lpxC: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

lpxC

Gene Synonym(s)

ECK0097, b0096, JW0094, asmB, envA[1], envA

Product Desc.

UDP-3-O-acyl N-acetylglucosamine deacetylase Lipid A biosynthesis, UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase; zinc metalloamidase; cell envelope and cell separation[2]

Product Synonyms(s)

UDP-3-O-acyl N-acetylglucosamine deacetylase[1], B0096[3][1], EnvA[3][1], AsmB[3][1], LpxC[3][1] , asmB, ECK0097, envA, JW0094, b0096

Function from GO

<GO_nr />

Knock-Out Phenotype

lethal (see PMID:2824434)

Regulation/Expression

transcription unit(s): lpxC[3]

Regulation/Activity

LPS biosynthesis

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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LpxC regulated degradation is facilitated by FtsH.[2]



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

lpxC

Mnemonic

Lipid A expression/biosynthesis

Synonyms

ECK0097, b0096, JW0094, asmB, envA[1], envA

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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

2.3 minutes 

MG1655: 106557..107474
<gbrowseImage> name=NC_000913:106557..107474 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 109361..110278
<gbrowseImage> name=NC_012967:109361..110278 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 106556..107473
<gbrowseImage> name=NC_012759:106556..107473 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 106557..107474
<gbrowseImage> name=NC_007779:106557..107474 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 80661..81578
<gbrowseImage> name=NC_010473:80661..81578 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

106557

Edman degradation

PMID:8530464


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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

lpxCF50S

F50S

(in ASMB2/3; reduced activity)

PMID:8752330

Strain variation; seeded from UniProt:P0A725

lpxCG210S

G210S

(in ASMB1; reduced activity)

PMID:8752330

Strain variation; seeded from UniProt:P0A725

lpxC101

C to T

His19Tyr

Cell Shape

Septation is inhibited forming chains of cells. Shows increased sensitivity to certain antibiotics.

PMID:2824434

PMID:4887513

CGSC:10013

Same as envA1 first described by S. Normark et al., PMID:4887513.

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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

JW0094

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCATCAAACAAAGGACACTTAA

Primer 2:CCTGCCAGTACAGCTGAAGGCGC

15B8

Kohara Phage

Genobase

PMID:3038334

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[4]

est. P1 cotransduction: 42% [5]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[4]

est. P1 cotransduction: 16% [5]

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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:EG10265

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10265

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944816

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000259

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0261

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000336

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

LpxC

Synonyms

UDP-3-O-acyl N-acetylglucosamine deacetylase[1], B0096[3][1], EnvA[3][1], AsmB[3][1], LpxC[3][1] , asmB, ECK0097, envA, JW0094, b0096

Product description

UDP-3-O-acyl N-acetylglucosamine deacetylase Lipid A biosynthesis, UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase; zinc metalloamidase; cell envelope and cell separation[2]

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:0008759

UDP-3-O-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00388

F

Seeded from EcoCyc (v14.0)

complete

GO:0008759

UDP-3-O-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004463

F

Seeded from EcoCyc (v14.0)

complete

GO:0008759

UDP-3-O-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011334

F

Seeded from EcoCyc (v14.0)

complete

GO:0008759

UDP-3-O-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015870

F

Seeded from EcoCyc (v14.0)

complete

GO:0009245

lipid A biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00388

P

Seeded from EcoCyc (v14.0)

complete

GO:0009245

lipid A biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004463

P

Seeded from EcoCyc (v14.0)

complete

GO:0009245

lipid A biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011334

P

Seeded from EcoCyc (v14.0)

complete

GO:0009245

lipid A biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015870

P

Seeded from EcoCyc (v14.0)

complete

GO:0009245

lipid A biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0441

P

Seeded from EcoCyc (v14.0)

complete

GO:0009245

lipid A biosynthetic process

PMID:8530464

IMP: Inferred from Mutant Phenotype

P

complete

GO:0019213

deacetylase activity

PMID:3288280

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

sucB

PMID:16606699

Experiment(s):EBI-1135572

Protein

groL

PMID:16606699

Experiment(s):EBI-1135572

Protein

ccmB

PMID:19402753

LCMS(ID Probability):99.0

Small Molecule

N-ethyl maleimide

Inhibits the activity of LpxC when added to membrane free extracts at 1mM concentration (see PMID:3288280).


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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

cytoplasm

From EcoCyc[6]


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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 

MIKQRTLKRI VQATGVGLHT GKKVTLTLRP APANTGVIYR RTDLNPPVDF PADAKSVRDT
MLCTCLVNEH DVRISTVEHL NAALAGLGID NIVIEVNAPE IPIMDGSAAP FVYLLLDAGI
DELNCAKKFV RIKETVRVED GDKWAEFKPY NGFSLDFTID FNHPAIDSSN QRYAMNFSAD
AFMRQISRAR TFGFMRDIEY LQSRGLCLGG SFDCAIVVDD YRVLNEDGLR FEDEFVRHKM
LDAIGDLFMC GHNIIGAFTA YKSGHALNNK LLQAVLAKQE AWEYVTFQDD AELPLAFKAP
SAVLA
Length

305

Mol. Wt

33.956 kDa

pI

5.7 (calculated)

Extinction coefficient

22,920 - 23,670 (calc based on 8 Y, 2 W, and 6 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

2..280

PF03331 UDP-3-O-acyl N-acetylglycosamine deacetylase

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=lpxC 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:16128089

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944816

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000336

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A725

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10265

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10265

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944816

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000259

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0261

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 MG1655

5806

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

2844

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

3773

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)

lpxC

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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_000913:106537..106577 source=MG1655 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:b0096 (EcoliWiki Page)

NCBI GEO profiles for lpxC

microarray

GenExpDB:b0096 (EcoliWiki Page)

Summary of data for lpxC 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

GFP Fusion

Intergenic region (106359..106582) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ09; Well:D2[7]

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Notes

Accessions Related to lpxC Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10265

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0261

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0096

EcoGene

EcoGene:EG10265

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000259

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000336

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

Arabidopsis thaliana

  • AT1G25210 (score: 1.000; bootstrap: 100%)
  • AT1G25054 (score: 0.989)
  • AT1G24793 (score: 0.877)
  • AT1G25141 (score: 0.877)
  • AT1G24880 (score: 0.834)
  • AT3G13680 (score: 0.115)
  • AT4G17200 (score: 0.108)
  • AT3G20030 (score: 0.085)
  • AT3G49520 (score: 0.084)
  • AT3G16740 (score: 0.077)
  • AT3G19890 (score: 0.076)
  • AT1G32140 (score: 0.076)
  • AT3G13820 (score: 0.072)
  • AT5G60560 (score: 0.071)
  • AT3G17620 (score: 0.070)
  • AT3G19880 (score: 0.069)
  • AT3G17320 (score: 0.066)
  • AT2G18780 (score: 0.065)
  • AT1G66490 (score: 0.065)
  • AT2G17830 (score: 0.063)
  • AT1G54550 (score: 0.061)
  • AT5G51000 (score: 0.060)
  • AT5G42460 (score: 0.058)
  • AT4G05080 (score: 0.058)
  • AT5G36730 (score: 0.058)
  • AT5G36820 (score: 0.058)
  • AT5G36200 (score: 0.058)
  • AT3G19560 (score: 0.057)
  • AT3G22421 (score: 0.056)
  • AT3G16880 (score: 0.054)
  • AT3G19470 (score: 0.053)
  • AT3G22940 (score: 0.053)
  • AT3G24580 (score: 0.051)
  • AT5G47300 (score: 0.050)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000016283 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

LPXC

From SHIGELLACYC

E. coli O157

LPXC

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)

PF03331 UDP-3-O-acyl N-acetylglycosamine deacetylase

Superfamily (EcoliWiki Page)

SUPERFAMILY:54211

Superfamily (EcoliWiki Page)

SUPERFAMILY:54211

EcoCyc

EcoCyc:EG10265

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10265

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000259

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0261

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000336

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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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).
  6. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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