holB:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

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)
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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[5]

Experiment(s):EBI-880223

Protein

dnaX

PMID:15690043[5]

Experiment(s):EBI-880223, EBI-885437

Protein

holA

PMID:15690043[5]

Experiment(s):EBI-880223

Protein

rplA

PMID:15690043[5]

Experiment(s):EBI-880223, EBI-885437

Protein

rplC

PMID:15690043[5]

Experiment(s):EBI-880223

Protein

rpsJ

PMID:15690043[5]

Experiment(s):EBI-880223

Protein

secA

PMID:15690043[5]

Experiment(s):EBI-880223

Protein

cysJ

PMID:15690043[5]

Experiment(s):EBI-885437

Protein

rplJ

PMID:15690043[5]

Experiment(s):EBI-885437

Protein

rpmB

PMID:15690043[5]

Experiment(s):EBI-885437

Protein

rpsP

PMID:15690043[5]

Experiment(s):EBI-885437

Protein

ugpB

PMID:15690043[5]

Experiment(s):EBI-885437

Protein

ybbN

PMID:15690043[5]

Experiment(s):EBI-885437

Protein

fabF

PMID:16606699[6]

Experiment(s):EBI-1138862

Protein

nadE

PMID:16606699[6]

Experiment(s):EBI-1138862

Protein

rplB

PMID:16606699[6]

Experiment(s):EBI-1138862

Protein

cysJ

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

ybbN

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

yfiF

PMID:19402753[7]

MALDI(Z-score):32.699703

Protein

rplA

PMID:19402753[7]

LCMS(ID Probability):99.0 MALDI(Z-score):17.053160

Protein

holA

PMID:19402753[7]

MALDI(Z-score):32.803073

Protein

dnaX

PMID:19402753[7]

LCMS(ID Probability):99.0 MALDI(Z-score):28.610934

Protein

holD

PMID:19402753[7]

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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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 

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[8]

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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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References

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

  1. ↑ 1.0 1.1 1.2 1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 5.11 5.12 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  6. ↑ 6.0 6.1 6.2 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  8. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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