
Protein	rplC		PMID:15690043	Experiment(s):EBI-880223
Protein	rpsJ		PMID:15690043	Experiment(s):EBI-880223
Protein	secA		PMID:15690043	Experiment(s):EBI-880223
Protein	cysJ		PMID:15690043	Experiment(s):EBI-885437
Protein	rplJ		PMID:15690043	Experiment(s):EBI-885437
Protein	rpmB		PMID:15690043	Experiment(s):EBI-885437
Protein	rpsP		PMID:15690043	Experiment(s):EBI-885437
Protein	ugpB		PMID:15690043	Experiment(s):EBI-885437
Protein	ybbN		PMID:15690043	Experiment(s):EBI-885437
Protein	fabF		PMID:16606699	Experiment(s):EBI-1138862
Protein	nadE		PMID:16606699	Experiment(s):EBI-1138862
Protein	rplB		PMID:16606699	Experiment(s):EBI-1138862
Protein	cysJ		PMID:19402753	LCMS(ID Probability):99.6
Protein	rpmB		PMID:19402753	LCMS(ID Probability):99.6
Protein	ybbN		PMID:19402753	LCMS(ID Probability):99.6
Protein	yfiF		PMID:19402753	MALDI(Z-score):32.699703
Protein	rplA		PMID:19402753	LCMS(ID Probability):99.0 MALDI(Z-score):17.053160
Protein	holA		PMID:19402753	MALDI(Z-score):32.803073
Protein	dnaX		PMID:19402753	LCMS(ID Probability):99.0 MALDI(Z-score):28.610934
Protein	holD		PMID:19402753	LCMS(ID Probability):99.0 MALDI(Z-score):38.856895
Protein	Subunits of DNA polymerase III, holoenzyme	could be indirect
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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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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 MRWYPWLRPD FEKLVASYQA GRGHHALLIQ ALPGMGDDAL IYALSRYLLC QQPQGHKSCG HCRGCQLMQA GTHPDYYTLA PEKGKNTLGV DAVREVTEKL NEHARLGGAK VVWVTDAALL TDAAANALLK TLEEPPAETW FFLATREPER LLATLRSRCR LHYLAPPPEQ YAVTWLSREV TMSQDALLAA LRLSAGSPGA ALALFQGDNW QARETLCQAL AYSVPSGDWY SLLAALNHEQ APARLHWLAT LLMDALKRHH GAAQVTNVDV PGLVAELANH LSPSRLQAIL GDVCHIREQL MSVTGINREL LITDLLLRIE HYLQPGVVLP VPHL
Length	334
Mol. Wt	36.936 kDa
pI	7.1 (calculated)
Extinction coefficient	60,390 - 61,265 (calc based on 11 Y, 8 W, and 7 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	Notes	References
Domain	206..323	PF09115 DNA polymerase III, delta subunit, C terminal		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=holB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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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:16129062	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945661	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003716	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P28631	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11500	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11500	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945661	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001456	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1463	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	Notes	Reference(s)
Protein	Ecoli K-12	11.615+/-0.085	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.03436255	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	218	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	77	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	105	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)
pabC
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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_000913:1154965..1155005 source=MG1655 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:b1099 (EcoliWiki Page)	NCBI GEO profiles for holB
microarray	GenExpDB:b1099 (EcoliWiki Page)	Summary of data for holB 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 holB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11500	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1463	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1099
EcoGene	EcoGene:EG11500	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001456	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003716	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
Shigella flexneri	HOLB	From SHIGELLACYC
E. coli O157	HOLB	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF09115 DNA polymerase III, delta subunit, C terminal
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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 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).

holB: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 holB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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