glyS:On One Page

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

Quickview

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Standard Name

glyS

Gene Synonym(s)

ECK3547, b3559, JW3530, act, gly, glySb, gly-act, glySbeta, glyS(B)[1], glyS

Product Desc.

glycyl-tRNA synthetase, β subunit[2][3];

Component of glycyl-tRNA synthetase[2][3]

Glycine--tRNA ligase, beta-subunit[4]

Product Synonyms(s)

glycine tRNA synthetase, beta subunit[1], B3559[2][1], Gly[2][1], GlyS[2][1], GlyS(B)[2][1] , ECK3547, gly-act, glyS, JW3530, b3559

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): glyQS[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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glyS is an essential gene; the glyS mutants in the Keio collection have a second intact copy of glyS (R. D'Ari and K. Nakahihashi, personal communication cited in Baba, 2000).[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

glyS

Mnemonic

Glycine

Synonyms

ECK3547, b3559, JW3530, act, gly, glySb, gly-act, glySbeta, glyS(B)[1], glyS

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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

80.19 minutes 

MG1655: 3722420..3720351
<gbrowseImage> name=NC_000913:3720351..3722420 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3654855..3652786
<gbrowseImage> name=NC_012967:3652786..3654855 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3608677..3610746
<gbrowseImage> name=NC_012759:3608677..3610746 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3916018..3918087
<gbrowseImage> name=NC_007779:3916018..3918087 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3819997..3817928
<gbrowseImage> name=NC_010473:3817928..3819997 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

3720354

Edman degradation

PMID:9298646


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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

ΔglyS (Keio:JW3530)

deletion

deletion

PMID:16738554

Shigen
CGSC10605[5]

Strain contains duplication detected by PCR PMID:18652654

glyS2(ts)

temperature sensitive

CGSC:9416

glyS3(ts)

temperature sensitive

CGSC:9426

ΔglyS742::kan

PMID:16738554

CGSC:101222


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Notes

The Keio collection[6] lists a deletion of glyS. The insertion in this strain is a duplication of the glyS region.[7]


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

JW3530

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCTGAGAAAACTTTTCTGGT

Primer 2:CCTTGCAACAGCGAAATATCCGC

6F2

Kohara Phage

Genobase

PMID:3038334

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: % [8]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: % [8]

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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:EG10410

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10410

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000403

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948080

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0405

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011624

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

GlyS

Synonyms

glycine tRNA synthetase, beta subunit[1], B3559[2][1], Gly[2][1], GlyS[2][1], GlyS(B)[2][1] , ECK3547, gly-act, glyS, JW3530, b3559

Product description

glycyl-tRNA synthetase, β subunit[2][3];

Component of glycyl-tRNA synthetase[2][3]

Glycine--tRNA ligase, beta-subunit[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:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002311

F

Seeded from EcoCyc (v14.0)

complete

GO:0006418

tRNA aminoacylation for protein translation

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006194

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015944

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0004812

aminoacyl-tRNA ligase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0030

F

Seeded from EcoCyc (v14.0)

complete

GO:0004814

arginine-tRNA ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008909

F

Seeded from EcoCyc (v14.0)

complete

GO:0004820

glycine-tRNA ligase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00255

F

Seeded from EcoCyc (v14.0)

complete

GO:0004820

glycine-tRNA ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002311

F

Seeded from EcoCyc (v14.0)

complete

GO:0004820

glycine-tRNA ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006194

F

Seeded from EcoCyc (v14.0)

complete

GO:0004820

glycine-tRNA ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015944

F

Seeded from EcoCyc (v14.0)

complete

GO:0004820

glycine-tRNA ligase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:6.1.1.14

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00255

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002311

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006194

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008909

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015944

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005829

cytosol

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002311

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006194

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015944

P

Seeded from EcoCyc (v14.0)

complete

GO:0006412

translation

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0648

P

Seeded from EcoCyc (v14.0)

complete

GO:0006420

arginyl-tRNA aminoacylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008909

P

Seeded from EcoCyc (v14.0)

complete

GO:0006426

glycyl-tRNA aminoacylation

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00255

P

Seeded from EcoCyc (v14.0)

complete

GO:0006426

glycyl-tRNA aminoacylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002311

P

Seeded from EcoCyc (v14.0)

complete

GO:0006426

glycyl-tRNA aminoacylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006194

P

Seeded from EcoCyc (v14.0)

complete

GO:0006426

glycyl-tRNA aminoacylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015944

P

Seeded from EcoCyc (v14.0)

complete

GO:0016874

ligase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0436

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 glycyl-tRNA synthetase

could be indirect

Protein

helD

PMID:16606699

Experiment(s):EBI-1146135

Protein

ttdA

PMID:16606699

Experiment(s):EBI-1146135

Protein

dnaC

PMID:16606699

Experiment(s):EBI-1146135
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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 

MSEKTFLVEI GTEELPPKAL RSLAESFAAN FTAELDNAGL AHGTVQWFAA PRRLALKVAN
LAEAQPDREI EKRGPAIAQA FDAEGKPSKA AEGWARGCGI TVDQAERLTT DKGEWLLYRA
HVKGESTEAL LPNMVATSLA KLPIPKLMRW GASDVHFVRP VHTVTLLLGD KVIPATILGI
QSDRVIRGHR FMGEPEFTID NADQYPEILR ERGKVIADYE ERKAKIKADA EEAARKIGGN
ADLSESLLEE VASLVEWPVV LTAKFEEKFL AVPAEALVYT MKGDQKYFPV YANDGKLLPN
FIFVANIESK DPQQIISGNE KVVRPRLADA EFFFNTDRKK RLEDNLPRLQ TVLFQQQLGT
LRDKTDRIQA LAGWIAEQIG ADVNHATRAG LLSKCDLMTN MVFEFTDTQG VMGMHYARHD
GEAEDVAVAL NEQYQPRFAG DDLPSNPVAC ALAIADKMDT LAGIFGIGQH PKGDKDPFAL
RRAALGVLRI IVEKNLNLDL QTLTEEAVRL YGDKLTNANV VDDVIDFMLG RFRAWYQDEG
YTVDTIQAVL ARRPTRPADF DARMKAVSHF RTLDAAAALA AANKRVSNIL AKSDEVLSDR
VNASTLKEPE EIKLAMQVVV LRDKLEPYFT EGRYQDALVE LAELREPVDA FFDKVMVMVD
DKELRINRLT MLEKLRELFL RVADISLLQ
Length

689

Mol. Wt

76.814 kDa

pI

5.2 (calculated)

Extinction coefficient

57,870 - 58,245 (calc based on 13 Y, 7 W, and 3 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:P00961

Modification Site

604

phosphorylation site at S604

probability less than 75%

PMID:17938405

Modification Site

605

phosphorylation site at T605

probability less than 75%

PMID:17938405

Modification Site

598

phosphorylation site at S598

probability less than 75%

PMID:17938405

Domain

6..553

PF02092 Glycyl-tRNA synthetase beta subunit

PMID:19920124

Domain

579..685

PF05746 DALR anticodon binding 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=glyS 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:16131430

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948080

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011624

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P00961

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10410

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10410

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948080

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000403

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0405

Escherichia coli str. K-12 substr. MG1655

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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

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

Protein

E. coli K-12 MC4100

2.42E+03

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 EMG2

80

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: M57

PMID: 9298646

Protein

E. coli K-12 MG1655

12974

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

1945

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

6020

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)

glyQS

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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

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<protect><gbrowseImage> name=NC_000913:3722400..3722440 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

</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

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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:b3559 (EcoliWiki Page)

NCBI GEO profiles for glyS

microarray

GenExpDB:b3559 (EcoliWiki Page)

Summary of data for glyS 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 glyS Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10410

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0405

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3559

EcoGene

EcoGene:EG10410

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000403

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011624

Escherichia coli str. K-12 substr. MG1655

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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.

Organism Homologs (Statistics) Comments

Arabidopsis thaliana

  • AT3G48110 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q5VRH2 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

GLYS

From SHIGELLACYC

E. coli O157

GLYS

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)

PF02092 Glycyl-tRNA synthetase beta subunit

Pfam (EcoliWiki Page)

PF05746 DALR anticodon binding domain

EcoCyc

EcoCyc:EG10410

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10410

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000403

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0405

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011624

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 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 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 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  7. ↑ Yamamoto, N et al. (2009) Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol. Syst. Biol. 5 335 PubMed
  8. ↑ 8.0 8.1 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

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