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Expression|

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Standard Name	rlmH
Gene Synonym(s)	ECK0629, b0636, JW0631, ybeA^[1], JW0631, ybeA
Product Desc.	conserved protein^[2]^[3]; Component of conserved protein^[3]. Sequence similarity indicates rlmH is an S-adenosylmethionine-dependent (SPOUT) methyltransferase ^[4]. Inactivation of the rlmH gene (Keio collection knockout ^[5]) leads to loss of methylation at nucleotide Psi1915 in 23S rRNA ^[4]. Computational docking suggests that a YbeA methyltransferase homodimer fits comfortably into the ribosomal A site without encroaching into the P site ^[4]. Purta et al. suggest that a more suitable designation for the SPOUT-superfamily member YbeA would be the rRNA large subunit methyltransferase RlmH, consistent with the terminology used for the other rRNA methyltransferase characterized in E. coli (see also Ofengand and Del Campo, 2004 ^[6]^[7], and Andersen and Douthwaite, 2006 ^[8]. Putative methyltransferase, function unknown^[9]
Product Synonyms(s)	conserved protein^[1], B0636^[2]^[1], YbeA^[2]^[1] , ECK0629, JW0631, ybeA, b0636
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rlpA^[2]
Regulation/Activity
Quick Links
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Notes

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AFMB Structural Genomics target No. 125 (http://afmb.cnrs-mrs.fr/article171.html). Structural similarity to known SAM-dependent SPOUT family methyltransferases.^[9]

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	rlmH
Mnemonic	rRNA large-subunit methylation
Synonyms	ECK0629, b0636, JW0631, ybeA^[1], JW0631, ybeA
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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	14.39 minutes	MG1655: 667938..667471 <gbrowseImage> name=NC_000913:667471..667938 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 570231..570698 <gbrowseImage> name=NC_012759:570231..570698 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 669137..668670 <gbrowseImage> name=NC_007779:668670..669137 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 607270..606803 <gbrowseImage> name=NC_010473:606803..607270 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
DH10B		DH10B: 720530..720063 <gbrowseImage> name=NC_010473:720063..720530 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
ΔybeA (Keio:JW0631)	deletion	deletion	PMID:16738554	Shigen CGSC8735^[10]
ΔybeA773::kan			PMID:16738554	CGSC:103730
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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
JW0631	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGCTGCAACTTGTCGCCGT Primer 2:CCCTCACGGTGATAAGGATGGTT
15D7	Kohara Phage	Genobase	PMID:3038334
crcA280::Tn10	Linked marker	CAG12077 = CGSC7347^[10]	est. P1 cotransduction: 63% ^[11] Synonyms:zbe-280::Tn10
asnB3057::Tn10	Linked marker	CAG18433 = CGSC7349^[10]	est. P1 cotransduction: 27% ^[11] Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.
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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
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0636
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C0727
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:YBEA
EcoCyc (EcoliWiki Page)	ECOCYC:EG11254	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945239	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	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	rlmH, rRNA large subunit methyltransferase
Synonyms	conserved protein^[1], B0636^[2]^[1], YbeA^[2]^[1] , ECK0629, JW0631, ybeA, b0636
Product description	conserved protein^[2]^[3]; Component of conserved protein^[3]. Sequence similarity indicates rlmH is an S-adenosylmethionine-dependent (SPOUT) methyltransferase ^[4]. Inactivation of the rlmH gene (Keio collection knockout ^[5]) leads to loss of methylation at nucleotide Psi1915 in 23S rRNA ^[4]. Computational docking suggests that a YbeA methyltransferase homodimer fits comfortably into the ribosomal A site without encroaching into the P site ^[4]. Purta et al. suggest that a more suitable designation for the SPOUT-superfamily member YbeA would be the rRNA large subunit methyltransferase RlmH, consistent with the terminology used for the other rRNA methyltransferase characterized in E. coli (see also Ofengand and Del Campo, 2004 ^[6]^[7], and Andersen and Douthwaite, 2006 ^[8]. Putative methyltransferase, function unknown^[9]
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:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00658	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003742	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:0005737	cytoplasm	PMID:18755835	IC: Inferred by Curator	GO:0070038	C	Seeded from EcoCyc (v14.0)	complete
	GO:0031167	rRNA methylation	PMID:18755836	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0042803	protein homodimerization activity	PMID:18755835	NAS: Non-traceable Author Statement		F	Seeded from EcoCyc (v14.0)	complete
	GO:0043022	ribosome binding	PMID:18755835	NAS: Non-traceable Author Statement		F	Seeded from EcoCyc (v14.0)	complete
	GO:0070038	rRNA (pseudouridine-N3-)-methyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00658	F	Seeded from EcoCyc (v14.0)	complete
	GO:0070475	rRNA base methylation	PMID:18755835	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0070475	rRNA base methylation	PMID:18755836	IMP: Inferred from Mutant Phenotype		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	Notes	References	Evidence
Protein	Subunits of conserved protein	could be indirect
Protein	rpsB		PMID:15690043	Experiment(s):EBI-887739
Protein	groL		PMID:16606699	Experiment(s):EBI-1137503
Protein	gfcD		PMID:16606699	Experiment(s):EBI-1137503
Protein	Homodimer	Docking simulation and sequence similarity ^[4]
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Notes

Localization

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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 MKLQLVAVGT KMPDWVQTGF TEYLRRFPKD MPFELIEIPA GKRGKNADIK RILDKEGEQM LAAAGKNRIV TLDIPGKPWD TPQLAAELER WKLDGRDVSL LIGGPEGLSP ACKAAAEQSW SLSALTLPHP LVRVLVAESL YRAWSITTNH PYHRE
Length	155
Mol. Wt	17.341 kDa
pI	8.9 (calculated)
Extinction coefficient	31,970 - 32,095 (calc based on 3 Y, 5 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	1..153	PF02590 Predicted SPOUT methyltransferase		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=ybeA 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:16128619	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945239	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A8I8	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945239	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	14.628+/-0.128	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.065310493	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	1099	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	177	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	420	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)
rlpA
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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_000913:667918..667958 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:b0636 (EcoliWiki Page)	NCBI GEO profiles for ybeA
microarray	GenExpDB:b0636 (EcoliWiki Page)	Summary of data for ybeA 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 rlmH 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:b0636
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
Arabidopsis thaliana	AT5G10620 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000051823 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YBEA	From SHIGELLACYC
E. coli O157	YBEA	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)	PF02590 Predicted SPOUT methyltransferase
Superfamily (EcoliWiki Page)	SUPERFAMILY:75217
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 ^3.2 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 ^4.3 ^4.4 ^4.5 ^4.6 Purta, E et al. (2008) YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. RNA 14 2234-44 PubMed
↑ ^5.0 ^5.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
↑ ^6.0 ^6.1
↑ ^7.0 ^7.1
↑ ^8.0 ^8.1 Andersen, NM & Douthwaite, S (2006) YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407. J. Mol. Biol. 359 777-86 PubMed
↑ ^9.0 ^9.1 ^9.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^10.0 ^10.1 ^10.2 CGSC: The Coli Genetics Stock Center
↑ ^11.0 ^11.1 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).

rlmH: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 rlmH Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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