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Gene |

Product(s) |

Expression|

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Standard Name	cho
Gene Synonym(s)	ydjQ, ECK1739, b1741, JW1730, sosD^[1]^[2], dinM, sosD
Product Desc.	endonuclease of nucleotide excision repair^[2]^[3] Endonuclease involved in excision repair, cuts 3' of lesion; requires UvrAB^[4]
Product Synonyms(s)	endonuclease of nucleotide excision repair^[1], YdjQ^[2]^[1], Cho^[2]^[1], B1741^[2]^[1] , dinM, ECK1739, JW1730, sosD, ydjQ, b1741
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): cho^[2], ydjQ
Regulation/Activity
Quick Links
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Notes

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Homologous to N-terminal domain of UvrC. LexA regulon.^[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	cho
Mnemonic	uvrC HOmolog
Synonyms	ydjQ, ECK1739, b1741, JW1730, sosD^[1]^[2], dinM, sosD
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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	39.26 minutes	MG1655: 1821539..1822426 <gbrowseImage> name=NC_000913:1821539..1822426 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1800780..1801667 <gbrowseImage> name=NC_012967:1800780..1801667 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1713598..1714485 <gbrowseImage> name=NC_012759:1713598..1714485 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1825229..1826116 <gbrowseImage> name=NC_007779:1825229..1826116 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1912110..1912997 <gbrowseImage> name=NC_010473:1912110..1912997 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: Type	Phenotype: Description	Reference	Availability	Comments
Δcho-739::kan					PMID:16738554	CGSC:106142
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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:
4F7	Kohara Phage	Genobase	PMID:3038334
5E12	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:G6937	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13993	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003525	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948996	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3749	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005807	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	Cho
Synonyms	endonuclease of nucleotide excision repair^[1], YdjQ^[2]^[1], Cho^[2]^[1], B1741^[2]^[1] , dinM, ECK1739, JW1730, sosD, ydjQ, b1741
Product description	endonuclease of nucleotide excision repair^[2]^[3] Endonuclease involved in excision repair, cuts 3' of lesion; requires UvrAB^[4]
EC number (for enzymes)	3.1.25.-^[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:0004518	nuclease activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000305	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004518	nuclease activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0267	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000305	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006281	DNA repair	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000305	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006281	DNA repair	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0228	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006281	DNA repair	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0234	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0227	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009432	SOS response	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0742	P	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:0006974	response to DNA damage stimulus	PMID:10760155	IEP: Inferred from Expression Pattern		P		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	groL	PMID:15690043	Experiment(s):EBI-883032
Protein	rplQ	PMID:16606699	Experiment(s):EBI-1140667
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1140667
Protein	rpsI	PMID:16606699	Experiment(s):EBI-1140667
Protein	groL	PMID:16606699	Experiment(s):EBI-1140667
Protein	uspG	PMID:16606699	Experiment(s):EBI-1140667
Protein	groL	PMID:19402753	MALDI(Z-score):17.053160
Protein	groS	PMID:19402753	MALDI(Z-score):28.255864
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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 MVRRLTSPRL EFEAAAIYEY PEHLRSFLND LPTRPGVYLF HGESDTMPLY IGKSVNIRSR VLSHLRTPDE AAMLRQSRRI SWICTAGEIG ALLLEARLIK EQQPLFNKRL RRNRQLCALQ LNEKRVDVVY AKEVDFSRAP NLFGLFANRR AALQALQTIA DEQKLCYGLL GLEPLSRGRA CFRSALKRCA GACCGKESHE EHALRLRQSL ERLRVVCWPW QGAVALKEQH PEMTQYHIIQ NWLWLGAVNS LEEATTLIRT PAGFDHDGYK ILCKPLLSGN YEITELDPAN DQRAS
Length	295
Mol. Wt	33.739 kDa
pI	9.0 (calculated)
Extinction coefficient	40,910 - 42,035 (calc based on 9 Y, 5 W, and 9 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	34..109	PF01541 GIY-YIG catalytic 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=cho 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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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:16129695	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948996	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005807	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76213	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6937	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13993	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948996	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003525	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3749	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	110	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	53	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	74	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)
cho
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Figure courtesy of RegulonDB

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Notes

LexA-regulated^[5]

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:1821519..1821559 source=MG1655 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:b1741 (EcoliWiki Page)	NCBI GEO profiles for cho
microarray	GenExpDB:b1741 (EcoliWiki Page)	Summary of data for cho 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 cho Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6937	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3749	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1741
EcoGene	EcoGene:EG13993	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003525	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005807	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	S1602	From SHIGELLACYC
E. coli O157	Z2771	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)	PF01541 GIY-YIG catalytic domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:82771
EcoCyc	EcoCyc:G6937	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13993	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003525	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3749	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005807	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 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 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.
↑ Fernández De Henestrosa, AR et al. (2000) Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol. Microbiol. 35 1560-72 PubMed

cho: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 cho Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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