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On One Page

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Gene |

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Expression|

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Standard Name	ybaZ
Gene Synonym(s)	ECK0448, b0454, JW0444^[1], JW0444
Product Desc.	putative methyltransferase^[2]; predicted methyltransferase^[3] Binds DNA with O(6)-meG or an abasic site; physiological role unknown^[4]
Product Synonyms(s)	predicted methyltransferase^[1], YbaZ^[2]^[1], B0454^[2]^[1] , ECK0448, JW0444, b0454
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ybaZ^[2]
Regulation/Activity
Quick Links
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Notes

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YbaZ is homologous to methylated-DNA--protein-cysteine methyltransferases Ada and Ogt, but lacks the active site cysteine. YbaZ binds O(6)-alkylguanine residues in DNA and blocks alkyltransferase action; YbaZ does not remove methyl groups from O(6)-methylguanine-containing DNA nor does it have glycosylase or endonuclease activity (Margison, 2007). YbaZ preferentially binds DNA with an abasic site, has base-flipping activity, and binds HelD (Chen, 2008).^[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	ybaZ
Mnemonic	Systematic nomenclature
Synonyms	ECK0448, b0454, JW0444^[1], JW0444
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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	10.24 minutes	MG1655: 475595..475206 <gbrowseImage> name=NC_000913:475206..475595 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 448438..448049 <gbrowseImage> name=NC_012967:448049..448438 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 377965..378354 <gbrowseImage> name=NC_012759:377965..378354 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 475595..475206 <gbrowseImage> name=NC_007779:475206..475595 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 414926..414537 <gbrowseImage> name=NC_010473:414537..414926 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
ΔybaZ (Keio:JW0444)	deletion	deletion			PMID:16738554	Shigen CGSC8605^[5]
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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
JW0444	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCTGGTTTCTTGCGCAATGCG Primer 2:CCGTAGTTCCAGCGATAACGCTG
7E2	Kohara Phage	Genobase	PMID:3038334
19B7	Kohara Phage	Genobase	PMID:3038334
zaj-3054::Tn10	Linked marker	CAG12017 = CGSC7339^[5]	est. P1 cotransduction: 57% ^[6] Synonyms:zba-3054::Tn10
gsk-3055::Tn10	Linked marker	CAG12154 = CGSC7341^[5]	est. P1 cotransduction: 37% ^[6] Synonyms:zbb-30-55::TnlO, zba-3055::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
NCBI (EcoliWiki Page)	GeneID:945094	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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	YbaZ
Synonyms	predicted methyltransferase^[1], YbaZ^[2]^[1], B0454^[2]^[1] , ECK0448, JW0444, b0454
Product description	putative methyltransferase^[2]; predicted methyltransferase^[3] Binds DNA with O(6)-meG or an abasic site; physiological role 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
		<input name="field[2]" type="hidden" value="" />	PMID:18084297			<input name="field[6]" type="hidden" value="" />		Missing: GO ID, evidence
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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	ygcA	PMID:15690043	Experiment(s):EBI-892264
Protein	ydgJ	PMID:15690043	Experiment(s):EBI-892264
Protein	hupA	PMID:15690043	Experiment(s):EBI-892264
Protein	lysS	PMID:15690043	Experiment(s):EBI-892264
Protein	marA	PMID:15690043	Experiment(s):EBI-892264
Protein	rplA	PMID:15690043	Experiment(s):EBI-892264
Protein	rplJ	PMID:15690043	Experiment(s):EBI-892264
Protein	rplL	PMID:15690043	Experiment(s):EBI-892264
Protein	rpsB	PMID:15690043	Experiment(s):EBI-892264
Protein	rpsJ	PMID:15690043	Experiment(s):EBI-892264
Protein	ydgA	PMID:15690043	Experiment(s):EBI-892264
Protein	rplD	PMID:16606699	Experiment(s):EBI-1136740
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1136740
Protein	rplA	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplJ	PMID:19402753	LCMS(ID Probability):99.6
Protein	lysS	PMID:19402753	LCMS(ID Probability):99.6
Protein	ydgJ	PMID:19402753	LCMS(ID Probability):99.6
Protein	ydgA	PMID:19402753	LCMS(ID Probability):99.6
Protein	rumA	PMID:19402753	LCMS(ID Probability):99.6
Protein	marA	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplL	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
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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 MLVSCAMRLH SGVFPDYAEK LPQEEKMEKE DSFPQRVWQI VAAIPEGYVT TYGDVAKLAG SPRAARQVGG VLKRLPEGST LPWHRVVNRH GTISLTGPDL QRQRQALLAE GVMVSGSGQI DLQRYRWNY
Length	129
Mol. Wt	14.448 kDa
pI	9.5 (calculated)
Extinction coefficient	23,950 - 24,075 (calc based on 5 Y, 3 W, and 1 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	31..115	PF01035 6-O-methylguanine DNA methyltransferase, DNA 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=ybaZ 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:16128439	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945094	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AFP2	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945094	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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	4.021+/-0.047	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.007712082	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	116	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	66	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	78^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
ybaZ
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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_000913:475575..475615 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:b0454 (EcoliWiki Page)	NCBI GEO profiles for ybaZ
microarray	GenExpDB:b0454 (EcoliWiki Page)	Summary of data for ybaZ 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 ybaZ Expression

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0454
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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
Schizosaccharomyces pombe	SPAC12504c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YBAZ	From SHIGELLACYC
E. coli O157	YBAZ	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)	PF01035 6-O-methylguanine DNA methyltransferase, DNA binding domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:46767
PFAM (EcoliWiki Page)	PFAM:PF01035
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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).

ybaZ: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 ybaZ Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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