P0A873 (TRMD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
tRNA (guanine-N(1)-)-methyltransferase
EC=2.1.1.228

Alternative name(s):
M1G-methyltransferase
tRNA [GM37] methyltransferase

Gene names

Name:	trmD
Ordered Locus Names:	b2607, JW2588

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	255 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Specifically methylates guanosine-37 in various tRNAs. Ref.6
Catalytic activity	S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA. HAMAP MF_00605
Subunit structure	Homodimer. Ref.6
Subcellular location	Cytoplasm Potential HAMAP MF_00605.
Induction	Part of the rpsP-rimM-trmD-rplS operon. HAMAP MF_00605
Miscellaneous	The specific activity of this enzyme increases only slightly with increased growth rate. HAMAP MF_00605 This enzyme is present at ca. 80 molecules/genome. HAMAP MF_00605
Sequence similarities	Belongs to the RNA methyltransferase TrmD family.

Ontologies

Keywords
Biological process	tRNA processing
Cellular component	Cytoplasm
Ligand	S-adenosyl-L-methionine
Molecular function	Methyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	RNA binding Inferred from electronic annotation. Source: InterPro tRNA (guanine-N1-)-methyltransferase activity Inferred from direct assay Ref.5. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 255

255

tRNA (guanine-N(1)-)-methyltransferase HAMAP MF_00605

PRO_0000060375

Regions

Region

133 – 138

6

S-adenosyl-L-methionine binding HAMAP MF_00605

Sites

Active site

169

1

Proton acceptor Potential

Binding site

86

1

S-adenosyl-L-methionine

Binding site

113

1

S-adenosyl-L-methionine; via amide nitrogen By similarity

Experimental info

Mutagenesis

59

1

G → A: Loss of activity. Ref.6

Mutagenesis

91

1

G → A: Loss of activity; no effect on tRNA binding. Ref.6

Mutagenesis

114

1

R → A: Loss of activity. Ref.6

Mutagenesis

115

1

Y → A: Increases Km for S-adenosyl-L-methionine 24-fold. Ref.6

Mutagenesis

117

1

G → A: Loss of activity. Ref.6

Mutagenesis

119

1

D → A: Loss of activity. Ref.6

Mutagenesis

121

1

R → A: Loss of activity; no effect on tRNA binding. Ref.6

Mutagenesis

128

1

D → A: Loss of activity. Ref.6

Mutagenesis

135

1

D → A: Loss of activity; no effect on tRNA binding. Ref.6

Mutagenesis

136

1

Y → A: Increases Km for S-adenosyl-L-methionine 68-fold. Ref.6

Mutagenesis

141

1

G → A: Increases Km for S-adenosyl-L-methionine 82-fold. Ref.6

Mutagenesis

154

1

R → A: Loss of activity; no effect on tRNA binding. Ref.6

Mutagenesis

169

1

D → A: Loss of activity. Ref.6

Mutagenesis

171

1

F → A: Loss of activity. Ref.6

Mutagenesis

184

1

P → A: Loss of activity; no effect on tRNA binding. Ref.6

Mutagenesis

192

1

V → A: Loss of activity; no effect on tRNA binding. Ref.6

Mutagenesis

193

1

P → A: Loss of activity; no effect on tRNA binding. Ref.6

Mutagenesis

196

1

L → A: Loss of activity; no effect on tRNA binding. Ref.6

Mutagenesis

197

1

L → A: Loss of activity; no effect on tRNA binding. Ref.6

Mutagenesis

204

1

I → A: Loss of activity; no effect on tRNA binding. Ref.6

Mutagenesis

207

1

W → A: Loss of activity; no effect on tRNA binding. Ref.6

Mutagenesis

207

1

W → F or H: Small decrease in activity. Ref.6

Mutagenesis

208

1

R → A: Loss of activity; no effect on tRNA binding. Ref.6

Secondary structure

1

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255

Helix Strand Turn

Details...

Beta strand

2 – 6

5

Helix

10 – 13

4

Helix

14 – 17

4

Helix

20 – 27

8

Beta strand

32 – 36

5

Helix

38 – 41

4

Helix

64 – 78

15

Beta strand

83 – 87

5

Beta strand

91 – 93

3

Helix

96 – 103

8

Beta strand

106 – 111

6

Helix

120 – 126

7

Beta strand

128 – 136

9

Helix

142 – 153

12

Turn

157 – 159

3

Beta strand

185 – 187

3

Helix

194 – 197

4

Helix

201 – 219

19

Helix

221 – 225

5

Helix

231 – 245

15

Sequences

	Sequence		Length	Mass (Da)
	P0A873 [UniParc]. Last modified April 1, 1988. Version 1. Checksum: B101087229B4CDBD	FASTA	255	28,422
	10 20 30 40 50 60 MWIGIISLFP EMFRAITDYG VTGRAVKNGL LSIQSWSPRD FTHDRHRTVD DRPYGGGPGM 70 80 90 100 110 120 LMMVQPLRDA IHAAKAAAGE GAKVIYLSPQ GRKLDQAGVS ELATNQKLIL VCGRYEGIDE 130 140 150 160 170 180 RVIQTEIDEE WSIGDYVLSG GELPAMTLID SVSRFIPGVL GHEASATEDS FAEGLLDCPH 190 200 210 220 230 240 YTRPEVLEGM EVPPVLLSGN HAEIRRWRLK QSLGRTWLRR PELLENLALT EEQARLLAEF 250 KTEHAQQQHK HDGMA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of an Escherichia coli operon containing genes for the tRNA(m1G)methyltransferase, the ribosomal proteins S16 and L19 and a 21-K polypeptide." Bystroem A.S., Hjalmarsson K.J., Wikstroem P.M., Bjoerk G.R. EMBO J. 2:899-905(1983) [PubMed: 6357787] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], OPERON STRUCTURE. Strain: K12.
[2]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed: 9205837] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Purification and characterization of transfer RNA (guanine-1)methyltransferase from Escherichia coli." Hjalmarsson K.J., Bystroem A.S., Bjoerk G.R. J. Biol. Chem. 258:1343-1351(1983) [PubMed: 6337136] [Abstract] Cited for: CHARACTERIZATION, PROTEIN SEQUENCE OF 1-10.
[6]	"Insights into catalysis by a knotted TrmD tRNA methyltransferase." Elkins P.A., Watts J.M., Zalacain M., van Thiel A., Vitazka P.R., Redlak M., Andraos-Selim C., Rastinejad F., Holmes W.M. J. Mol. Biol. 333:931-949(2003) [PubMed: 14583191] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, FUNCTION, SUBUNIT, MUTAGENESIS OF GLY-59; GLY-91; ARG-114; TYR-115; GLY-117; ASP-119; ARG-121; ASP-128; ASP-135; TYR-136; GLY-141; ARG-154; ASP-169; PHE-171; PRO-184; VAL-192; PRO-193; LEU-196; LEU-197; ILE-204; TRP-207 AND ARG-208.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X01818 Genomic DNA. Translation: CAA25959.1.
U00096 Genomic DNA. Translation: AAC75656.1.
AP009048 Genomic DNA. Translation: BAA16492.1.

PIR

XYECG1. A30380.

RefSeq

NP_417098.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1P9P	X-ray	2.50	A	1-255	[»]

ProteinModelPortal

P0A873.

SMR

P0A873. Positions 1-246.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48264N.

IntAct

P0A873. 1 interaction.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000001239; EBESCP00000001239; EBESCG00000001025.
EBESCT00000014588; EBESCP00000013879; EBESCG00000013649.

GeneID

947099.

GenomeReviews

Gene locus JW2588 in contig AP009048_GR.
Gene locus b2607 in contig U00096_GR.

KEGG

ecj:JW2588.
eco:b2607.

PATRIC

32120613. VBIEscCol129921_2705.

Organism-specific databases

EchoBASE

EB1016.

EcoGene

EG11023. trmD.

Phylogenomic databases

eggNOG

COG0336.

GeneTree

EBGT00050000009415.

HOGENOM

HBG285805.

OMA

VCGRFEG.

PhylomeDB

P0A873.

ProtClustDB

PRK00026.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11023-MONOMER.
MetaCyc:EG11023-MONOMER.

Gene expression databases

Genevestigator

P0A873.

Family and domain databases

HAMAP

MF_00605. TrmD.
[Tree]

InterPro

IPR016009. tRNA_m1G_MeTrfase.
IPR002649. tRNA_m1G_MeTrfase_bac.
IPR023148. tRNA_m1G_MeTrfase_C.
[Graphical view]

Gene3D

G3DSA:1.10.1270.20. tRNA_m1G_MeTrfase_C. 1 hit.

KO

K00554.

PANTHER

PTHR10056. PTHR10056. 1 hit.

Pfam

PF01746. tRNA_m1G_MT. 1 hit.
[Graphical view]

PIRSF

PIRSF000386. tRNA_mtase. 1 hit.

TIGRFAMs

TIGR00088. TrmD. 1 hit.

ProtoNet

Search...

Entry information

Entry name

TRMD_ECOLI

Accession

Primary (citable) accession number: P0A873
Secondary accession number(s): P07020

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	April 1, 1988
Last modified:	January 25, 2012
This is version 59 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program