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Gene |

Product(s) |

Expression|

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Standard Name	nadK
Gene Synonym(s)	yfjB, ECK2611, b2615, JW2596, ppnK, yfjE^[1]^[2], yfjE
Product Desc.	NAD kinase^[2]^[3]; Component of NAD kinase^[3] ATP-NAD kinase^[4]
Product Synonyms(s)	NAD kinase^[1], B2615^[2]^[1], YfjE^[2]^[1], NadK^[2]^[1], YfjB^[2]^[1] , ECK2611, JW2596, yfjB, yfjE, b2615
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yfjB^[2]
Regulation/Activity
Quick Links
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Notes

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nadK is probably an essential gene since mutants could not be obtained. Polyphosphates do not serve as P donors. yfjB is renamed as nadK, personal comm., Kousaku Murata, Kyoto Univ., 11/02.^[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	nadK
Mnemonic	Nicotinamide adenine dinucleotide
Synonyms	yfjB, ECK2611, b2615, JW2596, ppnK, yfjE^[1]^[2], yfjE
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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	59.25 minutes	MG1655: 2748853..2749731 <gbrowseImage> name=NC_000913:2748853..2749731 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2634665..2635543 <gbrowseImage> name=NC_012759:2634665..2635543 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2749487..2750365 <gbrowseImage> name=NC_007779:2749487..2750365 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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	2748853	Edman degradation	PMID:11488932
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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

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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:EG12192	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12192	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002081	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947092	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2109	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008603	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	YfjB
Synonyms	NAD kinase^[1], B2615^[2]^[1], YfjE^[2]^[1], NadK^[2]^[1], YfjB^[2]^[1] , ECK2611, JW2596, yfjB, yfjE, b2615
Product description	NAD kinase^[2]^[3]; Component of NAD kinase^[3] ATP-NAD kinase^[4]
EC number (for enzymes)	2.7.1.23^[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: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:0003951	NAD+ kinase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00361	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003951	NAD+ kinase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002504	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003951	NAD+ kinase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016064	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003951	NAD+ kinase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017437	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003951	NAD+ kinase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.1.23	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:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00361	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00361	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 NAD kinase	could be indirect
Protein	galU		PMID:16606699	Experiment(s):EBI-1143495
Protein	dnaK		PMID:16606699	Experiment(s):EBI-1143495
Protein	groL		PMID:16606699	Experiment(s):EBI-1143495
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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 MNNHFKCIGI VGHPRHPTAL TTHEMLYRWL CTKGYEVIVE QQIAHELQLK NVKTGTLAEI GQLADLAVVV GGDGNMLGAA RTLARYDIKV IGINRGNLGF LTDLDPDNAQ QQLADVLEGH YISEKRFLLE AQVCQQDCQK RISTAINEVV LHPGKVAHMI EFEVYIDEIF AFSQRSDGLI ISTPTGSTAY SLSAGGPILT PSLDAITLVP MFPHTLSARP LVINSSSTIR LRFSHRRNDL EISCDSQIAL PIQEGEDVLI RRCDYHLNLI HPKDYSYFNT LSTKLGWSKK LF
Length	292
Mol. Wt	32.566 kDa
pI	6.9 (calculated)
Extinction coefficient	24,410 - 25,160 (calc based on 9 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	7..272	PF01513 ATP-NAD kinase		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=nadK 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:16130534	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947092	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008603	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A7B3	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12192	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12192	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947092	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002081	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2109	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	Ecoli K-12	16.726+/-0.115	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.025626424	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	218	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	173	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	160	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)
yfjB
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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_000913:2748833..2748873 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

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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:b2615 (EcoliWiki Page)	NCBI GEO profiles for nadK
microarray	GenExpDB:b2615 (EcoliWiki Page)	Summary of data for nadK 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 (2748635..2748924) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ05; Well:H9^[5]
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Notes

Accessions Related to nadK Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12192	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2109	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2615
EcoGene	EcoGene:EG12192	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002081	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008603	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
Anopheles gambiae	ENSANGP00000012587 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000006353 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G21640 (score: 1.000; bootstrap: 100%) AT3G21070 (score: 0.086)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000000255 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00034605 (score: 1.000; bootstrap: 100%) WBGene00039904 (score: 0.250)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00022307 (score: 1.000; bootstrap: 100%) WBGene00012463 (score: 0.246)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000028345 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000010957 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-050417-39 (score: 1.000; bootstrap: 100%) ZDB-CDNA-050417-40 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231370 (score: 1.000; bootstrap: 100%) DDB0231371 (score: 0.062) DDB0205758 (score: 0.061)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0053156 (score: 1.000; bootstrap: 100%) FBgn0033853 (score: 0.626)	From Inparanoid:20070104
Drosophila pseudoobscura	GA17329-PA (score: 1.000; bootstrap: 100%) GA19389-PA (score: 0.677)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000034525 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000246422 (score: 1.000; bootstrap: 100%) ENSP00000340925 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000014257 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000008479 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:2183149 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q5JK52 (score: 1.000; bootstrap: 100%) Q60E60 (score: 0.586) Q53NI2 (score: 0.161)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000022900 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YEL041W (score: 1.000; bootstrap: 100%) YJR049C (score: 0.438)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC3231c (score: 1.000; bootstrap: 100%) SPAC3H51 (score: 0.061)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000152107 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000144351 (score: 0.508)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00020619001 (score: 1.000; bootstrap: 100%) GSTENP00021473001 (score: 0.303) GSTENP00001411001 (score: 0.151) GSTENP00001412001 (score: 0.058)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000042402 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YFJB	From SHIGELLACYC
E. coli O157	YFJB	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)	PF01513 ATP-NAD kinase
Panther (EcoliWiki Page)	PTHR20275:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:111331
EcoCyc	EcoCyc:EG12192	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12192	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002081	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2109	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008603	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 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 ^3.2 ^3.3 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.
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

nadK:On One Page

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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 nadK Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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