holC:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

holC

Gene Synonym(s)

ECK4252, b4259, JW4216[1], JW4216

Product Desc.

DNA polymerase III, χ subunit[2][3];

Component of DNA polymerase III, preinitiation complex[3]; DNA polymerase III, holoenzyme[3]

DNA polymerase III, chi subunit[4]

Product Synonyms(s)

DNA polymerase III, chi subunit[1], B4259[2][1], HolC[2][1] , ECK4252, JW4216, b4259

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s):

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]





Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


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

Standard name

holC

Mnemonic

Holoenzyme

Synonyms

ECK4252, b4259, JW4216[1], JW4216

edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

96.6 minutes 

MG1655: 4482303..4481860
<gbrowseImage> name=NC_000913:4481860..4482303 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4467313..4466870
<gbrowseImage> name=NC_012967:4466870..4467313 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4420595..4421038
<gbrowseImage> name=NC_012759:4420595..4421038 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4488960..4488517
<gbrowseImage> name=NC_007779:4488517..4488960 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4584111..4583668
<gbrowseImage> name=NC_010473:4583668..4584111 source=DH10B preset=GeneLocation </gbrowseImage>

edit table

</protect>

Notes

Sequence Features

[back to top]


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

4481860

Edman degradation

PMID:8246893
PMID:8389364


edit table

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

ΔholC (Keio:JW4216)

deletion

deletion

PMID:16738554

Shigen
CGSC11033[5]

ΔholC732::kan

PMID:16738554

CGSC:101400


edit table

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

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

</protect>

Notes

Genetic Resources

[back to top]


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

Resource Resource Type Source Notes/Reference

JW4216

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAAAACGCGACGTTCTACCT

Primer 2:CCTTTCCAGGTTGCCGTATTCAG

E1F5

Kohara Phage

Genobase

PMID:3038334

5C4

Kohara Phage

Genobase

PMID:3038334

zjf-920::Tn10

Linked marker

CAG12019 = CGSC7484[5]

est. P1 cotransduction: 22% [6]
Synonyms:zjh-901::Tn10, zjg-920::Tn10

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[5]

est. P1 cotransduction: % [6]
Synonyms:zjj-202::Tn10, zji-202::Tn10

edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG11413

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11413

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001379

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948787

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1385

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013948

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name

HolC

Synonyms

DNA polymerase III, chi subunit[1], B4259[2][1], HolC[2][1] , ECK4252, JW4216, b4259

Product description

DNA polymerase III, χ subunit[2][3];

Component of DNA polymerase III, preinitiation complex[3]; DNA polymerase III, holoenzyme[3]

DNA polymerase III, chi subunit[4]

EC number (for enzymes)
edit table

<protect></protect>

Notes

Function

[back to top]


<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:IPR007459

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:IPR007459

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:IPR007459

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: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:0043847

DNA polymerase III, DnaX complex, chi/psi subcomplex

PMID:12888503

IPI: Inferred from Physical Interaction

UniProtKB:P0AGE0


C

complete

GO:0032298

positive regulation of DNA-dependent DNA replication initiation

PMID:9989506

IDA: Inferred from Direct Assay

P

complete

GO:0003887

DNA-directed DNA polymerase activity

PMID:9722585

IPI: Inferred from Physical Interaction

UniProtKB:P18022


F

complete

GO:0043847

DNA polymerase III, DnaX complex, chi/psi subcomplex

PMID:9722585

IPI: Inferred from Physical Interaction

UniProtKB:P0AGE0


C

complete

edit table

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

ssb

PMID:15690043

Experiment(s):EBI-880166, EBI-885330

Protein

yoaA

PMID:15690043

Experiment(s):EBI-880166

Protein

clpA

PMID:15690043

Experiment(s):EBI-880166

Protein

dnaK

PMID:15690043

Experiment(s):EBI-880166

Protein

dnaX

PMID:15690043

Experiment(s):EBI-880166, EBI-885330

Protein

glnD

PMID:15690043

Experiment(s):EBI-880166

Protein

holA

PMID:15690043

Experiment(s):EBI-880166, EBI-885330

Protein

holB

PMID:15690043

Experiment(s):EBI-880166, EBI-885330

Protein

intE

PMID:15690043

Experiment(s):EBI-880166

Protein

lon

PMID:15690043

Experiment(s):EBI-880166

Protein

priA

PMID:15690043

Experiment(s):EBI-880166

Protein

recQ

PMID:15690043

Experiment(s):EBI-880166

Protein

rplB

PMID:15690043

Experiment(s):EBI-880166, EBI-885330

Protein

rplC

PMID:15690043

Experiment(s):EBI-880166, EBI-885330

Protein

rplD

PMID:15690043

Experiment(s):EBI-880166, EBI-885330

Protein

rpsB

PMID:15690043

Experiment(s):EBI-880166

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-880166

Protein

sbcB

PMID:15690043

Experiment(s):EBI-880166

Protein

secA

PMID:15690043

Experiment(s):EBI-880166

Protein

topA

PMID:15690043

Experiment(s):EBI-880166, EBI-885330

Protein

topB

PMID:15690043

Experiment(s):EBI-880166

Protein

uvrA

PMID:15690043

Experiment(s):EBI-880166

Protein

yhiR

PMID:15690043

Experiment(s):EBI-880166

Protein

pinR

PMID:15690043

Experiment(s):EBI-885330

Protein

holE

PMID:15690043

Experiment(s):EBI-885330

Protein

rplL

PMID:15690043

Experiment(s):EBI-885330

Protein

rplS

PMID:15690043

Experiment(s):EBI-885330

Protein

rplV

PMID:15690043

Experiment(s):EBI-885330

Protein

rpmB

PMID:15690043

Experiment(s):EBI-885330

Protein

rpmC

PMID:15690043

Experiment(s):EBI-885330

Protein

rpmG

PMID:15690043

Experiment(s):EBI-885330

Protein

rpsE

PMID:15690043

Experiment(s):EBI-885330

Protein

rpsN

PMID:15690043

Experiment(s):EBI-885330

Protein

ubiB

PMID:16606699

Experiment(s):EBI-1147770

Protein

ygjN

PMID:16606699

Experiment(s):EBI-1147770

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmC

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):37.515585

Protein

rpmG

PMID:19402753

LCMS(ID Probability):99.6

Protein

pinR

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):19.138029

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

topA

PMID:19402753

LCMS(ID Probability):99.4 MALDI(Z-score):26.853643

Protein

topB

PMID:19402753

LCMS(ID Probability):92.5 MALDI(Z-score):29.045604

Protein

yoaA

PMID:19402753

MALDI(Z-score):52.626611

Protein

guaB

PMID:19402753

LCMS(ID Probability):99.0

Protein

holA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.190892

Protein

ssb

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.945294

Protein

holE

PMID:19402753

LCMS(ID Probability):99.6

Protein

dnaQ

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):36.204812

Protein

dnaX

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.856428

Protein

holB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.273953

Protein

recQ

PMID:19402753

MALDI(Z-score):27.692516

Protein

priA

PMID:19402753

MALDI(Z-score):25.941626

Protein

holD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

Protein

Subunits of DNA polymerase III, holoenzyme

could be indirect


edit table

</protect>

Notes

Localization

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

Compartment Description Evidence Reference/Source Notes
edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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 

MKNATFYLLD NDTTVDGLSA VEQLVCEIAA ERWRSGKRVL IACEDEKQAY RLDEALWARP
AESFVPHNLA GEGPRGGAPV EIAWPQKRSS SRRDILISLR TSFADFATAF TEVVDFVPYE
DSLKQLARER YKAYRVAGFN LNTATWK
Length

147

Mol. Wt

16.632 kDa

pI

6.1 (calculated)

Extinction coefficient

29,450 - 29,700 (calc based on 5 Y, 4 W, and 2 C residues)

edit table


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

1..143

PF04364 DNA polymerase III chi subunit, HolC

PMID:19920124

edit table

<motif_map/>

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

Structures

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

Models

View models at:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16132081

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948787

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013948

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P28905

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11413

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11413

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948787

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001379

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1385

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

Ecoli K-12

31.382+/-0.126

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.089164786

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

266

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

167

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

243

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

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

Transcription unit(s)
edit table
Figure courtesy of RegulonDB

</protect>

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

[back to top]


<protect><gbrowseImage> name=NC_000913:4482283..4482323 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]


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

Allele Name Mutation Phenotype Reference
edit table


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b4259 (EcoliWiki Page)

NCBI GEO profiles for holC

microarray

GenExpDB:b4259 (EcoliWiki Page)

Summary of data for holC from multiple microarray studies

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes
edit table

<protect></protect>

Notes

Accessions Related to holC Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG11413

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1385

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4259

EcoGene

EcoGene:EG11413

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001379

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013948

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Shigella flexneri

HOLC

From SHIGELLACYC

E. coli O157

HOLC

From ECOO157CYC

edit table


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Pfam (EcoliWiki Page)

PF04364 DNA polymerase III chi subunit, HolC

Panther (EcoliWiki Page)

PTHR11963:SF9

Superfamily (EcoliWiki Page)

SUPERFAMILY:102400

EcoCyc

EcoCyc:EG11413

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11413

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001379

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1385

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013948

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


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 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 5.2 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).

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=holC:On_One_Page&oldid=222650"