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Standard Name	nudK
Gene Synonym(s)	yffH, ECK2462, b2467, JW2451^[1]^[2], JW2451
Product Desc.	nucleotide-sugar hydrolase^[2]^[3]; Component of nucleotide-sugar hydrolase^[3] GDP-mannose pyrophosphatase^[4]
Product Synonyms(s)	predicted NUDIX hydrolase^[1], B2467^[2]^[1], YffH^[2]^[1], NudK^[2]^[1] , ECK2462, JW2451, yffH, b2467
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yffH^[2]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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Nudix hydrolase.^[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	nudK
Mnemonic	Nudix hydrolase
Synonyms	yffH, ECK2462, b2467, JW2451^[1]^[2], JW2451
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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	55.63 minutes	MG1655: 2581500..2580925 <gbrowseImage> name=NC_000913:2580925..2581500 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 2466730..2467305 <gbrowseImage> name=NC_012759:2466730..2467305 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2582134..2581559 <gbrowseImage> name=NC_007779:2581559..2582134 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
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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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
yffH::Tn5KAN-I-SceI (FB20813)	Insertion at nt 198 in Minus orientation			PMID:15262929	E. coli Genome Project:FB20813	contains pKD46
yffH::Tn5KAN-I-SceI (FB20814)	Insertion at nt 198 in Minus orientation			PMID:15262929	E. coli Genome Project:FB20814	does not contain pKD46
ΔyffH::kan	deletion	Biolog:respiration	unable to respire N-Acetyl-D-glucosamine	PMID:16095938
ΔyffH::kan	deletion	Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔyffH::kan	deletion	Biolog:respiration	unable to respire a-Ketobutyrate	PMID:16095938
ΔnudK787::kan				PMID:16738554	CGSC:106270
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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:

7A8

Kohara Phage

Genobase

PMID:3038334

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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:EG12410	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12410	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002271	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947072	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2309	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008123	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	YffH
Synonyms	predicted NUDIX hydrolase^[1], B2467^[2]^[1], YffH^[2]^[1], NudK^[2]^[1] , ECK2462, JW2451, yffH, b2467
Product description	nucleotide-sugar hydrolase^[2]^[3]; Component of nucleotide-sugar hydrolase^[3] GDP-mannose pyrophosphatase^[4]
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:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000086	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015797	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
	GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004385	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004385	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 nucleotide-sugar hydrolase	could be indirect
Protein	eutQ		PMID:16606699	Experiment(s):EBI-1142937
Protein	narL		PMID:16606699	Experiment(s):EBI-1142937
Protein	uvrC		PMID:16606699	Experiment(s):EBI-1142937
Protein	pta		PMID:16606699	Experiment(s):EBI-1142937
Protein	aceE		PMID:16606699	Experiment(s):EBI-1142937
Protein	ahpC		PMID:16606699	Experiment(s):EBI-1142937
Protein	acnB		PMID:16606699	Experiment(s):EBI-1142937
Protein	rplF		PMID:16606699	Experiment(s):EBI-1142937
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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 MTQQITLIKD KILSDNYFTL HNITYDLTRK DGEVIRHKRE VYDRGNGATI LLYNTKKKTV VLIRQFRVAT WVNGNESGQL IESCAGLLDN DEPEVCIRKE AIEETGYEVG EVRKLFELYM SPGGVTELIH FFIAEYSDNQ RANAGGGVED EDIEVLELPF SQALEMIKTG EIRDGKTVLL LNYLQTSHLM D
Length	191
Mol. Wt	21.748 kDa
pI	4.7 (calculated)
Extinction coefficient	17,420 - 17,670 (calc based on 8 Y, 1 W, and 2 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	44..184	PF00293 NUDIX domain		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=nudK 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:16130392	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947072	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008123	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P37128	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12410	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12410	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947072	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002271	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2309	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	14.4+/-0.148	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.03826087	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	326	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	215	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	198	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)
yffH
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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_000913:2581480..2581520 source=MG1655 flip=1 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:b2467 (EcoliWiki Page)	NCBI GEO profiles for nudK
microarray	GenExpDB:b2467 (EcoliWiki Page)	Summary of data for nudK 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 (2581410..2581585) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ10; Well:D3^[5]
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Notes

Accessions Related to nudK Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12410	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2309	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2467
EcoGene	EcoGene:EG12410	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002271	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008123	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	ENSANGP00000011673 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000021683 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000032528 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000027181 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0051063 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA15978-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000339175 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000006230 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1913424 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000011592 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000019550 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YFFH	From SHIGELLACYC
E. coli O157	YFFH	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)	PF00293 NUDIX domain
Panther (EcoliWiki Page)	PTHR11839:SF1
Superfamily (EcoliWiki Page)	SUPERFAMILY:55811
EcoCyc	EcoCyc:EG12410	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12410	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002271	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2309	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008123	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 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 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

nudK: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 nudK Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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