nagB: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

nagB

Gene Synonym(s)

ECK0666, b0678, JW0664, glmD[1], glmD

Product Desc.

NagB[2][3];

Component of glucosamine-6-phosphate deaminase[2][3]

Glucosamine-6-phosphate deaminase; hexameric trimer of dimers[4]

Product Synonyms(s)

glucosamine-6-phosphate deaminase[1], B0678[2][1], GlmD[2][1], NagB[2][1] , ECK0666, glmD, JW0664, b0678

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): nagBACD[2], OP00058, nagB

Regulation/Activity
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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

nagB

Mnemonic

N-Acetylglucosamine

Synonyms

ECK0666, b0678, JW0664, glmD[1], glmD

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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.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

15.13 minutes 

MG1655: 702834..702034
<gbrowseImage> name=NC_000913:702034..702834 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 685706..684906
<gbrowseImage> name=NC_012967:684906..685706 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 604794..605594
<gbrowseImage> name=NC_012759:604794..605594 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 704033..703233
<gbrowseImage> name=NC_007779:703233..704033 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 755426..754626
<gbrowseImage> name=NC_010473:754626..755426 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
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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

ΔnagB (Keio:JW0664)

deletion

deletion

PMID:16738554

Shigen
CGSC8755[5]

nagBF174A

F174A

Loss of activity in the absence of the allosteric activator

seeded from UniProt:P0A759

nagB::Tn5KAN-2 (FB20219)

Insertion at nt 212 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20219

does not contain pKD46

nagBC239S

C239S

50% of wild-type activity, but 2- fold decrease in substrate affinity; decrease in allosteric interaction energy

seeded from UniProt:P0A759

nagBE148Q

E148Q

Large decrease in activity

seeded from UniProt:P0A759

nagBH143Q

H143Q

Loss of activity for the deamination reaction but not for the reverse reaction; complete loss of the homotropic cooperativity

seeded from UniProt:P0A759

nagBC118S

C118S

50% of wild-type activity, but 2- fold decrease in substrate affinity

seeded from UniProt:P0A759

nagBD141N

D141N

Large decrease in activity

seeded from UniProt:P0A759

nagB2

CGSC:5376

nagB3

CGSC:6276

nagB22

CGSC:15703

ΔnagB727::kan

PMID:16738554

CGSC:101990

nagB

Resistant to

Resistance to Iodoacetylglucosamine resistance

PMID:4919471

Table 4

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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

JW0664

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGACTGATCCCCCTGACTAC

Primer 2:CCCAGACCTTTGATATTTTCTGC

16A8

Kohara Phage

Genobase

PMID:3038334

3A6

Kohara Phage

Genobase

PMID:3038334

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[5]

est. P1 cotransduction: 95% [6]
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.

nadA57::Tn10

Linked marker

CAG12147 = CGSC7351[5]

est. P1 cotransduction: % [6]

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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:EG10633

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10633

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000626

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945290

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0627

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002304

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

NagB

Synonyms

glucosamine-6-phosphate deaminase[1], B0678[2][1], GlmD[2][1], NagB[2][1] , ECK0666, glmD, JW0664, b0678

Product description

NagB[2][3];

Component of glucosamine-6-phosphate deaminase[2][3]

Glucosamine-6-phosphate deaminase; hexameric trimer of dimers[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.

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:0004342

glucosamine-6-phosphate deaminase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01241

F

Seeded from EcoCyc (v14.0)

complete

GO:0004342

glucosamine-6-phosphate deaminase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004547

F

Seeded from EcoCyc (v14.0)

complete

GO:0004342

glucosamine-6-phosphate deaminase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018321

F

Seeded from EcoCyc (v14.0)

complete

GO:0004342

glucosamine-6-phosphate deaminase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018322

F

Seeded from EcoCyc (v14.0)

complete

GO:0004342

glucosamine-6-phosphate deaminase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.5.99.6

F

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

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 glucosamine-6-phosphate deaminase

could be indirect

Protein

dnaK

PMID:16606699[7]

Experiment(s):EBI-1137674

Protein

nuoE

PMID:16606699[7]

Experiment(s):EBI-1137674

Protein

tatE

PMID:16606699[7]

Experiment(s):EBI-1137674

Protein

arnA

PMID:16606699[7]

Experiment(s):EBI-1137674

Protein

stpA

PMID:16606699[7]

Experiment(s):EBI-1137674

Protein

nuoI

PMID:16606699[7]

Experiment(s):EBI-1137674

Protein

nadE

PMID:16606699[7]

Experiment(s):EBI-1137674

Protein

gntK

PMID:16606699[7]

Experiment(s):EBI-1137674

Protein

sapA

PMID:16606699[7]

Experiment(s):EBI-1137674

Protein

rplE

PMID:19402753[8]

MALDI(Z-score):22.075684

Protein

rplF

PMID:19402753[8]

MALDI(Z-score):22.056595

Protein

lysS

PMID:19402753[8]

MALDI(Z-score):16.833311

Protein

fusA

PMID:19402753[8]

MALDI(Z-score):26.805477

Protein

pflB

PMID:19402753[8]

MALDI(Z-score):28.448012

Protein

gapA

PMID:19402753[8]

MALDI(Z-score):36.355695

Protein

ugpB

PMID:19402753[8]

MALDI(Z-score):19.729265

Protein

adhE

PMID:19402753[8]

MALDI(Z-score):20.072346

Protein

rpsD

PMID:19402753[8]

MALDI(Z-score):23.814236

Protein

gadB

PMID:19402753[8]

MALDI(Z-score):18.408656

Protein

rplB

PMID:19402753[8]

MALDI(Z-score):33.537668

Protein

tig

PMID:19402753[8]

MALDI(Z-score):23.396279

Protein

eno

PMID:19402753[8]

MALDI(Z-score):32.621331

Protein

rpsJ

PMID:19402753[8]

MALDI(Z-score):19.132228

Protein

pgk

PMID:19402753[8]

MALDI(Z-score):32.169687

Protein

glpK

PMID:19402753[8]

MALDI(Z-score):24.698600

Protein

groS

PMID:19402753[8]

MALDI(Z-score):18.597115

Protein

tufB

PMID:19402753[8]

MALDI(Z-score):18.634822

Protein

phoA

PMID:19402753[8]

MALDI(Z-score):24.656734

Protein

tnaA

PMID:19402753[8]

MALDI(Z-score):23.947841

Protein

clpB

PMID:19402753[8]

MALDI(Z-score):27.905538

Protein

pstS

PMID:19402753[8]

MALDI(Z-score):36.912658

Protein

pta

PMID:19402753[8]

MALDI(Z-score):21.943806

Protein

sucC

PMID:19402753[8]

MALDI(Z-score):21.749805

Protein

rpoA

PMID:19402753[8]

MALDI(Z-score):28.657556

Protein

deoD

PMID:19402753[8]

MALDI(Z-score):24.591325

Protein

fbaB

PMID:19402753[8]

MALDI(Z-score):30.826109

Protein

cdd

PMID:19402753[8]

MALDI(Z-score):25.864730

Protein

treC

PMID:19402753[8]

MALDI(Z-score):19.284473

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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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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 

MRLIPLTTAE QVGKWAARHI VNRINAFKPT ADRPFVLGLP TGGTPMTTYK ALVEMHKAGQ
VSFKHVVTFN MDEYVGLPKE HPESYYSFMH RNFFDHVDIP AENINLLNGN APDIDAECRQ
YEEKIRSYGK IHLFMGGVGN DGHIAFNEPA SSLASRTRIK TLTHDTRVAN SRFFDNDVNQ
VPKYALTVGV GTLLDAEEVM ILVLGSQKAL ALQAAVEGCV NHMWTISCLQ LHPKAIMVCD
EPSTMELKVK TLRYFNELEA ENIKGL
Length

266

Mol. Wt

29.773 kDa

pI

6.9 (calculated)

Extinction coefficient

22,920 - 23,420 (calc based on 8 Y, 2 W, and 4 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

15..250

PF01182 Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase

PMID:19920124[9]

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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=nagB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

Notes

Gene Product Resources

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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:16128654

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945290

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002304

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A759

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10633

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10633

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945290

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000626

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0627

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

5.46E+02

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

1391

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

687

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

866

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

Transcription unit(s)

nagBACD

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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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<gbrowseImage> name=NC_000913:702814..702854 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> 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

</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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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:b0678 (EcoliWiki Page)

NCBI GEO profiles for nagB

microarray

GenExpDB:b0678 (EcoliWiki Page)

Summary of data for nagB 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 (702739..703185) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ17; Well:D9[10]

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<protect>

Notes

Accessions Related to nagB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10633

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0627

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0678

EcoGene

EcoGene:EG10633

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000626

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002304

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

Anopheles gambiae

  • ENSANGP00000027824 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000033350 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT5G24400 (score: 1.000; bootstrap: 100%)
  • AT3G49360 (score: 0.418)
  • AT5G24410 (score: 0.353)
  • AT5G24420 (score: 0.350)
  • AT1G13700 (score: 0.313)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000010347 (score: 1.000; bootstrap: 100%)
  • ENSBTAP00000000357 (score: 0.173)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00040062 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00011399 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000002748 (score: 1.000; bootstrap: 100%)
  • ENSCAFP00000009366 (score: 0.741)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000018019 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-050417-417 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-050417-418 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0206255 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0031717 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA19983-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000011819 (score: 1.000; bootstrap: 100%)
  • ENSGALP00000022938 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000295448 (score: 1.000; bootstrap: 100%)
  • ENSP00000311876 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000012780 (score: 1.000; bootstrap: 100%)
  • ENSMMUP00000012149 (score: 0.374)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000025757 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000013035 (score: 0.404)

From Inparanoid:20070104

Mus musculus

  • MGI:1915230 (score: 1.000; bootstrap: 100%)
  • MGI:1347054 (score: 0.722)
  • MGI:3647532 (score: 0.478)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000027571 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000002992 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000152425 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00017024001 (score: 1.000; bootstrap: 100%)
  • GSTENP00011336001 (score: 0.300)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000009054 (score: 1.000; bootstrap: 100%)
  • ENSXETP00000018475 (score: 0.360)

From Inparanoid:20070104

Shigella flexneri

NAGB

From SHIGELLACYC

E. coli O157

NAGB

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.

Database Accession Notes

Pfam (EcoliWiki Page)

PF01182 Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase

Superfamily (EcoliWiki Page)

SUPERFAMILY:100950

EcoCyc

EcoCyc:EG10633

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10633

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000626

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0627

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002304

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. ↑ 2.00 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 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 5.2 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 7.2 7.3 7.4 7.5 7.6 7.7 7.8 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 8.18 8.19 8.20 8.21 8.22 8.23 8.24 8.25 8.26 8.27 8.28 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  9. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
  10. ↑ 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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