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Expression|

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Standard Name	trmD
Gene Synonym(s)	ECK2604, b2607, JW2588^[1], JW2588
Product Desc.	TrmD^[2]^[3]; Component of tRNA (guanine-1-)-methyltransferase^[3] tRNA m(1)G37 methyltransferase^[4]
Product Synonyms(s)	tRNA (guanine-1-)-methyltransferase^[1], B2607^[2]^[1], TrmD^[2]^[1] , ECK2604, JW2588, b2607
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rpsP-rimM-trmD-rplS^[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	trmD
Mnemonic	tRNA methyltransferase
Synonyms	ECK2604, b2607, JW2588^[1], JW2588
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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	59.11 minutes, 59.11 minutes	MG1655: 2743361..2742594 <gbrowseImage> name=NC_000913:2742594..2743361 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2666746..2665979 <gbrowseImage> name=NC_012967:2665979..2666746 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2628406..2629173 <gbrowseImage> name=NC_012759:2628406..2629173 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2743995..2743228 <gbrowseImage> name=NC_007779:2743228..2743995 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2835126..2834359 <gbrowseImage> name=NC_010473:2834359..2835126 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	2742594	Edman degradation	PMID:6337136
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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	AA change(s)	Phenotype: Description	Comments
trmDD169A	D169A	Loss of activity	seeded from UniProt:P0A873
trmDL197A	L197A	Loss of activity; no effect on tRNA binding	seeded from UniProt:P0A873
trmDF171A	F171A	Loss of activity	seeded from UniProt:P0A873
trmDP184A	P184A	Loss of activity; no effect on tRNA binding	seeded from UniProt:P0A873
trmDG59A	G59A	Loss of activity	seeded from UniProt:P0A873
trmDG91A	G91A	Loss of activity; no effect on tRNA binding	seeded from UniProt:P0A873
trmDR114A	R114A	Loss of activity	seeded from UniProt:P0A873
trmDY115A	Y115A	Increases Km for S-adenosyl-L- methionine 24-fold	seeded from UniProt:P0A873
trmDG117A	G117A	Loss of activity	seeded from UniProt:P0A873
trmDD119A	D119A	Loss of activity	seeded from UniProt:P0A873
trmDR121A	R121A	Loss of activity; no effect on tRNA binding	seeded from UniProt:P0A873
trmDL196A	L196A	Loss of activity; no effect on tRNA binding	seeded from UniProt:P0A873
trmDV192A	V192A	Loss of activity; no effect on tRNA binding	seeded from UniProt:P0A873
trmDG141A	G141A	Increases Km for S-adenosyl-L- methionine 82-fold	seeded from UniProt:P0A873
trmDR154A	R154A	Loss of activity; no effect on tRNA binding	seeded from UniProt:P0A873
trmDD135A	D135A	Loss of activity; no effect on tRNA binding	seeded from UniProt:P0A873
trmDY136A	Y136A	Increases Km for S-adenosyl-L- methionine 68-fold	seeded from UniProt:P0A873
trmDP193A	P193A	Loss of activity; no effect on tRNA binding	seeded from UniProt:P0A873
trmDD128A	D128A	Loss of activity	seeded from UniProt:P0A873
trmDW207A	W207A	Loss of activity; no effect on tRNA binding	seeded from UniProt:P0A873
trmDW207F,H	W207F,H	Small decrease in activity	seeded from UniProt:P0A873
trmDR208A	R208A	Loss of activity; no effect on tRNA binding	seeded from UniProt:P0A873
trmDI204A	I204A	Loss of activity; no effect on tRNA binding	seeded from UniProt:P0A873
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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
JW2588	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTGGATTGGCATAATTAGCCT Primer 2:CCgGCCATCCCATCATGTTTATG
E8F2	Kohara Phage	Genobase	PMID:3038334
22D7	Kohara Phage	Genobase	PMID:3038334
pheA18::Tn10	Linked marker	CAG12158 = CGSC7421^[5]	est. P1 cotransduction: 84% ^[6]
srlD3131::Tn10	Linked marker	CAG18642 = CGSC7423^[5]	est. P1 cotransduction: % ^[6] Synonyms:zfh-3131::Tn10, zfi-3131::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:EG11023	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11023	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001012	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947099	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1016	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008576	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	TrmD
Synonyms	tRNA (guanine-1-)-methyltransferase^[1], B2607^[2]^[1], TrmD^[2]^[1] , ECK2604, JW2588, b2607
Product description	TrmD^[2]^[3]; Component of tRNA (guanine-1-)-methyltransferase^[3] tRNA m(1)G37 methyltransferase^[4]
EC number (for enzymes)	2.1.1.31^[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:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002649	F	Seeded from EcoCyc (v14.0)	complete
	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_00605	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:0009019	tRNA (guanine-N1-)-methyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00605	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009019	tRNA (guanine-N1-)-methyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002649	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009019	tRNA (guanine-N1-)-methyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.1.1.31	F	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 tRNA (guanine-1-)-methyltransferase	could be indirect
Protein	dnaX		PMID:19402753	MALDI(Z-score):28.759733
Protein	holA		PMID:19402753	MALDI(Z-score):32.609818
Protein	dnaE		PMID:19402753	MALDI(Z-score):18.854791
Protein	holD		PMID:19402753	MALDI(Z-score):21.182048
Protein	holC		PMID:19402753	MALDI(Z-score):27.442857
Protein	dnaQ		PMID:19402753	MALDI(Z-score):29.343986
Protein	holB		PMID:19402753	MALDI(Z-score):38.943183
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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 MWIGIISLFP EMFRAITDYG VTGRAVKNGL LSIQSWSPRD FTHDRHRTVD DRPYGGGPGM LMMVQPLRDA IHAAKAAAGE GAKVIYLSPQ GRKLDQAGVS ELATNQKLIL VCGRYEGIDE RVIQTEIDEE WSIGDYVLSG GELPAMTLID SVSRFIPGVL GHEASATEDS FAEGLLDCPH YTRPEVLEGM EVPPVLLSGN HAEIRRWRLK QSLGRTWLRR PELLENLALT EEQARLLAEF KTEHAQQQHK HDGMA
Length	255
Mol. Wt	28.422 kDa
pI	5.7 (calculated)
Extinction coefficient	36,440 - 36,690 (calc based on 6 Y, 5 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
Domain	22..221	PF01746 tRNA (Guanine-1)-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=trmD 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:16130528	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947099	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008576	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A873	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11023	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11023	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947099	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001012	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1016	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	3.15E+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	1778	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	318	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	683	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)
rpsP-rimM-trmD-rplS
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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_000913:2743341..2743381 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:b2607 (EcoliWiki Page)	NCBI GEO profiles for trmD
microarray	GenExpDB:b2607 (EcoliWiki Page)	Summary of data for trmD 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 trmD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11023	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1016	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2607
EcoGene	EcoGene:EG11023	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001012	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008576	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
Xenopus tropicalis	ENSXETP00000004503 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	TRMD	From SHIGELLACYC
E. coli O157	TRMD	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)	PTHR10056:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:75217
Pfam (EcoliWiki Page)	PF01746 tRNA (Guanine-1)-methyltransferase
EcoCyc	EcoCyc:EG11023	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11023	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001012	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1016	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008576	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 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 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).

trmD: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 trmD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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