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Standard Name	prmA
Gene Synonym(s)	ECK3246, b3259, JW3227, prm-1, yhdI^[1], yhdI
Product Desc.	methylase for 50S ribosomal subunit protein L11^[2]^[3] 50S subunit L11 protein lysine methyltransferase^[4]
Product Synonyms(s)	methylase for 50S ribosomal subunit protein L11^[1], B3259^[2]^[1], YhdI^[2]^[1], PrmA^[2]^[1] , ECK3246, JW3227, prm-1, yhdI, b3259
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yhdT-panF-prmA^[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	prmA
Mnemonic	Protein methylation
Synonyms	ECK3246, b3259, JW3227, prm-1, yhdI^[1], yhdI
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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	73.43 minutes	MG1655: 3407092..3407973 <gbrowseImage> name=NC_000913:3407092..3407973 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3336961..3337842 <gbrowseImage> name=NC_012967:3336961..3337842 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3294240..3295121 <gbrowseImage> name=NC_012759:3294240..3295121 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3408925..3409806 <gbrowseImage> name=NC_007779:3408925..3409806 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3504837..3505718 <gbrowseImage> name=NC_010473:3504837..3505718 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
prmA(del) (Keio:JW3227)	deletion	deletion			PMID:16738554	Shigen CGSC10441^[5]
prmAW285R		W285R		Great decrease in activity			seeded from UniProt:P0A8T1
prmA777(del)::kan					PMID:16738554	CGSC:102464
Ksg^d prmA MV9			Resistant to	Kasugamycin dependence	PMID:363701		See Figure 2 for partial to dimensional gel electropherogram of the 70S ribosomal protein.
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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
JW3227	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCCTTGGATCCAACTGAAACT Primer 2:CCATTCTTACGACCGGTAATACG
6G3	Kohara Phage	Genobase	PMID:3038334
6G9	Kohara Phage	Genobase	PMID:3038334
zhc-6::Tn10	Linked marker	CAG12153 = CGSC7442^[5]	est. P1 cotransduction: 15% ^[6] Synonyms:zha-6::Tn10
acrF3083::Tn10	Linked marker	CAG12075 = CGSC7447^[5]	est. P1 cotransduction: 77% ^[6] Synonyms:zhd-3083::Tn10, zhe-3083::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:EG11497	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11497	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001453	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947708	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1460	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010697	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	PrmA
Synonyms	methylase for 50S ribosomal subunit protein L11^[1], B3259^[2]^[1], YhdI^[2]^[1], PrmA^[2]^[1] , ECK3246, JW3227, prm-1, yhdI, b3259
Product description	methylase for 50S ribosomal subunit protein L11^[2]^[3] 50S subunit L11 protein lysine 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:0009451	RNA modification				P	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00735	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010456	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
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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	rplK	PMID:15690043	Experiment(s):EBI-881872, EBI-890083
Protein	insO2	PMID:16606699	Experiment(s):EBI-1145321
Protein	rpsG	PMID:16606699	Experiment(s):EBI-1145321
Protein	rplK	PMID:16606699	Experiment(s):EBI-1145321
Protein	bioH	PMID:16606699	Experiment(s):EBI-1145321
Protein	rpsB	PMID:16606699	Experiment(s):EBI-1145321
Protein	rpsD	PMID:16606699	Experiment(s):EBI-1145321
Protein	nadE	PMID:16606699	Experiment(s):EBI-1145321
Protein	malS	PMID:15690043	Experiment(s):EBI-890083
Protein	msbA	PMID:15690043	Experiment(s):EBI-890083
Protein	ydaY	PMID:15690043	Experiment(s):EBI-890083
Protein	mdtD	PMID:15690043	Experiment(s):EBI-890083
Protein	yejO	PMID:15690043	Experiment(s):EBI-890083
Protein	rplK	PMID:19402753	LCMS(ID Probability):99.0 MALDI(Z-score):17.053160
Protein	msbA	PMID:19402753	LCMS(ID Probability):99.0
Protein	mdtD	PMID:19402753	LCMS(ID Probability):99.0
Protein	malS	PMID:19402753	LCMS(ID Probability):99.0
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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 MPWIQLKLNT TGANAEDLSD ALMEAGAVSI TFQDTHDTPV FEPLPGETRL WGDTDVIGLF DAETDMNDVV AILENHPLLG AGFAHKIEQL EDKDWEREWM DNFHPMRFGE RLWICPSWRD VPDENAVNVM LDPGLAFGTG THPTTSLCLQ WLDSLDLTGK TVIDFGCGSG ILAIAALKLG AAKAIGIDID PQAIQASRDN AERNGVSDRL ELYLPKDQPE EMKADVVVAN ILAGPLRELA PLISVLPVSG GLLGLSGILA SQAESVCEAY ADSFALDPVV EKEEWCRITG RKN
Length	293
Mol. Wt	31.877 kDa
pI	4.2 (calculated)
Extinction coefficient	46,980 - 47,605 (calc based on 2 Y, 8 W, and 5 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	2..293	PF06325 Ribosomal protein L11 methyltransferase (PrmA)		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=prmA 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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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:16131147	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947708	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010697	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A8T1	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11497	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11497	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947708	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001453	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1460	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	E. coli K-12 MC4100	2.29E+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	Ecoli K-12	11.378+/-0.098	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.034052213	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	3883	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	384	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	1716	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)
yhdT-panF-prmA
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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_000913:3407072..3407112 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:b3259 (EcoliWiki Page)	NCBI GEO profiles for prmA
microarray	GenExpDB:b3259 (EcoliWiki Page)	Summary of data for prmA 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 prmA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11497	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1460	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3259
EcoGene	EcoGene:EG11497	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001453	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010697	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
Arabidopsis thaliana	AT5G53920 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q6L4V6 (score: 1.000; bootstrap: 100%) Q5ZBT1 (score: 0.257)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000169322 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PRMA	From SHIGELLACYC
E. coli O157	PRMA	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
Panther (EcoliWiki Page)	PTHR18895:SF3
Superfamily (EcoliWiki Page)	SUPERFAMILY:53335
Pfam (EcoliWiki Page)	PF06325 Ribosomal protein L11 methyltransferase (PrmA)
EcoCyc	EcoCyc:EG11497	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11497	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001453	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1460	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010697	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)
↑ ^2.0 ^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 ^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).

prmA: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 prmA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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