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Product(s) |

Expression|

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Standard Name	ygfZ
Gene Synonym(s)	ECK2893, b2898, JW2866, up14, yzzW^[1], yzzW
Product Desc.	predicted folate-dependent regulatory protein^[2]^[3] Hda suppressor; also involved in methylthio modification at 2-methylthio-6-iodeadenosine in tRNA; mutants grow slowly, especially at low temperature; slow growth is suppressed by MnmE; binds folate^[4]
Product Synonyms(s)	predicted folate-dependent regulatory protein^[1], B2898^[2]^[1], YzzW^[2]^[1], YgfZ^[2]^[1] , ECK2893, JW2866, yzzW, b2898
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ygfZ^[2]
Regulation/Activity
Quick Links
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Notes

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A null ygfZ mutation suppresses a null hda mutation. YgfZ may be a regulatory working through modified tRNAs. YgfZ is structurally similar to an enzyme involved in the betaine catabolism pathway (DMGO) of A. globiformis. YgfZ has a yeast homolog, CAF17, that is a component of the transcriptional regulatory complex. Induced by plumbagin.^[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	ygfZ
Mnemonic	Systematic nomenclature
Synonyms	ECK2893, b2898, JW2866, up14, yzzW^[1], yzzW
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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	65.51 minutes	MG1655: 3039335..3040315 <gbrowseImage> name=NC_000913:3039335..3040315 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2927066..2928046 <gbrowseImage> name=NC_012967:2927066..2928046 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2926483..2927463 <gbrowseImage> name=NC_012759:2926483..2927463 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3039969..3040949 <gbrowseImage> name=NC_007779:3039969..3040949 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3133205..3134185 <gbrowseImage> name=NC_010473:3133205..3134185 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	3039338	Edman degradation	PMID:9298646
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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
ΔygfZ (Keio:JW2866)	deletion	deletion	PMID:16738554	Shigen CGSC10222^[5]
ΔygfZ749::kan			PMID:16738554	CGSC:104984
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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
JW2866	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTTTTACACCTTTTCCTCC Primer 2:CCtTCTTCGAGCGAATACGGCAG
22H4	Kohara Phage	Genobase	PMID:3038334
5E11	Kohara Phage	Genobase	PMID:3038334
recD1901::Tn10	Linked marker	CAG12135 = CGSC7429^[5]	est. P1 cotransduction: % ^[6]
speA210::Tn10	Linked marker	CAG12168 = CGSC7431^[5]	est. P1 cotransduction: 13% ^[6] Synonyms:zgd-210::Tn10, zgf-210::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:G7511	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12685	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004073	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947384	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2549	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009512	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	YgfZ
Synonyms	predicted folate-dependent regulatory protein^[1], B2898^[2]^[1], YzzW^[2]^[1], YgfZ^[2]^[1] , ECK2893, JW2866, yzzW, b2898
Product description	predicted folate-dependent regulatory protein^[2]^[3] Hda suppressor; also involved in methylthio modification at 2-methylthio-6-iodeadenosine in tRNA; mutants grow slowly, especially at low temperature; slow growth is suppressed by MnmE; binds folate^[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:0004047	aminomethyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006222	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005542	folic acid binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01175	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005542	folic acid binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0290	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01175	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006222	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006546	glycine catabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006222	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008033	tRNA processing	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01175	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008033	tRNA processing	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0819	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	References	Evidence
Protein	yibL	PMID:16606699	Experiment(s):EBI-1144233
Protein	yfdE	PMID:16606699	Experiment(s):EBI-1144233
Protein	rplT	PMID:16606699	Experiment(s):EBI-1144233
Protein	nadE	PMID:16606699	Experiment(s):EBI-1144233
Protein	yhhX	PMID:19402753	MALDI(Z-score):39.042988
Protein	erpA	PMID:19402753	LCMS(ID Probability):99.6
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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
Cytoplasm		PMID:9298646	EchoLocation:ygfZ
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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 MAFTPFPPRQ PTASARLPLT LMTLDDWALA TITGADSEKY MQGQVTADVS QMAEDQHLLA AHCDAKGKMW SNLRLFRDGD GFAWIERRSV REPQLTELKK YAVFSKVTIA PDDERVLLGV AGFQARAALA NLFSELPSKE KQVVKEGATT LLWFEHPAER FLIVTDEATA NMLTDKLRGE AELNNSQQWL ALNIEAGFPV IDAANSGQFI PQATNLQALG GISFKKGCYT GQEMVARAKF RGANKRALWL LAGSASRLPE AGEDLELKMG ENWRRTGTVL AAVKLEDGQV VVQVVMNNDM EPDSIFRVRD DANTLHIEPL PYSLEE
Length	326
Mol. Wt	36.094 kDa
pI	5.0 (calculated)
Extinction coefficient	44,460 - 44,710 (calc based on 4 Y, 7 W, and 2 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
Initiator Methionine	1	Removed	UniProt:P0ADE8
Domain	21..219	PF01571 Aminomethyltransferase folate-binding 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=ygfZ taxon=562,83333 </beststructure>

Models

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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:16130800	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947384	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009512	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ADE8	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7511	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12685	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947384	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004073	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2549	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	5476	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	1708	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	3323	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)
ygfZ
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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_000913:3039315..3039355 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:b2898 (EcoliWiki Page)	NCBI GEO profiles for ygfZ
microarray	GenExpDB:b2898 (EcoliWiki Page)	Summary of data for ygfZ 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 ygfZ Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7511	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2549	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2898
EcoGene	EcoGene:EG12685	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004073	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009512	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
Caenorhabditis briggsae	WBGene00035254 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00009563 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000017223 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000144305 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00016137001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000013591 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YGFZ	From SHIGELLACYC
E. coli O157	YGFZ	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)	PF01571 Aminomethyltransferase folate-binding domain
Panther (EcoliWiki Page)	PTHR22602:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:101790
Superfamily (EcoliWiki Page)	SUPERFAMILY:103025
EcoCyc	EcoCyc:G7511	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12685	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004073	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2549	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009512	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)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 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).

ygfZ: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 ygfZ Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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