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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	dut
Gene Synonym(s)	ECK3630, b3640, JW3615, dnaS, sof^[1], sof
Product Desc.	Dut^[2]^[3]; Component of deoxyuridine triphosphatase^[2]^[3] dUTP pyrophosphatase; dUTPase^[4]
Product Synonyms(s)	deoxyuridinetriphosphatase^[1], B3640^[2]^[1], sof^[2]^[1], DnaS^[2]^[1], Dut^[2]^[1] , dnaS, ECK3630, JW3615, sof, b3640
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): dut-slmA^[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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dut is an essential gene.^[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	dut
Mnemonic	dUTPase
Synonyms	ECK3630, b3640, JW3615, dnaS, sof^[1], sof
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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	82.16 minutes	MG1655: 3811955..3812410 <gbrowseImage> name=NC_000913:3811955..3812410 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3752287..3752742 <gbrowseImage> name=NC_012967:3752287..3752742 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3700281..3700736 <gbrowseImage> name=NC_012759:3700281..3700736 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3826483..3826028 <gbrowseImage> name=NC_007779:3826028..3826483 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3909532..3909987 <gbrowseImage> name=NC_010473:3909532..3909987 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
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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	AA change(s)	Phenotype: Description	Reference	Availability	Comments
dutD89N	D89N	Reduces catalytic activity 40000- fold			seeded from UniProt:P06968
dut-1			PMID:148458	CGSC:6840
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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
JW3615	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAAAAATCGACGTTAAGAT Primer 2:CCtTGACGACCAGAGTGACCAAA
2A6	Kohara Phage	Genobase	PMID:3038334
4D2	Kohara Phage	Genobase	PMID:3038334
zhg-50::Tn10	Linked marker	CAG18450 = CGSC7450^[5]	est. P1 cotransduction: % ^[6] Synonyms:zhf-50::Tn10, zhf-5::Tn10
zic-4901::Tn10	Linked marker	CAG18492 = CGSC7457^[5]	est. P1 cotransduction: 57% ^[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:EG10251	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10251	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000245	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948607	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0247	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011899	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	Dut
Synonyms	deoxyuridinetriphosphatase^[1], B3640^[2]^[1], sof^[2]^[1], DnaS^[2]^[1], Dut^[2]^[1] , dnaS, ECK3630, JW3615, sof, b3640
Product description	Dut^[2]^[3]; Component of deoxyuridine triphosphatase^[2]^[3] dUTP pyrophosphatase; dUTPase^[4]
EC number (for enzymes)	3.6.1.23^[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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0000287	magnesium ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00116	F	Seeded from EcoCyc (v14.0)	complete
	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:0004170	dUTP diphosphatase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00116	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004170	dUTP diphosphatase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008181	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004170	dUTP diphosphatase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.6.1.23	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0006220	pyrimidine nucleotide metabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00116	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009117	nucleotide metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0546	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046080	dUTP metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008180	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046080	dUTP metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008181	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	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 deoxyuridine triphosphatase	could be indirect
Protein	trkA		PMID:16606699	Experiment(s):EBI-1146377
Protein	moaE		PMID:16606699	Experiment(s):EBI-1146377
Protein	stfR		PMID:16606699	Experiment(s):EBI-1146377
Protein	lacZ		PMID:16606699	Experiment(s):EBI-1146377
Protein	pepD		PMID:16606699	Experiment(s):EBI-1146377
Protein	clpB		PMID:16606699	Experiment(s):EBI-1146377
Protein	metH		PMID:16606699	Experiment(s):EBI-1146377
Protein	rplW		PMID:16606699	Experiment(s):EBI-1146377
Protein	stpA		PMID:16606699	Experiment(s):EBI-1146377
Protein	ydbH		PMID:16606699	Experiment(s):EBI-1146377
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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 MKKIDVKILD PRVGKEFPLP TYATSGSAGL DLRACLNDAV ELAPGDTTLV PTGLAIHIAD PSLAAMMLPR SGLGHKHGIV LGNLVGLIDS DYQGQLMISV WNRGQDSFTI QPGERIAQMI FVPVVQAEFN LVEDFDATDR GEGGFGHSGR Q
Length	151
Mol. Wt	16.155 kDa
pI	5.0 (calculated)
Extinction coefficient	8,480 - 8,605 (calc based on 2 Y, 1 W, and 1 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..149	PF00692 dUTPase		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=dut 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:16131511	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948607	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011899	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P06968	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10251	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10251	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948607	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000245	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0247	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	2.66E+03	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	119.921+/-0.498	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.072527473	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	6571	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	1435	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	1948	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)
dut-slmA
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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_000913:3811935..3811975 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:b3640 (EcoliWiki Page)	NCBI GEO profiles for dut
microarray	GenExpDB:b3640 (EcoliWiki Page)	Summary of data for dut 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 dut Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10251	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0247	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3640
EcoGene	EcoGene:EG10251	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000245	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011899	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	ENSANGP00000001952 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000009358 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT3G46940 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000015916 (score: 1.000; bootstrap: 63%) ENSBTAP00000012947 (score: 0.288) ENSBTAP00000031396 (score: 0.135)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00026525 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00010609 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000021075 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000000051 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-041010-93 (score: 1.000; bootstrap: 100%) ZDB-CDNA-041010-93 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0230111 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0013349 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA18276-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000007930 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000249783 (score: 1.000; bootstrap: 100%) ENSP00000303742 (score: 0.061)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000022213 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000003255 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1346051 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000009549 (score: 1.000; bootstrap: 80%) ENSRNOP00000023387 (score: 0.688)	From Inparanoid:20070104
Saccharomyces cerevisiae	YBR252W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC6445c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000133083 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00018078001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000000815 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	DUT	From SHIGELLACYC
E. coli O157	DUT	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)	PF00692 dUTPase
Superfamily (EcoliWiki Page)	SUPERFAMILY:51283
Panther (EcoliWiki Page)	PTHR11241:SF0
EcoCyc	EcoCyc:EG10251	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10251	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000245	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0247	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011899	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 ^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.
↑ ^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).

dut: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 dut Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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