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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	yrdD
Gene Synonym(s)	ECK3270, b3283, JW5949^[1], JW5949
Product Desc.	putative DNA topoisomerase^[2]; predicted DNA topoisomerase^[3] Function unknown^[4]
Product Synonyms(s)	predicted DNA topoisomerase^[1], B3283^[2]^[1], YrdD^[2]^[1] , ECK3270, JW5949, b3283
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yrdD-rimN-aroE-yrdB^[2]
Regulation/Activity
Quick Links
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Notes

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AFMB Structural Genomics target No. 20 (http://afmb.cnrs-mrs.fr/article171.html).^[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	yrdD
Mnemonic	Systematic nomenclature
Synonyms	ECK3270, b3283, JW5949^[1], JW5949
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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	73.92 minutes	MG1655: 3429984..3429442 <gbrowseImage> name=NC_000913:3429442..3429984 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3359867..3359325 <gbrowseImage> name=NC_012967:3359325..3359867 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3316599..3317141 <gbrowseImage> name=NC_012759:3316599..3317141 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4208454..4208996 <gbrowseImage> name=NC_007779:4208454..4208996 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3527729..3527187 <gbrowseImage> name=NC_010473:3527187..3527729 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)	Reference	Availability
ΔyrdD (Keio:JW5949)	deletion	deletion	PMID:16738554	Shigen CGSC11591^[5]
ΔyrdD722::kan			PMID:16738554	CGSC:111620
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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:
smg-3082::Tn10	Linked marker	CAG12071 = CGSC7444^[5]	est. P1 cotransduction: 98% ^[6] Synonyms:zhb-3082::Tn10, zhd-3082::Tn10
zhf-3084::Tn10	Linked marker	CAG18456 = CGSC7576^[5]	est. P1 cotransduction: 1% ^[6] Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).
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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:G7699	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12841	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004245	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947782	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2690	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010768	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	YrdD
Synonyms	predicted DNA topoisomerase^[1], B3283^[2]^[1], YrdD^[2]^[1] , ECK3270, JW5949, b3283
Product description	putative DNA topoisomerase^[2]; predicted DNA topoisomerase^[3] Function unknown^[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:0003916	DNA topoisomerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013498	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005694	chromosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013498	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006265	DNA topological change	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013498	P	Seeded from EcoCyc (v14.0)	complete
	GO:0003674	molecular function	n/a	ND: No biological Data available		F		Missing: reference
	GO:0005575	cellular component	n/a	ND: No biological Data available		C		Missing: reference
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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
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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 MAKSALFTVR NNESCPKCGA ELVIRSGKHG PFLGCSQYPA CDYVRPLKSS ADGHIVKVLE GQVCPACGAN LVLRQGRFGM FIGCINYPEC EHTELIDKPD ETAITCPQCR TGHLVQRRSR YGKTFHSCDR YPECQFAINF KPIAGECPEC HYPLLIEKKT AQGVKHFCAS KQCGKPVSAE
Length	180
Mol. Wt	19.87 kDa
pI	8.3 (calculated)
Extinction coefficient	8,940 - 10,940 (calc based on 6 Y, 0 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	12..50	PF01396 Topoisomerase DNA binding C4 zinc finger	PMID:19920124
Domain	61..99	PF01396 Topoisomerase DNA binding C4 zinc finger	PMID:19920124
Domain	103..143	PF01396 Topoisomerase DNA binding C4 zinc finger	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=yrdD 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:49176335	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947782	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010768	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P45771	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7699	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12841	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947782	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004245	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2690	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 MG1655	347	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	169	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	307	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)
yrdD-rimN-aroE-yrdB
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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_000913:3429964..3430004 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:b3283 (EcoliWiki Page)	NCBI GEO profiles for yrdD
microarray	GenExpDB:b3283 (EcoliWiki Page)	Summary of data for yrdD 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 yrdD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7699	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2690	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3283
EcoGene	EcoGene:EG12841	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004245	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010768	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	YRDD	From SHIGELLACYC
E. coli O157	YRDD	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:57783
Superfamily (EcoliWiki Page)	SUPERFAMILY:57783
Pfam (EcoliWiki Page)	PF01396 Topoisomerase DNA binding C4 zinc finger
Pfam (EcoliWiki Page)	PF01396 Topoisomerase DNA binding C4 zinc finger
Pfam (EcoliWiki Page)	PF01396 Topoisomerase DNA binding C4 zinc finger
EcoCyc	EcoCyc:G7699	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12841	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004245	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2690	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010768	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 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).

yrdD:On One Page

Quickview

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 yrdD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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