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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	nadE
Gene Synonym(s)	ECK1738, b1740, JW1729, efg, ntrL^[1], ntrL
Product Desc.	NadE^[2]^[3]; Component of NAD-SYNTH-CPLX^[2] NAD synthase, ammonia dependent^[4]
Product Synonyms(s)	NAD synthetase, NH3/glutamine-dependent^[1], B1740^[2]^[1], Efg^[2]^[1], NtrL^[2]^[1], NadE^[2]^[1] , ECK1738, efg, JW1729, ntrL, b1740
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): nadE^[2]
Regulation/Activity
Quick Links
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Notes

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NadE is regulated by cyaR sRNA (De Lay, 2009).^[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	nadE
Mnemonic	Nicotinamide adenine dinucleotide
Synonyms	ECK1738, b1740, JW1729, efg, ntrL^[1], ntrL
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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	39.24 minutes	MG1655: 1820482..1821309 <gbrowseImage> name=NC_000913:1820482..1821309 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1799723..1800550 <gbrowseImage> name=NC_012967:1799723..1800550 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1712541..1713368 <gbrowseImage> name=NC_012759:1712541..1713368 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1824172..1824999 <gbrowseImage> name=NC_007779:1824172..1824999 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1911053..1911880 <gbrowseImage> name=NC_010473:1911053..1911880 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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	1820482	Edman degradation	PMID:3025172 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
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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
JW1729	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACATTGCAACAACAAATAAT Primer 2:CCtTTTTTCCAGAAATCATCGAA
4F7	Kohara Phage	Genobase	PMID:3038334
5E12	Kohara Phage	Genobase	PMID:3038334
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[5]	est. P1 cotransduction: 15% ^[6] Synonyms:zdh-925::Tn10
zdj-276::Tn10	Linked marker	CAG18464 = CGSC7387^[5]	est. P1 cotransduction: 66% ^[6] Synonyms:zdi-276::Tn10
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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:EG10663	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10663	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000656	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946946	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0657	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005803	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	NadE
Synonyms	NAD synthetase, NH3/glutamine-dependent^[1], B1740^[2]^[1], Efg^[2]^[1], NtrL^[2]^[1], NadE^[2]^[1] , ECK1738, efg, JW1729, ntrL, b1740
Product description	NadE^[2]^[3]; Component of NAD-SYNTH-CPLX^[2] NAD synthase, ammonia dependent^[4]
EC number (for enzymes)	6.3.5.1^[1]
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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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	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:0003952	NAD+ synthase (glutamine-hydrolyzing) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003694	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00193	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003694	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:0008795	NAD+ synthase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:6.3.1.5	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		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 NAD-SYNTH-CPLX	could be indirect
Protein	arnA		PMID:15690043	Experiment(s):EBI-887727
Protein	ygfH		PMID:15690043	Experiment(s):EBI-887727
Protein	yhcA		PMID:16606699	Experiment(s):EBI-1140662
Protein	clpA		PMID:19402753	MALDI(Z-score):19.681648
Protein	rpsA		PMID:19402753	MALDI(Z-score):19.102974
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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 MTLQQQIIKA LGAKPQINAE EEIRRSVDFL KSYLQTYPFI KSLVLGISGG QDSTLAGKLC QMAINELRLE TGNESLQFIA VRLPYGVQAD EQDCQDAIAF IQPDRVLTVN IKGAVLASEQ ALREAGIELS DFVRGNEKAR ERMKAQYSIA GMTSGVVVGT DHAAEAITGF FTKYGDGGTD INPLYRLNKR QGKQLLAALA CPEHLYKKAP TADLEDDRPS LPDEVALGVT YDNIDDYLEG KNVPQQVART IENWYLKTEH KRRPPITVFD DFWKK
Length	275
Mol. Wt	30.637 kDa
pI	5.3 (calculated)
Extinction coefficient	25,900 - 26,275 (calc based on 10 Y, 2 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
Domain	22..265	PF02540 NAD synthase		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=nadE taxon=562,83333 </beststructure>

Models

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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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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:16129694	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946946	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005803	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P18843	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10663	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10663	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946946	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000656	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0657	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	7.46E+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	Ecoli K-12	30.911+/-0.141	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.125151149	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 EMG2	100	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: Ml l2	PMID: 9298646
Protein	E. coli K-12 MG1655	3352	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	2198	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	2478	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)
nadE
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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_000913:1820462..1820502 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:b1740 (EcoliWiki Page)	NCBI GEO profiles for nadE
microarray	GenExpDB:b1740 (EcoliWiki Page)	Summary of data for nadE 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 nadE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10663	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0657	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1740
EcoGene	EcoGene:EG10663	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000656	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005803	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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
Shigella flexneri	NADE	From SHIGELLACYC
E. coli O157	NADE	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)	PF02540 NAD synthase
Superfamily (EcoliWiki Page)	SUPERFAMILY:52402
Panther (EcoliWiki Page)	PTHR23090:SF2
EcoCyc	EcoCyc:EG10663	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10663	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000656	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0657	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005803	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^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)
↑ ^2.00 ^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
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^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.
↑ ^5.0 ^5.1 CGSC: The Coli Genetics Stock Center
↑ ^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).

nadE:On One Page

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to nadE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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