P25745 (MNMA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
tRNA-specific 2-thiouridylase MnmA
EC=2.8.1.-

Gene names

Name:	mnmA
Synonyms:	asuE, trmU, ycfB
Ordered Locus Names:	b1133, JW1119

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	368 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA(Lys), tRNA(Glu) and tRNA(Gln), leading to the formation of s2U34, the first step of tRNA-mnm5s2U34 synthesis. Sulfur is provided by IscS, via a sulfur-relay system. Binds ATP and its substrate tRNAs. Ref.7
Subunit structure	Interacts with TusE. Ref.8
Subcellular location	Cytoplasm HAMAP-Rule MF_00144.
Miscellaneous	During the reaction, ATP is used to activate the C2 atom of U34 by adenylation. After this, the persulfide sulfur on the catalytic cysteine is transferred to the C2 atom of U34. The reaction probably involves hydrogen sulfide that is generated from the persulfide intermediate and that acts as nucleophile towards the activated C2 atom on U34. Subsequently, Cys-102 acts as nucleophile towards Cys-199, and a transient disulfide bond is formed. HAMAP-Rule MF_00144
Sequence similarities	Belongs to the MnmA/TRMU family.
Caution	Was originally thought to be a 5-methylaminomethyl-2-methyltransferase involved in tRNA modification.
Sequence caution	The sequence CAA41994.1 differs from that shown. Reason: Frameshift at positions 175 and 215.

Ontologies

Keywords
Biological process	tRNA processing
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding RNA-binding tRNA-binding
Molecular function	Transferase
PTM	Disulfide bond
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	tRNA wobble position uridine thiolation Inferred from direct assay Ref.7. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW sulfurtransferase activity Inferred from direct assay Ref.7. Source: EcoCyc tRNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 368

368

tRNA-specific 2-thiouridylase MnmA HAMAP-Rule MF_00144

PRO_0000121588

Regions

Nucleotide binding

11 – 18

8

ATP HAMAP-Rule MF_00144

Region

97 – 99

3

Interaction with target base in tRNA HAMAP-Rule MF_00144

Region

149 – 151

3

Interaction with tRNA HAMAP-Rule MF_00144

Region

243 – 252

10

Interaction with tRNA HAMAP-Rule MF_00144

Region

311 – 312

2

Interaction with tRNA HAMAP-Rule MF_00144

Sites

Active site

102

1

Nucleophile

Active site

199

1

Cysteine persulfide intermediate

Binding site

37

1

ATP; via amide nitrogen and carbonyl oxygen

Binding site

127

1

ATP; via amide nitrogen

Site

128

1

Interaction with tRNA

Site

344

1

Interaction with tRNA

Amino acid modifications

Disulfide bond

102 ↔ 199

Alternate HAMAP-Rule MF_00144

Experimental info

Mutagenesis

17

1

D → A: Loss of activity. Ref.10

Mutagenesis

37

1

M → A: Reduces activity by 60%. Ref.10

Mutagenesis

97

1

N → A: Loss of activity. Ref.10

Mutagenesis

99

1

D → A: Loss of activity. Ref.10

Mutagenesis

102

1

C → A: Loss of activity. Ref.10

Mutagenesis

107

1

K → M: Reduces activity by 75%. Ref.10

Mutagenesis

128

1

H → A: Reduces activity by 90%. Ref.10

Mutagenesis

149

1

K → A: Loss of activity. Ref.10

Mutagenesis

151

1

Q → E: Loss of activity. Ref.10

Mutagenesis

199

1

C → A: Abolishes the incorporation of sulfur from the sulfur-relay system; loss of activity. Ref.10

Mutagenesis

200

1

F → A: Reduces activity by 60%. Ref.10

Mutagenesis

239

1

T → A: Reduces activity by 50%. Ref.10

Mutagenesis

311

1

R → A: Reduces activity by 75%. Ref.10

Mutagenesis

344

1

Q → A: Loss of activity. Ref.10

Secondary structure

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368

Helix Strand Turn

Details...

Beta strand

7 – 11

5

Helix

19 – 26

8

Beta strand

31 – 38

8

Helix

45 – 65

21

Beta strand

69 – 73

5

Helix

75 – 81

7

Helix

83 – 91

9

Helix

98 – 105

8

Turn

106 – 109

4

Helix

110 – 117

8

Beta strand

122 – 125

4

Beta strand

131 – 135

5

Beta strand

138 – 142

5

Turn

147 – 149

3

Helix

152 – 155

4

Helix

160 – 165

6

Helix

170 – 172

3

Helix

175 – 184

10

Beta strand

197 – 201

5

Helix

206 – 211

6

Beta strand

220 – 223

4

Beta strand

224 – 226

3

Beta strand

228 – 231

4

Beta strand

252 – 254

3

Beta strand

259 – 265

7

Turn

266 – 269

4

Beta strand

270 – 276

7

Turn

280 – 282

3

Beta strand

284 – 294

11

Beta strand

302 – 311

10

Beta strand

317 – 322

6

Beta strand

325 – 327

3

Beta strand

329 – 338

10

Beta strand

344 – 350

7

Beta strand

353 – 365

13

Sequences

	Sequence		Length	Mass (Da)
	P25745 [UniParc]. Last modified May 30, 2000. Version 4. Checksum: 22CA92676D0805CC	FASTA	368	40,959
	10 20 30 40 50 60 MSETAKKVIV GMSGGVDSSV SAWLLQQQGY QVEGLFMKNW EEDDGEEYCT AAADLADAQA 70 80 90 100 110 120 VCDKLGIELH TVNFAAEYWD NVFELFLAEY KAGRTPNPDI LCNKEIKFKA FLEFAAEDLG 130 140 150 160 170 180 ADYIATGHYV RRADVDGKSR LLRGLDSNKD QSYFLYTLSH EQIAQSLFPV GELEKPQVRK 190 200 210 220 230 240 IAEDLGLVTA KKKDSTGICF IGERKFREFL GRYLPAQPGK IITVDGDEIG EHQGLMYHTL 250 260 270 280 290 300 GQRKGLGIGG TKEGTEEPWY VVDKDVENNI LVVAQGHEHP RLMSVGLIAQ QLHWVDREPF 310 320 330 340 350 360 TGTMRCTVKT RYRQTDIPCT VKALDDDRIE VIFDEPVAAV TPGQSAVFYN GEVCLGGGII EQRLPLPV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"The purB gene of Escherichia coli K-12 is located in an operon." Green S.M., Malik T., Giles I.G., Drabble W.T. Microbiology 142:3219-3230(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 138-368. Strain: K12.
[5]	"Escherichia coli purB gene: cloning, nucleotide sequence, and regulation by purR." He B., Smith J.M., Zalkin H. J. Bacteriol. 174:130-136(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 254-368. Strain: K12.
[6]	"Antisuppressor mutation in Escherichia coli defective in biosynthesis of 5-methylaminomethyl-2-thiouridine." Sullivan M.A., Cannon J.F., Webb F.H., Bock R.M. J. Bacteriol. 161:368-376(1985) [PubMed] [Europe PMC] [Abstract] Cited for: MUTANT STUDIES. Strain: K12.
[7]	"MnmA and IscS are required for in vitro 2-thiouridine biosynthesis in Escherichia coli." Kambampati R., Lauhon C.T. Biochemistry 42:1109-1117(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, ATP-BINDING, TRNA-BINDING. Strain: K12 / MC1061 / ATCC 53338 / DSM 7140.
[8]	"Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions." Ikeuchi Y., Shigi N., Kato J., Nishimura A., Suzuki T. Mol. Cell 21:97-108(2006) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH TUSE.
[9]	"Crystallization and preliminary X-ray analysis of the tRNA thiolation enzyme MnmA from Escherichia coli complexed with tRNA(Glu)." Numata T., Ikeuchi Y., Fukai S., Adachi H., Matsumura H., Takano K., Murakami S., Inoue T., Mori Y., Sasaki T., Suzuki T., Nureki O. Acta Crystallogr. F 62:368-371(2006) [PubMed] [Europe PMC] [Abstract] Cited for: CRYSTALLIZATION.
[10]	"Snapshots of tRNA sulphuration via an adenylated intermediate." Numata T., Ikeuchi Y., Fukai S., Suzuki T., Nureki O. Nature 442:419-424(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) IN COMPLEXES WITH AMP AND TRNA, MUTAGENESIS OF ASP-17; MET-37; ASN-97; ASP-99; CYS-102; LYS-107; HIS-128; LYS-149; GLN-151; CYS-199; PHE-200; THR-239; ARG-311 AND GLN-344.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U00096 Genomic DNA. Translation: AAC74217.2.
AP009048 Genomic DNA. Translation: BAA35955.1.
X59307 Genomic DNA. Translation: CAA41994.1. Frameshift.
M74924 Genomic DNA. No translation available.

PIR

B64858.

RefSeq

NP_415651.4. NC_000913.2.
YP_489401.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2DER	X-ray	3.10	A/B	1-368	[»]
2DET	X-ray	3.40	A	1-368	[»]
2DEU	X-ray	3.40	A/B	1-368	[»]

ProteinModelPortal

P25745.

SMR

P25745. Positions 4-368.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-11035N.

IntAct

P25745. 2 interactions.

STRING

511145.b1133.

Proteomic databases

PaxDb

P25745.

PRIDE

P25745.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74217; AAC74217; b1133.
BAA35955; BAA35955; BAA35955.

GeneID

12934135.
945690.

KEGG

ecj:Y75_p1103.
eco:b1133.

PATRIC

32117515. VBIEscCol129921_1180.

Organism-specific databases

EchoBASE

EB1320.

EcoGene

EG11344. mnmA.

Phylogenomic databases

eggNOG

COG0482.

HOGENOM

HOG000218046.

KO

K00566.

OMA

QPGNIET.

ProtClustDB

PRK00143.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11344-MONOMER.
ECOL316407:JW1119-MONOMER.
MetaCyc:EG11344-MONOMER.

Gene expression databases

Genevestigator

P25745.

Family and domain databases

Gene3D

2.30.30.280. 1 hit.
3.40.50.620. 1 hit.

HAMAP

MF_00144. tRNA_thiouridyl_MnmA.

InterPro

IPR023382. Adenine_a_hdrlase_dom.
IPR014729. Rossmann-like_a/b/a_fold.
IPR004506. tRNA-specific_2-thiouridylase.
[Graphical view]

PANTHER

PTHR11933. PTHR11933. 1 hit.

Pfam

PF03054. tRNA_Me_trans. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00420. trmU. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P25745.

Entry information

Entry name

MNMA_ECOLI

Accession

Primary (citable) accession number: P25745
Secondary accession number(s): P75964

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	May 30, 2000
Last modified:	May 1, 2013
This is version 114 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program