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Standard Name	prmB
Gene Synonym(s)	ECK2324, b2330, JW5841, yfcB^[1], yfcB
Product Desc.	EG12449^[2]^[3] 50S subunit L3 protein glutamine methyltransferase^[4]
Product Synonyms(s)	N5-glutamine methyltransferase^[1], PrmB^[2]^[1], YfcB^[2]^[1], B2330^[2]^[1] , ECK2324, JW5841, yfcB, b2330
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yfcL^[2]
Regulation/Activity
Quick Links
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Notes

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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	prmB
Mnemonic	Protein methylation
Synonyms	ECK2324, b2330, JW5841, yfcB^[1], yfcB
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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	52.71 minutes	MG1655: 2446462..2445530 <gbrowseImage> name=NC_000913:2445530..2446462 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2391100..2392032 <gbrowseImage> name=NC_012967:2391100..2392032 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2331335..2332267 <gbrowseImage> name=NC_012759:2331335..2332267 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2453886..2452954 <gbrowseImage> name=NC_007779:2452954..2453886 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2538227..2537295 <gbrowseImage> name=NC_010473:2537295..2538227 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	Comments
ΔprmB (Keio:JW5841)	deletion	deletion	PMID:16738554	Shigen
yfcB::Tn5KAN-I-SceI (FB20768)	Insertion at nt 691 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20768	contains pKD46
yfcB::Tn5KAN-I-SceI (FB20769)	Insertion at nt 691 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20769	does not contain pKD46
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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
JW5841	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGATAAAATTTTCGTTGATGA Primer 2:CCATCTTTATAAATCGCGAAATG
12F12	Kohara Phage	Genobase	PMID:3038334
2G11	Kohara Phage	Genobase	PMID:3038334
2C9	Kohara Phage	Genobase	PMID:3038334
zfb-223::Tn10	Linked marker	CAG18484 = CGSC7406^[5]	est. P1 cotransduction: 6% ^[6] Synonyms:zej-223::Tn10
zfd-1::Tn10	Linked marker	CAG18467 = CGSC7408^[5]	est. P1 cotransduction: 13% ^[6] Synonyms:zfb-1::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:EG12449	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12449	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002301	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946805	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2343	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007695	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	PrmB
Synonyms	N5-glutamine methyltransferase^[1], PrmB^[2]^[1], YfcB^[2]^[1], B2330^[2]^[1] , ECK2324, JW5841, yfcB, b2330
Product description	EG12449^[2]^[3] 50S subunit L3 protein glutamine methyltransferase^[4]
EC number (for enzymes)	2.1.1.-^[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:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002052	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017127	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006306	DNA methylation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017127	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006479	protein amino acid methylation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004556	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008168	methyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002052	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008168	methyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR007848	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008168	methyltransferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0489	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008276	protein methyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004556	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009007	site-specific DNA-methyltransferase (adenine-specific) activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017127	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009007	site-specific DNA-methyltransferase (adenine-specific) activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.1.1.72	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0032259	methylation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002052	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	rpsJ	PMID:19402753	LCMS(ID Probability):99.6
Protein	tig	PMID:19402753	LCMS(ID Probability):99.4 MALDI(Z-score):26.555363
Protein	mcbR	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 MAGISLLLDQ AFHRHFADFF TLRSVDNRVL LNLASPRHQL AKQSLVLLAK CCFLFHLSVS ISNFPTVYPT RSAIDRFKRI FPHSPRVNAD LSSSSWQTSR RNYCDHALEE YVDKIFVDEA VNELQTIQDM LRWSVSRFSA ANIWYGHGTD NPWDEAVQLV LPSLYLPLDI PEDMRTARLT SSEKHRIVER VIRRVNERIP VAYLTNKAWF CGHEFYVDER VLVPRSPIGE LINNKFAGLI SKQPQHILDM CTGSGCIAIA CAYAFPDAEV DAVDISPDAL AVAEQNIEEH GLIHNVIPIR SDLFRDLPKV QYDLIVTNPP YVDAEDMSDL PNEYRHEPEL GLASGTDGLK LTRRILGNAA DYLADDGVLI CEVGNSMVHL MEQYPDVPFT WLEFDNGGDG VFMLTKEQLI AAREHFAIYK D
Length	421
Mol. Wt	47.762 kDa
pI	5.2 (calculated)
Extinction coefficient	53,860 - 54,860 (calc based on 14 Y, 6 W, and 8 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	124..273	PF05175 Methyltransferase small 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=prmB 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:90111419	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946805	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007695	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P39199	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12449	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12449	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946805	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002301	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2343	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 MC4100	6.13E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	1886	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	939	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	1573	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)
yfcL
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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_000913:2446442..2446482 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:b2330 (EcoliWiki Page)	NCBI GEO profiles for prmB
microarray	GenExpDB:b2330 (EcoliWiki Page)	Summary of data for prmB 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 prmB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12449	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2343	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2330
EcoGene	EcoGene:EG12449	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002301	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007695	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
Saccharomyces cerevisiae	YNL063W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC29B125c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000026087 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YFCB	From SHIGELLACYC
E. coli O157	YFCB	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF05175 Methyltransferase small domain
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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)
↑ ^2.0 ^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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 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).

prmB: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 prmB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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