tRNA modification GTPase mnmE - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P25522 (MNME_ECOLI)

Last modified November 3, 2009. Version 101. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
tRNA modification GTPase mnmE
EC=3.6.-.-

Gene names

Name:	mnmE
Synonyms:	thdF, trmE
Ordered Locus Names:	b3706, JW3684

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	454 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm₅s₂U34. HAMAP MF_00379
Cofactor	Binds 1 potassium ion per subunit. HAMAP MF_00379
Enzyme regulation	GTPase activity is strongly activated by potassium ions. HAMAP MF_00379
Subunit structure	Homodimer. Heterotetramer of two mnmE and two mnmG subunits. Ref.9
Subcellular location	Cytoplasm. Note: Partially associated with the inner membrane. Ref.5
Sequence similarities	Belongs to the era/mnmE GTP-binding protein family. MnmE subfamily.
Biophysicochemical properties	Kinetic parameters: K_M=511 µM for GTP HAMAP MF_00379 K_M=346 µM for XTP V_max=193 nmol/min/mg enzyme with GTP as substrate V_max=100 nmol/min/mg enzyme with XTP as substrate pH dependence: Optimum pH is 7.5-9.5.
Sequence caution	The sequence AAB19981.1 differs from that shown. Reason: Miscellaneous discrepancy.

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Ontologies

Keywords
Biological process	tRNA processing
Cellular component	Cytoplasm
Ligand	GTP-binding Magnesium Metal-binding Nucleotide-binding Potassium
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	tRNA modification Inferred from electronic annotation. Source: HAMAP
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	GTP binding Inferred from electronic annotation. Source: HAMAP GTPase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW potassium ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
mnmG	P0A6U3	1	EBI-550986,EBI-550977

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 454

454

tRNA modification GTPase mnmE HAMAP MF_00379

PRO_0000188874

Regions

Nucleotide binding

226 – 231

GTP HAMAP MF_00379

Nucleotide binding

245 – 251

GTP HAMAP MF_00379

Nucleotide binding

270 – 273

GTP HAMAP MF_00379

Nucleotide binding

335 – 338

GTP HAMAP MF_00379

Nucleotide binding

358 – 360

GTP HAMAP MF_00379

Sites

Metal binding

226

Potassium HAMAP MF_00379

Metal binding

230

Magnesium HAMAP MF_00379

Metal binding

245

Potassium; via carbonyl oxygen HAMAP MF_00379

Metal binding

247

Potassium; via carbonyl oxygen HAMAP MF_00379

Metal binding

250

Potassium HAMAP MF_00379

Metal binding

251

Magnesium HAMAP MF_00379

Binding site

Formyltetrahydrofolate By similarity

Binding site

Formyltetrahydrofolate By similarity

Binding site

120

Formyltetrahydrofolate By similarity

Binding site

454

Formyltetrahydrofolate By similarity

Experimental info

Mutagenesis

224

R → A: 1.5-fold decrease in GTPase activity and almost no change in affinity. Ref.7

Mutagenesis

226

N → A: 100-fold decrease in GTPase activity. 5-fold decrease of affinity for GTP. Ref.9

Mutagenesis

226

N → K: 70-fold decrease in GTPase activity. 2-fold decrease of affinity for GTP. Ref.9

Mutagenesis

228

G → A: Loss of GTP binding and hydrolase activity. Completely impairs tRNA modifying function. Ref.6

Mutagenesis

249

G → A: 22-fold decrease in GTPase activity and 7-fold increase of affinity. Ref.7

Mutagenesis

250

T → A: 4-fold decrease in GTPase activity and 1.5-fold increase of affinity. Ref.7

Mutagenesis

250

T → S: 1.8-fold decrease in GTPase activity and 1.5-fold increase of affinity. Ref.7

Mutagenesis

251

T → A: 92-fold decrease in GTPase activity and 59-fold increase of affinity. Ref.7

Mutagenesis

251

T → S: 4-fold decrease in GTPase activity and 1.2-fold decrease of affinity. Ref.7

Mutagenesis

252

R → A: 7-fold decrease in GTPase activity and 6-fold increase of affinity. Ref.7

Mutagenesis

252

R → K: 2-fold decrease in GTPase activity and no change in affinity. Ref.7

Mutagenesis

253

D → A: 9-fold decrease in GTPase activity and 13-fold increase of affinity. Ref.7

Mutagenesis

255

L → D: 1.5-fold decrease in affinity for GTP. Ref.9

Mutagenesis

256

R → A: 2-fold decrease in GTPase activity and almost no change in affinity. Ref.7

Mutagenesis

270

D → A: Does not affect GTP binding, but impairs hydrolase activity. Completely impairs tRNA modifying function. Ref.6

Mutagenesis

275

R → A: 6-fold decrease in GTPase activity and 1.9-fold increase of affinity. Ref.7

Mutagenesis

282

E → A: 1900-fold decrease in GTPase activity. Ref.9

Mutagenesis

282

E → Q: 370-fold decrease in GTPase activity. Ref.9

Mutagenesis

288

R → A: 1.7-fold decrease in GTPase activity and 1.5-fold increase of affinity. Ref.7

Mutagenesis

338

D → N: Strong decrease in GTP binding. Does not affect hydrolase activity, but has 10-fold higher affinity for XTP than for GTP. Partially impairs tRNA modifying function. Ref.6

Mutagenesis

451

C → S: No change in GTP binding and hydrolase activity. Does not affect association to the cell inner membrane. Completely impairs tRNA modifying function. Ref.6

Secondary structure

454

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P25522-1 [UniParc].

Last modified July 15, 1998. Version 3.
Checksum: 032211797805D2FE
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FASTA

454

49,231

        10         20         30         40         50         60 
MSDNDTIVAQ ATPPGRGGVG ILRISGFKAR EVAETVLGKL PKPRYADYLP FKDADGSVLD 

        70         80         90        100        110        120 
QGIALWFPGP NSFTGEDVLE LQGHGGPVIL DLLLKRILTI PGLRIARPGE FSERAFLNDK 

       130        140        150        160        170        180 
LDLAQAEAIA DLIDASSEQA ARSALNSLQG AFSARVNHLV EALTHLRIYV EAAIDFPDEE 

       190        200        210        220        230        240 
IDFLSDGKIE AQLNDVIADL DAVRAEARQG SLLREGMKVV IAGRPNAGKS SLLNALAGRE 

       250        260        270        280        290        300 
AAIVTDIAGT TRDVLREHIH IDGMPLHIID TAGLREASDE VERIGIERAW QEIEQADRVL 

       310        320        330        340        350        360 
FMVDGTTTDA VDPAEIWPEF IARLPAKLPI TVVRNKADIT GETLGMSEVN GHALIRLSAR 

       370        380        390        400        410        420 
TGEGVDVLRN HLKQSMGFDT NMEGGFLARR RHLQALEQAA EHLQQGKAQL LGAWAGELLA 

       430        440        450 
EELRLAQQNL SEITGEFTSD DLLGRIFSSF CIGK

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning and sequence of the thdF gene, which is involved in thiophene and furan oxidation by Escherichia coli." Alam K.Y., Clark D.P. J. Bacteriol. 173:6018-6024(1991) [PubMed: 1917835] [Abstract] Cited for: PRELIMINARY NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication." Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R. Genomics 16:551-561(1993) [PubMed: 7686882] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[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]	"The Escherichia coli trmE (mnmE) gene, involved in tRNA modification, codes for an evolutionarily conserved GTPase with unusual biochemical properties." Cabedo H., Macian F., Villarroya M., Escudero J.C., Martinez-Vicente M., Knecht E., Armengod M.-E. EMBO J. 18:7063-7076(1999) [PubMed: 10601028] [Abstract] Cited for: CHARACTERIZATION, SUBCELLULAR LOCATION.
[6]	"The GTPase activity and C-terminal cysteine of the Escherichia coli MnmE protein are essential for its tRNA modifying function." Yim L., Martinez-Vicente M., Villarroya M., Aguado C., Knecht E., Armengod M.-E. J. Biol. Chem. 278:28378-28387(2003) [PubMed: 12730230] [Abstract] Cited for: GTPASE ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF GLY-228; ASP-270; ASP-338 AND CYS-451.
[7]	"Effects of mutagenesis in the switch I region and conserved arginines of Escherichia coli MnmE protein, a GTPase involved in tRNA modification." Martinez-Vicente M., Yim L., Villarroya M., Mellado M., Perez-Paya E., Bjoerk G.R., Armengod M.-E. J. Biol. Chem. 280:30660-30670(2005) [PubMed: 15983041] [Abstract] Cited for: MUTAGENESIS OF ARG-224; GLY-249; THR-250; THR-251; ARG-252; ASP-253; ARG-256; ARG-275 AND ARG-288.
[8]	"Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli." Yim L., Moukadiri I., Bjoerk G.R., Armengod M.-E. Nucleic Acids Res. 34:5892-5905(2006) [PubMed: 17062623] [Abstract] Cited for: INTERACTION WITH MNMG. Strain: K12.
[9]	"Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element." Scrima A., Wittinghofer A. EMBO J. 25:2940-2951(2006) [PubMed: 16763562] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 216-384 IN COMPLEXES WITH GDP; TRANSITION STATE ANALOG; MAGNESIUM AND POTASSIUM IONS, SUBUNIT, MUTAGENESIS OF ASN-226; LEU-255 AND GLU-282.
[10]	"Structural insights into the GTPase domain of Escherichia coli MnmE protein." Monleon D., Martinez-Vicente M., Esteve V., Yim L., Prado S., Armengod M.-E., Celda B. Proteins 66:726-739(2007) [PubMed: 17143896] [Abstract] Cited for: STRUCTURE BY NMR OF 210-377, BIOPHYSICOCHEMICAL PROPERTIES.

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Cross-references

Sequence databases

S57109 Genomic DNA. Translation: AAB19981.1. Sequence problems.
L10328 Genomic DNA. Translation: AAA62057.1.
U00096 Genomic DNA. Translation: AAC76729.1.
AP009048 Genomic DNA. Translation: BAE77587.1.

PIR

A38160.
C65173.

RefSeq

AP_004086.1.
NP_418162.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1RFL	NMR	-	A	210-377	[»]
2GJ8	X-ray	1.70	A/B/C/D	216-384	[»]
2GJ9	X-ray	2.00	A/B/C/D	216-384	[»]
2GJA	X-ray	1.85	A/B	216-384	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:11033N.

IntAct

P25522. 23 interactions.

STRING

P25522.

Proteomic databases

PRIDE

P25522.

Genome annotation databases

GeneID

948222.

GenomeReviews

Gene locus JW3684 in contig AP009048_GR.
Gene locus b3706 in contig U00096_GR.

KEGG

ecj:JW3684.
eco:b3706.

Organism-specific databases

EchoBASE

EB0990.

EcoGene

EG10997. mnmE.

CMR

Search...

Phylogenomic databases

HOGENOM

P25522.

OMA

KGPNSFT.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10997-MON.

Gene expression databases

Genevestigator

P25522.

Family and domain databases

HAMAP

MF_00379.
[Tree]

InterPro

IPR018948. GTP_bd_TrmE_N.
IPR002917. MMR_HSR1_GTP_bd.
IPR005225. Small_GTP_bd.
IPR004520. ThdF.
[Graphical view]

Gene3D

G3DSA:3.30.1360.120. GTP_bd_TrmE_N. 1 hit.

Pfam

PF01926. MMR_HSR1. 1 hit.
PF10396. TrmE_N. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00450. mnmE_trmE_thdF. 1 hit.
TIGR00231. small_GTP. 1 hit.

ProtoNet

Search...

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Entry information

Entry name

MNME_ECOLI

Accession

Primary (citable) accession number: P25522
Secondary accession number(s): Q2M819

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	July 15, 1998
Last modified:	November 3, 2009
This is version 101 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents