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der:On One Page

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Standard Name

der

Gene Synonym(s)

ECK2507, b2511, JW5403, engA, yfgK[1]

Product Desc.

50S ribosomal subunit stability factor[2][3]

Multicopy suppressor of ftsJ; depleted cells form filaments with defective chromosome segregation; GTPase[4]

Product Synonyms(s)

predicted GTP-binding protein[1], B2511[2][1], Der[2][1], YfgK[2][1], EngA[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yfgL-der[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(der)    Textpresso(der)

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Notes

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Der-depletion alters ribosome stability and/or biogenesis, as evidenced by polysome profiles (Bharat, 2006). Der has two tandem GTP-binding domains. der is an essential gene.[4]



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

der

Mnemonic

Double ERa-like domains

Synonyms

ECK2507, b2511, JW5403, engA, yfgK[1]

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Notes

Location(s) and DNA Sequence

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

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

56.77 minutes 

MG1655: 2635378..2633906
gbrowse_img.php?coord=2633906..2635378&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 2636012..2634540
gbrowse_img.php?coord=2634540..2636012&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 2727143..2725671
gbrowse_img.php?coord=2725671..2727143&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 2519711..2521183
gbrowse_img.php?coord=2519711..2521183&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments
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Notes

Genetic Resources

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

ResourceResource TypeSourceNotes/Reference

JW5403

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGTACCTGTGGTCGCGCTTGT

Primer 2:CCTTTATTTTTCTTGATGTGCTT

purC80::Tn10

Linked marker

CAG18470 = CGSC7413[5]

est. P1 cotransduction: 18% [6]

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[5]

est. P1 cotransduction: 32% [6]
Synonyms:zff-208::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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7319

EchoBASE (EcoliWiki Page)

EchoBASE:EB3959

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2511

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3033

EcoGene (EcoliWiki Page)

EcoGene:EG14207

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z3774

ASAP (EcoliWikiPage)

ASAP:ABE-0008270


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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

Der

Synonyms

predicted GTP-binding protein[1], B2511[2][1], Der[2][1], YfgK[2][1], EngA[2][1]

Product description

50S ribosomal subunit stability factor[2][3]

Multicopy suppressor of ftsJ; depleted cells form filaments with defective chromosome segregation; GTPase[4]

EC number (for enzymes)


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Notes

Function

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

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0005622

intracellular

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002917

C

Seeded from EcoCyc [7]

complete

GO:0005525

GTP binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR002917
InterPro:IPR005225
InterPro:IPR005289
InterPro:IPR006073
SP_KW:KW-0342
HAMAP:MF_00195

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0000166

nucleotide binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc [7]

complete

GO:0009282

cytosolic large ribosomal subunit (sensu Bacteria)

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0000027

ribosomal large subunit assembly and maintenance

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0042273

ribosomal large subunit biogenesis and assembly

P

Seeded from EcoCyc 11.1[3].

required fields missing

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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 TypePartnerNotesReferencesEvidence

Protein

ynbC

PMID:15690043

Experiment(s):EBI-878632

Protein

rplB

PMID:15690043

Experiment(s):EBI-878632

Protein

rplD

PMID:15690043

Experiment(s):EBI-878632

Protein

rplN

PMID:15690043

Experiment(s):EBI-878632

Protein

rpsB

PMID:15690043

Experiment(s):EBI-878632

Protein

rpsC

PMID:15690043

Experiment(s):EBI-878632

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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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

Sequence

at EcoCyc 

MRCLMIYKNE ALNMVPVVAL VGRPNVGKST LFNRLTRTRD ALVADFPGLT RDRKYGRAEI
EGREFICIDT GGIDGTEDGV ETRMAEQSLL AIEEADVVLF MVDARAGLMP ADEAIAKHLR
SREKPTFLVA NKTDGLDPDQ AVVDFYSLGL GEIYPIAASH GRGVLSLLEH VLLPWMEDLA
PQEEVDEDAE YWAQFEAEEN GEEEEEDDFD PQSLPIKLAI VGRPNVGKST LTNRILGEER
VVVYDMPGTT RDSIYIPMER DGREYVLIDT AGVRKRGKIT DAVEKFSVIK TLQAIEDANV
VMLVIDAREG ISDQDLSLLG FILNSGRSLV IVVNKWDGLS QEVKEQVKET LDFRLGFIDF
ARVHFISALH GSGVGNLFES VREAYDSSTR RVGTSMLTRI MTMAVEDHQP PLVRGRRVKL
KYAHAGGYNP PIVVIHGNQV KDLPDSYKRY LMNYFRKSLD VMGSPIRIQF KEGENPYANK
RNTLTPTQMR KRKRLMKHIK KNK
Length

503

Mol. Wt

56.617 kDa

pI

5.8 (calculated)

Extinction coefficient

38,850 - 39,100 (calc based on 15 Y, 3 W, and 2 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.

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

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7319-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0A6P5

PFAM (EcoliWiki Page)

PFAM:PF01926

RefSeq (EcoliWiki Page)

RefSeq:NP_417006


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Notes

Links

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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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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)

yfgL-der

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Figure courtesy of RegulonDB

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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gbrowse_img.php?coord=2635358..2635398&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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

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

TypeReferenceNotes

microarray

GEO Profiles:b2511 (EcoliWiki Page)

NCBI GEO profiles for der

microarray

GenExpDB:b2511 (EcoliWiki Page)

Summary of data for der 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 NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (2635330..2635532) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ06; Well:C11[9]

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Notes

Accessions Related to der Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7319

EchoBASE (EcoliWiki Page)

EchoBASE:EB3959

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2511

EcoGene (EcoliWiki Page)

EcoGene:EG14207


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Notes

Links

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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.

OrganismHomologs (Statistics)Comments

Arabidopsis thaliana

  • AT3G12080 (score: 1.000; bootstrap: 80%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0205682 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

S2729

From SHIGELLACYC

E. coli O157

Z3774

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.

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF01926


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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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 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).
  7. ↑ 7.0 7.1 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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