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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	nagD
Gene Synonym(s)	ECK0663, b0675, JW0661^[1], JW0661
Product Desc.	ribonucleotide monophosphatase^[2]^[3] UMP phosphatase; HAD23^[4]
Product Synonyms(s)	UMP phosphatase^[1], B0675^[2]^[1], NagD^[2]^[1] , ECK0663, JW0661, b0675
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): nagD^[2], nagBACD^[2], OP00058, nagB
Regulation/Activity
Quick Links
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Notes

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Also has GMP phosphatase activity. HAD superfamily.^[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	nagD
Mnemonic	N-Acetylglucosamine
Synonyms	ECK0663, b0675, JW0661^[1], JW0661
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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	15.06 minutes	MG1655: 699549..698797 <gbrowseImage> name=NC_000913:698797..699549 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 682421..681669 <gbrowseImage> name=NC_012967:681669..682421 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 601557..602309 <gbrowseImage> name=NC_012759:601557..602309 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 700748..699996 <gbrowseImage> name=NC_007779:699996..700748 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 752141..751389 <gbrowseImage> name=NC_010473:751389..752141 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	Nt change(s)	AA change(s)	Phenotype: Description	Reference	Availability	Comments
Strain DH10B		H97Y	Nonsynonomous mutation	PMID:18245285	ASAP	This is a SNP in E. coli K-12 Strain DH10B
ΔnagD (Keio:JW0661)	deletion	deletion		PMID:16738554	Shigen CGSC8752^[5]
ΔnagD724::kan				PMID:16738554	CGSC:101994
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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
JW0661	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACCATTAAAAATGTAATTTG Primer 2:CCGATAACGTCGATTTCAGCGAC
16A8	Kohara Phage	Genobase	PMID:3038334
3A6	Kohara Phage	Genobase	PMID:3038334
crcA280::Tn10	Linked marker	CAG12077 = CGSC7347^[5]	est. P1 cotransduction: 14% ^[6] Synonyms:zbe-280::Tn10
asnB3057::Tn10	Linked marker	CAG18433 = CGSC7349^[5]	est. P1 cotransduction: 94% ^[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.
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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:EG10634	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10634	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000627	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945283	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0628	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002296	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	NagD
Synonyms	UMP phosphatase^[1], B0675^[2]^[1], NagD^[2]^[1] , ECK0663, JW0661, b0675
Product description	ribonucleotide monophosphatase^[2]^[3] UMP phosphatase; HAD23^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005834	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005975	carbohydrate metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0119	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005834	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006357	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006357	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	References	Evidence
Protein	asnB	PMID:16606699	Experiment(s):EBI-1137655
Protein	groL	PMID:16606699	Experiment(s):EBI-1137655
Protein	atpA	PMID:16606699	Experiment(s):EBI-1137655
Protein	sapA	PMID:16606699	Experiment(s):EBI-1137655
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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 MTIKNVICDI DGVLMHDNVA VPGAAEFLHG IMDKGLPLVL LTNYPSQTGQ DLANRFATAG VDVPDSVFYT SAMATADFLR RQEGKKAYVV GEGALIHELY KAGFTITDVN PDFVIVGETR SYNWDMMHKA AYFVANGARF IATNPDTHGR GFYPACGALC AGIEKISGRK PFYVGKPSPW IIRAALNKMQ AHSEETVIVG DNLRTDILAG FQAGLETILV LSGVSSLDDI DSMPFRPSWI YPSVAEIDVI
Length	250
Mol. Wt	27.163 kDa
pI	5.2 (calculated)
Extinction coefficient	29,910 - 30,285 (calc based on 9 Y, 3 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	3..214	PF00702 haloacid dehalogenase-like hydrolase		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=nagD 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:16128651	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945283	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002296	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AF24	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10634	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10634	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945283	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000627	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0628	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	Reference(s)
Protein	E. coli K-12 MC4100	2.89E+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	2085	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	709	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	1230	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)
nagD
nagBACD
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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_000913:699529..699569 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:b0675 (EcoliWiki Page)	NCBI GEO profiles for nagD
microarray	GenExpDB:b0675 (EcoliWiki Page)	Summary of data for nagD 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 nagD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10634	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0628	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0675
EcoGene	EcoGene:EG10634	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000627	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002296	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	ENSANGP00000018510 (score: 1.000; bootstrap: 86%) ENSANGP00000011965 (score: 0.119) ENSANGP00000019927 (score: 0.097) ENSANGP00000024232 (score: 0.097) ENSANGP00000011809 (score: 0.051)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000003008 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G36790 (score: 1.000; bootstrap: 100%) AT5G36700 (score: 1.000; bootstrap: 100%) AT5G47760 (score: 0.487)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000013127 (score: 1.000; bootstrap: 91%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00030926 (score: 1.000; bootstrap: 76%) WBGene00030927 (score: 0.884) WBGene00029103 (score: 0.166) WBGene00039013 (score: 0.109)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00016892 (score: 1.000; bootstrap: 77%) WBGene00018424 (score: 1.000; bootstrap: 76%) WBGene00019604 (score: 1.000; bootstrap: 77%) WBGene00019301 (score: 0.196) WBGene00016664 (score: 0.171)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000025912 (score: 1.000; bootstrap: 56%) ENSCAFP00000018755 (score: 0.226)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000000285 (score: 1.000; bootstrap: 59%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-030131-6240 (score: 1.000; bootstrap: 79%) ZDB-CDNA-040425-1460 (score: 1.000; bootstrap: 76%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0186160 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0036760 (score: 1.000; bootstrap: 83%) FBgn0052487 (score: 0.240) FBgn0052488 (score: 0.240) FBgn0034713 (score: 0.179) FBgn0036759 (score: 0.159) FBgn0030347 (score: 0.081)	From Inparanoid:20070104
Drosophila pseudoobscura	GA16942-PA (score: 1.000; bootstrap: 87%) GA16941-PA (score: 0.244) GA18976-PA (score: 0.228) GA18982-PA (score: 0.098)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000002892 (score: 1.000; bootstrap: 76%) ENSGALP00000022802 (score: 0.233)	From Inparanoid:20070104
Homo sapiens	ENSP00000330918 (score: 1.000; bootstrap: 78%) ENSP00000215904 (score: 0.292)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000025276 (score: 1.000; bootstrap: 81%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000019860 (score: 1.000; bootstrap: 94%) ENSMODP00000000548 (score: 0.276)	From Inparanoid:20070104
Mus musculus	MGI:1914328 (score: 1.000; bootstrap: 81%) MGI:1919282 (score: 0.279)	From Inparanoid:20070104
Oryza gramene	Q6EP66 (score: 1.000; bootstrap: 100%) Q7X7H3 (score: 0.601)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000024706 (score: 1.000; bootstrap: 70%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000012720 (score: 1.000; bootstrap: 88%) ENSRNOP00000050300 (score: 0.279)	From Inparanoid:20070104
Saccharomyces cerevisiae	YDL236W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC15D45 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000141793 (score: 1.000; bootstrap: 76%) NEWSINFRUP00000128523 (score: 0.311)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00024192001 (score: 1.000; bootstrap: 87%) GSTENP00030960001 (score: 0.287)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000035103 (score: 1.000; bootstrap: 80%)	From Inparanoid:20070104
E. coli O157	NAGD	From ECOO157CYC
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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)	PF00702 haloacid dehalogenase-like hydrolase
Panther (EcoliWiki Page)	PTHR19288:SF3
Superfamily (EcoliWiki Page)	SUPERFAMILY:56784
EcoCyc	EcoCyc:EG10634	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10634	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000627	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0628	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002296	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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 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 ^5.2 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).

nagD: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 nagD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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