holA:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

holA

Gene Synonym(s)

ECK0633, b0640, JW0635[1], JW0635

Product Desc.

DNA polymerase III, δ 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; acts as a wrench to open the sliding clamp[4]

Product Synonyms(s)

DNA polymerase III, delta subunit[1], B0640[2][1], HolA[2][1] , ECK0633, JW0635, b0640

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): cobC[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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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

holA

Mnemonic

Holoenzyme

Synonyms

ECK0633, b0640, JW0635[1], JW0635

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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

14.44 minutes 

MG1655: 670828..669797
<gbrowseImage> name=NC_000913:669797..670828 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 654189..653158
<gbrowseImage> name=NC_012967:653158..654189 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 572557..573588
<gbrowseImage> name=NC_012759:572557..573588 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 672027..670996
<gbrowseImage> name=NC_007779:670996..672027 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 610160..609129
<gbrowseImage> name=NC_010473:609129..610160 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 723420..722389
<gbrowseImage> name=NC_010473:722389..723420 source=DH10B preset=GeneLocation </gbrowseImage>

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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

669797

Edman degradation

PMID:1400251
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

JW0635

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCATTCGGTTGTACCCGGAACA

Primer 2:CCACCGTCGATAAATACGTCCGC

15D7

Kohara Phage

Genobase

PMID:3038334

crcA280::Tn10

Linked marker

CAG12077 = CGSC7347[5]

est. P1 cotransduction: 58% [6]
Synonyms:zbe-280::Tn10

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[5]

est. P1 cotransduction: 30% [6]
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.

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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:EG11412

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11412

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001378

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947573

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1384

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002192

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

HolA

Synonyms

DNA polymerase III, delta subunit[1], B0640[2][1], HolA[2][1] , ECK0633, JW0635, b0640

Product description

DNA polymerase III, δ 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; acts as a wrench to open the sliding clamp[4]

EC number (for enzymes)
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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:IPR005790

F

Seeded from EcoCyc (v14.0)

complete

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:IPR010372

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:IPR010372

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:IPR005790

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:IPR010372

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:0009360

DNA polymerase III complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010372

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

groL

PMID:16606699

Experiment(s):EBI-1137527

Protein

accB

PMID:15690043

Experiment(s):EBI-885490

Protein

accC

PMID:15690043

Experiment(s):EBI-885490

Protein

macA

PMID:15690043

Experiment(s):EBI-885490

Protein

ydcK

PMID:15690043

Experiment(s):EBI-885490

Protein

dnaK

PMID:15690043

Experiment(s):EBI-885490

Protein

fdnH

PMID:15690043

Experiment(s):EBI-885490

Protein

gcvP

PMID:15690043

Experiment(s):EBI-885490

Protein

grpE

PMID:15690043

Experiment(s):EBI-885490

Protein

infB

PMID:15690043

Experiment(s):EBI-885490

Protein

pepB

PMID:15690043

Experiment(s):EBI-885490

Protein

ppx

PMID:15690043

Experiment(s):EBI-885490

Protein

rplL

PMID:15690043

Experiment(s):EBI-885490

Protein

rplP

PMID:15690043

Experiment(s):EBI-885490

Protein

rplV

PMID:15690043

Experiment(s):EBI-885490

Protein

rpmG

PMID:15690043

Experiment(s):EBI-885490

Protein

rpsC

PMID:15690043

Experiment(s):EBI-885490

Protein

yehB

PMID:15690043

Experiment(s):EBI-885490

Protein

macA

PMID:19402753

LCMS(ID Probability):99.0

Protein

fdnH

PMID:19402753

LCMS(ID Probability):99.0

Protein

accB

PMID:19402753

LCMS(ID Probability):99.0

Protein

yehB

PMID:19402753

LCMS(ID Probability):99.0

Protein

ppx

PMID:19402753

LCMS(ID Probability):99.0

Protein

ydcK

PMID:19402753

LCMS(ID Probability):99.0

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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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 

MIRLYPEQLR AQLNEGLRAA YLLLGNDPLL LQESQDAVRQ VAAAQGFEEH HTFSIDPNTD
WNAIFSLCQA MSLFASRQTL LLLLPENGPN AAINEQLLTL TGLLHDDLLL IVRGNKLSKA
QENAAWFTAL ANRSVQVTCQ TPEQAQLPRW VAARAKQLNL ELDDAANQVL CYCYEGNLLA
LAQALERLSL LWPDGKLTLP RVEQAVNDAA HFTPFHWVDA LLMGKSKRAL HILQQLRLEG
SEPVILLRTL QRELLLLVNL KRQSAHTPLR ALFDKHRVWQ NRRGMMGEAL NRLSQTQLRQ
AVQLLTRTEL TLKQDYGQSV WAELEGLSLL LCHKPLADVF IDG
Length

343

Mol. Wt

38.704 kDa

pI

3.5 (calculated)

Extinction coefficient

45,950 - 46,575 (calc based on 5 Y, 7 W, and 5 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

21..190

PF06144 DNA polymerase III, delta subunit

PMID:19920124

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

Structures

<beststructure> gene=holA 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:16128623

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947573

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002192

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P28630

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11412

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11412

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947573

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001378

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1384

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

E. coli K-12 MG1655

140

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

82

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

70

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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<protect>

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

Transcription unit(s)

cobC

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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_000913:670808..670848 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:b0640 (EcoliWiki Page)

NCBI GEO profiles for holA

microarray

GenExpDB:b0640 (EcoliWiki Page)

Summary of data for holA 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 holA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11412

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1384

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0640

EcoGene

EcoGene:EG11412

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001378

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002192

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Xenopus tropicalis

  • ENSXETP00000027758 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

HOLA

From SHIGELLACYC

E. coli O157

HOLA

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Superfamily (EcoliWiki Page)

SUPERFAMILY:48019

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Pfam (EcoliWiki Page)

PF06144 DNA polymerase III, delta subunit

EcoCyc

EcoCyc:EG11412

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11412

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001378

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1384

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002192

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. ↑ 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. ↑ 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. ↑ 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. ↑ 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. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).

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