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Standard Name	nrdD
Gene Synonym(s)	ECK4233, b4238, JW4197^[1], JW4197
Product Desc.	ribonucleoside-triphosphate reductase^[2]^[3]; Component of ribonucleoside-triphosphate reductase^[2]^[3]; anaerobic nucleoside-triphosphate reductase activating system^[2]^[3] Ribonucleoside triphosphate reductase, class III, anaerobic^[4]
Product Synonyms(s)	anaerobic ribonucleoside-triphosphate reductase^[1], B4238^[2]^[1], NrdD^[2]^[1] , ECK4233, JW4197, b4238
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): nrdDG^[2]
Regulation/Activity
Quick Links
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Notes

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Activated NrdD is predicted to be cleaved by oxygen at the Gly681 radical, dropping the last 31 aa. Requires AdoMet for oxidation of the iron-sulfur center and glycine radical formation. FNR regulon. Binds TrxA (Kumar, 2004).^[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	nrdD
Mnemonic	Nucleotide reductase
Synonyms	ECK4233, b4238, JW4197^[1], JW4197
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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	96.1 minutes	MG1655: 4460683..4458545 <gbrowseImage> name=NC_000913:4458545..4460683 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4445937..4443799 <gbrowseImage> name=NC_012967:4443799..4445937 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4397280..4399418 <gbrowseImage> name=NC_012759:4397280..4399418 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4467340..4465202 <gbrowseImage> name=NC_007779:4465202..4467340 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4562491..4560353 <gbrowseImage> name=NC_010473:4560353..4562491 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	4458545	Edman degradation	PMID:8421692
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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)	Reference	Availability
ΔnrdD (Keio:JW4197)	deletion	deletion	PMID:16738554	Shigen CGSC11020^[5]
ΔnrdD785::kan			PMID:16738554	CGSC:102104
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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
JW4197	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACACCGCATGTGATGAAACG Primer 2:CCACCTATCTGCCCATTCCCCAA
zjf-920::Tn10	Linked marker	CAG12019 = CGSC7484^[5]	est. P1 cotransduction: 62% ^[6] Synonyms:zjh-901::Tn10, zjg-920::Tn10
mdoB202::Tn10	Linked marker	CAG18430 = CGSC7488^[5]	est. P1 cotransduction: % ^[6] Synonyms:zjj-202::Tn10, zji-202::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:EG11417	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11417	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001382	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948755	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1388	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013865	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	NrdD
Synonyms	anaerobic ribonucleoside-triphosphate reductase^[1], B4238^[2]^[1], NrdD^[2]^[1] , ECK4233, JW4197, b4238
Product description	ribonucleoside-triphosphate reductase^[2]^[3]; Component of ribonucleoside-triphosphate reductase^[2]^[3]; anaerobic nucleoside-triphosphate reductase activating system^[2]^[3] Ribonucleoside triphosphate reductase, class III, anaerobic^[4]
EC number (for enzymes)	1.17.4.2^[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:0031250	anaerobic ribonucleoside-triphosphate reductase complex	PMID:8954104	IMP: Inferred from Mutant Phenotype		C		complete
	GO:0015949	nucleobase, nucleoside and nucleotide interconversion	PMID:8954104	IMP: Inferred from Mutant Phenotype		P		complete
	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
Contributes to	GO:0004748	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor	PMID:8954104	IMP: Inferred from Mutant Phenotype		F	replaces obsolete GO:0016961	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:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	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
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012833	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	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 ribonucleoside-triphosphate reductase	could be indirect
Protein	nadE		PMID:16606699	Experiment(s):EBI-1147734
Protein	metG		PMID:19402753	LCMS(ID Probability):99.6
Protein	ybiS		PMID:19402753	LCMS(ID Probability):99.6
Protein	yohN		PMID:19402753	LCMS(ID Probability):99.6
Protein	nrdG		PMID:19402753	LCMS(ID Probability):99.6
Protein	Subunits of anaerobic nucleoside-triphosphate reductase activating system	could be indirect
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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 MTPHVMKRDG CKVPFKSERI KEAILRAAKA AEVDDADYCA TVAAVVSEQM QGRNQVDINE IQTAVENQLM SGPYKQLARA YIEYRHDRDI EREKRGRLNQ EIRGLVEQTN ASLLNENANK DSKVIPTQRD LLAGIVAKHY ARQHLLPRDV VQAHERGDIH YHDLDYSPFF PMFNCMLIDL KGMLTQGFKM GNAEIEPPKS ISTATAVTAQ IIAQVASHIY GGTTINRIDE VLAPFVTASY NKHRKTAEEW NIPDAEGYAN SRTIKECYDA FQSLEYEVNT LHTANGQTPF VTFGFGLGTS WESRLIQESI LRNRIAGLGK NRKTAVFPKL VFAIRDGLNH KKGDPNYDIK QLALECASKR MYPDILNYDQ VVKVTGSFKT PMGCRSFLGV WENENGEQIH DGRNNLGVIS LNLPRIALEA KGDEATFWKL LDERLVLARK ALMTRIARLE GVKARVAPIL YMEGACGVRL NADDDVSEIF KNGRASISLG YIGIHETINA LFGGEHVYDN EQLRAKGIAI VERLRQAVDQ WKEETGYGFS LYSTPSENLC DRFCRLDTAE FGVVPGVTDK GYYTNSFHLD VEKKVNPYDK IDFEAPYPPL ANGGFICYGE YPNIQHNLKA LEDVWDYSYQ HVPYYGTNTP IDECYECGFT GEFECTSKGF TCPKCGNHDA SRVSVTRRVC GYLGSPDARP FNAGKQEEVK RRVKHLGNGQ IG
Length	712
Mol. Wt	80.023 kDa
pI	6.8 (calculated)
Extinction coefficient	80,680 - 82,680 (calc based on 32 Y, 6 W, and 16 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	References
Domain	3..90	PF03477 ATP cone domain	PMID:19920124
Domain	581..687	PF01228 Glycine radical	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=nrdD 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:16132060	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948755	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013865	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P28903	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11417	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11417	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948755	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001382	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1388	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	5.183+/-0.119	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.016604303	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	256	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	92	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	140	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)
nrdDG
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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_000913:4460663..4460703 source=MG1655 flip=1 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:b4238 (EcoliWiki Page)	NCBI GEO profiles for nrdD
microarray	GenExpDB:b4238 (EcoliWiki Page)	Summary of data for nrdD 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 (4460150..4460669) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ17; Well:E10^[7]
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Notes

Accessions Related to nrdD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11417	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1388	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4238
EcoGene	EcoGene:EG11417	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001382	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013865	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	NRDD	From SHIGELLACYC
E. coli O157	NRDD	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)	PF03477 ATP cone domain
Pfam (EcoliWiki Page)	PF01228 Glycine radical
Superfamily (EcoliWiki Page)	SUPERFAMILY:51998
Panther (EcoliWiki Page)	PTHR21075:SF0
EcoCyc	EcoCyc:EG11417	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11417	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001382	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1388	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013865	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 ^3.4 ^3.5 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

nrdD:On One Page

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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 nrdD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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