murI: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

murI

Gene Synonym(s)

ECK3959, b3967, JW5550, dga, glr, yijA[1], yijA

Product Desc.

MurI[2][3];

Component of glutamate racemase[2][3]

Glutamate racemase; D-glutamate synthesis;[4]

Product Synonyms(s)

glutamate racemase[1], B3967[2][1], YijA[2][1], Glr[2][1], Dga[2][1], MurI[2][1] , dga, ECK3959, glr, JW5550, yijA, b3967

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): btuB[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

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

Notes

[back to top]


murI is an essential gene. MurI can inhibit DNA gyrase activity (Ashiuchi, 2002).[4]



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

murI

Mnemonic

Murein

Synonyms

ECK3959, b3967, JW5550, dga, glr, yijA[1], yijA

</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

89.74 minutes 

MG1655: 4163451..4164308
<gbrowseImage> name=NC_000913:4163451..4164308 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4145289..4146146
<gbrowseImage> name=NC_012967:4145289..4146146 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4053120..4053977
<gbrowseImage> name=NC_012759:4053120..4053977 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3471253..3470396
<gbrowseImage> name=NC_007779:3470396..3471253 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4263148..4264005
<gbrowseImage> name=NC_010473:4263148..4264005 source=DH10B preset=GeneLocation </gbrowseImage>

</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

<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

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

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

</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

JW5550

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCTACCAAACTGCAGGACGG

Primer 2:CCGCCTAAAACTGCCAGTTTTTC

E11C11

Kohara Phage

Genobase

PMID:3038334

argE86::Tn10

Linked marker

CAG12185 = CGSC7471[5]

est. P1 cotransduction: 69% [6]

thiC39::Tn10

Linked marker

CAG18500 = CGSC7472[5]

est. P1 cotransduction: 30% [6]
Synonyms:thi-39::Tn10

<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:EG11204

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11204

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001184

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948467

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1189

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012989

Escherichia coli str. K-12 substr. MG1655

<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

MurI

Synonyms

glutamate racemase[1], B3967[2][1], YijA[2][1], Glr[2][1], Dga[2][1], MurI[2][1] , dga, ECK3959, glr, JW5550, yijA, b3967

Product description

MurI[2][3];

Component of glutamate racemase[2][3]

Glutamate racemase; D-glutamate synthesis;[4]

EC number (for enzymes)

<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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0007047

cellular cell wall organization

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0961

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001920

P

Seeded from EcoCyc (v14.0)

complete

GO:0008360

regulation of cell shape

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0133

P

Seeded from EcoCyc (v14.0)

complete

GO:0008881

glutamate racemase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00258

F

Seeded from EcoCyc (v14.0)

complete

GO:0008881

glutamate racemase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004391

F

Seeded from EcoCyc (v14.0)

complete

GO:0008881

glutamate racemase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:5.1.1.3

F

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00258

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004391

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0573

P

Seeded from EcoCyc (v14.0)

complete

GO:0016853

isomerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0413

F

Seeded from EcoCyc (v14.0)

complete

GO:0016855

racemase and epimerase activity, acting on amino acids and derivatives

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001920

F

Seeded from EcoCyc (v14.0)

complete

GO:0016855

racemase and epimerase activity, acting on amino acids and derivatives

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018187

F

Seeded from EcoCyc (v14.0)

complete

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 glutamate racemase

could be indirect

Protein

tufA

PMID:15690043

Experiment(s):EBI-888865

Protein

nusG

PMID:15690043

Experiment(s):EBI-893999

Protein

rplK

PMID:15690043

Experiment(s):EBI-893999

Protein

rplL

PMID:15690043

Experiment(s):EBI-893999

Protein

rpsB

PMID:15690043

Experiment(s):EBI-893999

</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

<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

MRQSMATKLQ DGNTPCLAAT PSEPRPTVLV FDSGVGGLSV YDEIRHLLPD LHYIYAFDNV
AFPYGEKSEA FIVERVVAIV TAVQERYPLA LAVVACNTAS TVSLPALREK FDFPVVGVVP
AIKPAARLTA NGIVGLLATR GTVKRSYTHE LIARFANECQ IEMLGSAEMV ELAEAKLHGE
DVSLDALKRI LRPWLRMKEP PDTVVLGCTH FPLLQEELLQ VLPEGTRLVD SGAAIARRTA
WLLEHEAPDA KSADANIAFC MAMTPGAEQL LPVLQRYGFE TLEKLAVLG
Length

289

Mol. Wt

31.504 kDa

pI

5.3 (calculated)

Extinction coefficient

21,430 - 22,055 (calc based on 7 Y, 2 W, and 5 C residues)


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

24..236

PF01177 Asp/Glu/Hydantoin racemase

PMID:19920124

<motif_map/>

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

Structures

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

Models

View models at:

</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

<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:90111671

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948467

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012989

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P22634

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11204

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11204

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948467

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001184

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1189

Escherichia coli str. K-12 substr. MG1655

<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

13.395+/-0.076

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.017502917

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

989

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

159

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

424

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

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)

btuB

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.

murI inactivation leads to an inability to form colonies in the absence of D-glutamic acid. [7]

Translation and Regulation of Translation

[back to top]


<protect><gbrowseImage> name=NC_000913:4163431..4163471 source=MG1655 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


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

Type Reference Notes

microarray

GEO Profiles:b3967 (EcoliWiki Page)

NCBI GEO profiles for murI

microarray

GenExpDB:b3967 (EcoliWiki Page)

Summary of data for murI from multiple microarray studies


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

Resource Name Resource Type Description Source Notes

<protect></protect>

Notes

Accessions Related to murI Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG11204

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1189

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3967

EcoGene

EcoGene:EG11204

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001184

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012989

Escherichia coli str. K-12 substr. MG1655

<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

Xenopus tropicalis

  • ENSXETP00000038403 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

MURI

From SHIGELLACYC

E. coli O157

MURI

From ECOO157CYC


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)

PF01177 Asp/Glu/Hydantoin racemase

Superfamily (EcoliWiki Page)

SUPERFAMILY:53681

Superfamily (EcoliWiki Page)

SUPERFAMILY:53681

Panther (EcoliWiki Page)

PTHR21198:SF0

PFAM (EcoliWiki Page)

PFAM:PF01177

EcoCyc

EcoCyc:EG11204

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11204

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001184

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1189

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012989

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


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 1.14 1.15 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 2.13 2.14 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 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. Doublet, P et al. (1992) Identification of the Escherichia coli murI gene, which is required for the biosynthesis of D-glutamic acid, a specific component of bacterial peptidoglycan. J. Bacteriol. 174 5772-9 PubMed

Categories

[back to top]