rpsD: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

rpsD

Gene Synonym(s)

ECK3283, b3296, JW3258, ramA, sud(2), sud2[1], sud

Product Desc.

30S ribosomal subunit protein S4[2][3];

Component of 30S ribosomal subunit[2][3]; ribosome[2][3]

30S ribosomal subunit protein S4; NusA-like antitermination factor[4]

Product Synonyms(s)

30S ribosomal subunit protein S4[1], B3296[2][1], RamA[2][1], RpsD[2][1] , ECK3283, JW3258, ramA, sud, b3296

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rpsMKD-rpoA-rplQ[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

rpsD

Mnemonic

Ribosomal protein, small

Synonyms

ECK3283, b3296, JW3258, ramA, sud(2), sud2[1], sud

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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

74.12 minutes 

MG1655: 3439697..3439077
<gbrowseImage> name=NC_000913:3439077..3439697 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3369580..3368960
<gbrowseImage> name=NC_012967:3368960..3369580 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3326234..3326854
<gbrowseImage> name=NC_012759:3326234..3326854 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4198741..4199361
<gbrowseImage> name=NC_007779:4198741..4199361 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3537442..3536822
<gbrowseImage> name=NC_010473:3536822..3537442 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

3439080

Edman degradation

PMID:1100394
PMID:4587210


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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

rpsDY51D

Y51D

(in rpsD101; suppresses a temperature-sensitive mutant of release factor 1, R137P. Not a ram mutation)

Strain variation; seeded from UniProt:P0A7V8

rpsD

Deletion

rpsDKMEGTFKRKPERSDLSADINEHLIVELYSK177GRYV

KMEGTFKRKPERSDLSADINEHLIVELYSK177GRYV

(in rpsD12; suppresses streptomycin dependence in protein S12. A ram mutation)

Strain variation; seeded from UniProt:P0A7V8

rpsDEGTFKRKPERSDLSADINEHLIVELYSK179ARYV

EGTFKRKPERSDLSADINEHLIVELYSK179ARYV

(in rpsD14; suppresses streptomycin dependence in protein S12. A ram mutation)

Strain variation; seeded from UniProt:P0A7V8

rpsDRKPR44AKPA

RKPR44AKPA

Decreases mRNA unwinding ability of the ribosome

seeded from UniProt:P0A7V8

rpsD1

CGSC:10060

rpsD2000

CGSC:7735

rpsD2001

CGSC:12150

rpsD4

Insertion of ram mutation

Sensitivity to

Increased reactivity toward dimethyl sulfate at positions A8 16 S rRNA

PIMD:2477554

See Figure 1.

rpsD4

Insertion of ram mutation

Sensitivity to

Increased reactivity toward dimethyl sulfate at positions A26 16 S rRNA

PIMD:2477554

See Figure 1.

rpsD6

Insertion of ram mutation

Sensitivity to

Increased reactivity toward dimethyl sulfate at positions A8 16 S rRNA

PIMD:2477554

See Figure 1.

rpsL1rpsD4

Insertion of SmI mutation into proteins rpsL and rpsD

Sensitivity to

Insertion of streptomycin independence rpsL and rpsD induced significantly greater reactivity with DMS at position A8.

PMID:2477554

See Figure 1 for the Autoradiograph

rpsD6

Insertion of ram mutation

Sensitivity to

Increased reactivity toward dimethyl sulfate at positions A26 16 S rRNA

PIMD:2477554

See Figure 1.

rpsL1rpsD4

Insertion of SmI mutation into proteins rpsL and rpsD

Sensitivity to

Insertion of streptomycin independence into both the rpsL and rpsD induced significantly greater reactivity with DMS at position A26.

PMID:2477554

See Figure 1 for the Autoradiograph

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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

JW3258

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCAAGATATTTGGGTCCTAA

Primer 2:CCtTTGGAGTAAAGCTCGACGAT

E1H9

Kohara Phage

Genobase

PMID:3038334

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[5]

est. P1 cotransduction: 70% [6]
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[5]

est. P1 cotransduction: 3% [6]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

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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:EG10903

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10903

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000894

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947793

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0896

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010805

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

RpsD

Synonyms

30S ribosomal subunit protein S4[1], B3296[2][1], RamA[2][1], RpsD[2][1] , ECK3283, JW3258, ramA, sud, b3296

Product description

30S ribosomal subunit protein S4[2][3];

Component of 30S ribosomal subunit[2][3]; ribosome[2][3]

30S ribosomal subunit protein S4; NusA-like antitermination factor[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:0003735

structural constituent of ribosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005709

F

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006353

transcription termination

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0806

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01306

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005709

P

Seeded from EcoCyc (v14.0)

complete

GO:0022626

cytosolic ribosome

C

Missing: evidence, reference

GO:0006417

regulation of translation

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0810

P

Seeded from EcoCyc (v14.0)

complete

GO:0019843

rRNA binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01306

F

Seeded from EcoCyc (v14.0)

complete

GO:0019843

rRNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001912

F

Seeded from EcoCyc (v14.0)

complete

GO:0019843

rRNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018079

F

Seeded from EcoCyc (v14.0)

complete

GO:0019843

rRNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0699

F

Seeded from EcoCyc (v14.0)

complete

GO:0046677

response to antibiotic

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0046

P

Seeded from EcoCyc (v14.0)

complete

GO:0019843

rRNA binding

PMID:4912319

IDA: Inferred from Direct Assay

F

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 30S ribosomal subunit

could be indirect

Protein

ybeA

PMID:16606699

Experiment(s):EBI-1145434

Protein

nusG

PMID:16606699

Experiment(s):EBI-1145434

Protein

ydfK

PMID:16606699

Experiment(s):EBI-1145434

Protein

rpsM

PMID:16606699

Experiment(s):EBI-1145434, EBI-1145459

Protein

rpsC

PMID:16606699

Experiment(s):EBI-1145434

Protein

rplB

PMID:16606699

Experiment(s):EBI-1145434, EBI-1145434, EBI-1145550

Protein

rpsG

PMID:16606699

Experiment(s):EBI-1145434, EBI-1145434, EBI-1145603

Protein

yghW

PMID:16606699

Experiment(s):EBI-1145434

Protein

ynaE

PMID:16606699

Experiment(s):EBI-1145434

Protein

sxy

PMID:16606699

Experiment(s):EBI-1145434

Protein

rpsE

PMID:16606699

Experiment(s):EBI-1145434, EBI-1145472

Protein

rplA

PMID:16606699

Experiment(s):EBI-1145434

Protein

cybC

PMID:16606699

Experiment(s):EBI-1145434

Protein

yafO

PMID:16606699

Experiment(s):EBI-1145434

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1145434

Protein

Subunits of ribosome

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 

MARYLGPKLK LSRREGTDLF LKSGVRAIDT KCKIEQAPGQ HGARKPRLSD YGVQLREKQK
VRRIYGVLER QFRNYYKEAA RLKGNTGENL LALLEGRLDN VVYRMGFGAT RAEARQLVSH
KAIMVNGRVV NIASYQVSPN DVVSIREKAK KQSRVKAALE LAEQREKPTW LEVDAGKMEG
TFKRKPERSD LSADINEHLI VELYSK
Length

206

Mol. Wt

23.469 kDa

pI

10.4 (calculated)

Extinction coefficient

17,420 - 17,545 (calc based on 8 Y, 1 W, and 1 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

Initiator Methionine

1

Removed

UniProt:P0A7V8

Domain

96..143

PF01479 S4 domain

PMID:19920124

Domain

2..95

PF00163 Ribosomal protein S4/S9 N-terminal domain

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=rpsD 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:16131175

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947793

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010805

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A7V8

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10903

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10903

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947793

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000894

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0896

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 MC4100

9.11E+04

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

158063

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

25885

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

68110

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)

rpsMKD-rpoA-rplQ

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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_000913:3439677..3439717 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:b3296 (EcoliWiki Page)

NCBI GEO profiles for rpsD

microarray

GenExpDB:b3296 (EcoliWiki Page)

Summary of data for rpsD 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 rpsD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10903

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0896

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3296

EcoGene

EcoGene:EG10903

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000894

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010805

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

Oryza gramene

  • Q6QY73 (score: 1.000; bootstrap: 100%)
  • P12147 (score: 1.000; bootstrap: 100%)
  • Q6ENH2 (score: 1.000; bootstrap: 100%)
  • Q7G222 (score: 1.000; bootstrap: 100%)
  • Q9TJU6 (score: 0.963)
  • Q6ENW1 (score: 0.955)
  • Q6L397 (score: 0.955)
  • P02355 (score: 0.955)
  • P69649 (score: 0.937)
  • P69634 (score: 0.937)
  • Q6LB26 (score: 0.933)
  • P36454 (score: 0.933)
  • P36473 (score: 0.925)
  • P69654 (score: 0.925)
  • P69650 (score: 0.925)
  • Q9TJX9 (score: 0.925)
  • Q95H61 (score: 0.918)
  • P69653 (score: 0.918)
  • P69631 (score: 0.918)
  • Q9THJ9 (score: 0.907)
  • Q9TJV9 (score: 0.907)
  • Q6LB25 (score: 0.899)
  • P69648 (score: 0.899)
  • P36467 (score: 0.899)
  • P69645 (score: 0.899)
  • P69640 (score: 0.899)
  • P69638 (score: 0.899)
  • P69637 (score: 0.899)
  • P69636 (score: 0.899)
  • P69635 (score: 0.899)
  • P69630 (score: 0.899)
  • P36456 (score: 0.899)
  • P36447 (score: 0.896)
  • Q9TJX4 (score: 0.892)
  • P36472 (score: 0.892)
  • P36466 (score: 0.888)
  • P69644 (score: 0.888)
  • P69641 (score: 0.888)
  • P36451 (score: 0.888)
  • P69646 (score: 0.888)
  • P69642 (score: 0.888)
  • P36464 (score: 0.884)
  • Q9TJX5 (score: 0.881)
  • P36459 (score: 0.881)
  • P36465 (score: 0.873)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000043399 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

RPSD

From SHIGELLACYC

E. coli O157

RPSD

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

Pfam (EcoliWiki Page)

PF01479 S4 domain

Panther (EcoliWiki Page)

PTHR11831:SF4

Superfamily (EcoliWiki Page)

SUPERFAMILY:55174

Pfam (EcoliWiki Page)

PF00163 Ribosomal protein S4/S9 N-terminal domain

EcoCyc

EcoCyc:EG10903

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10903

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000894

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0896

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010805

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 1.9 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 2.11 2.12 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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