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Ligand tRNA UpsiC

Basic Ligand Information

Molecular Structure

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Roles as Enzyme Ligand

In Vivo Substrate in Enzyme-catalyzed Reactions (5 results)

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Show Natural Substrate (5 entries)

EC NUMBER

PROVEN IN VIVO REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.1.1.35

S-adenosyl-L-methionine + tRNA containing uridine at position 54 = S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54

689248, 705768, 689809, 705962

-

2.1.1.35

S-adenosyl-L-methionine + uridine54 in tRNA = S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA

441380, 441361, 441362, 441359, 441363, 441365, 441366, 441377, 441378, 441381, 441372, 441367

-

2.1.1.74

5,10-methylenetetrahydrofolate + tRNA containing uridine at position 54 + FADH2 = tetrahydrofolate + tRNA containing ribothymidine at position 54 + FAD

706541, 701488

-

2.1.1.74

5,10-methylenetetrahydrofolate + tRNA UpsiC + FADH2 = tetrahydrofolate + tRNA TpsiC + FAD

485582, 485581, 485583

-

2.1.1.35

2 entries

2.1.1.74

2 entries

5.4.99.B25

tRNA uridine54 = tRNA pseudouridine54

748425, 721041

-

Substrate in Enzyme-catalyzed Reactions (7 results)

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Show Substrate (7 entries)

EC NUMBER

REACTION

REACTION DIAGRAM

LITERATURE

ENZYME 3D STRUCTURE

2.1.1.35

S-adenosyl-L-methionine + tRNA containing uridine at position 54 = S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54

689248, 705768, 689809, 705962

-

2.1.1.35

S-adenosyl-L-methionine + uridine54 in tRNA = S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA

441341, 441373, 441380, 441338, 441339, 441299, 441362, 441372, 441379, 441363, 441361, 441358, 441367, 441378, 441375, 441364, 441357, 441359, 441376, 441365, 441366, 441374, 441377, 441360, 441381

-

2.1.1.74

5,10-methylenetetrahydrofolate + tRNA containing uridine at position 54 + FADH2 = tetrahydrofolate + tRNA containing ribothymidine at position 54 + FAD

706541, 701488

-

2.1.1.74

N5,N10-methylenetetrahydrofolate + tRNA containing uridine at position 54 + FADH2 = tetrahydrofolate + tRNA containing ribothymidine at position 54 + FAD

701488

-

2.1.1.74

5,10-methylenetetrahydrofolate + tRNA UpsiC + FADH2 = tetrahydrofolate + tRNA TpsiC + FAD

485581, 485582, 485583, 718903, 719972, 671555, 676202

-

2.1.1.74

5,10-methylenetetrahydrofolate + tRNA UpsiC + NADH = tetrahydrofolate + tRNA TpsiC + NAD+

720967

-

2.1.1.35

2 entries

2.1.1.74

4 entries

5.4.99.B25

tRNA uridine54 = tRNA pseudouridine54

716902, 748425, 721041, 695108, 728787

-

Enzyme Kinetic Parameters

k_cat Value (Turnover Number) (1 result)

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Show Turnover Number (1 entry)

EC NUMBER

TURNOVER NUMBER [1/S]

TURNOVER NUMBER MAXIMUM [1/S]

COMMENTARY

LITERATURE

2.1.1.35

0.317

-

-

441365

K_M Value (1 result)

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Show KM Value (1 entry)

EC NUMBER

KM VALUE [MM]

KM VALUE MAXIMUM [MM]

COMMENTARY

LITERATURE

2.1.1.35

0.00008

-

-

441365

References & Links

Literature References (44)

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Show Reference (44 entries)

BRENDA REFERENCE ID

PUBMED ID

TITLE

YEAR

AUTHORS

JOURNAL

VOLUME

PAGES

441299

4896260

Studies on microbial RNA. Fractionation of tRNA methylases from Saccharomyces cerevisiae

1969

Björk, G.R.; Svensson, I.

Eur. J. Biochem.

9

207-215

441338

14245404

The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid. III. Purification of soluble ribonucleic acid-methylating enzymes

1964

Hurwitz, J.; Gold, M.; Anders, M.

J. Biol. Chem.

239

3462-3473

441339

14245405

The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid. IV. The properties of the soluble ribonucleic acid-methylating enzymes

1964

Hurwitz, J.; Gold, M.; Anders, M.

J. Biol. Chem.

239

3474-3482

441341

6787407

Purification and properties of several transfer RNA methyltransferases from S. typhimurium

1981

Cimino, F.; Traboni, C.; Colonna, A.; Izzo, P.; Salvatore, F.

Mol. Cell. Biochem.

36

95-104

441357

4896261

Studies on microbial RNA. Properties of tRNA methylases from Saccharomyces cerevisiae

1969

Svensson, I.; Björk, G.R.; Lundahl, P.

Eur. J. Biochem.

9

216-221

441358

391549

Escherichia coli tRNA (uracil-5-)-methyltransferase: Inhibition by analogues of adenosylhomocysteine

1979

Shugart, L.; Chastain, B.

Enzyme

24

353-357

441359

6997293

Isolation and characterization of m5U-methyltransferase from Escherichia coli

1980

Greenberg, R.; Dudock, B.

J. Biol. Chem.

255

8296-8302

441360

374938

Bacterial tRNA methyltransferases

1979

Greenberg, R.; Dudock, B.

Methods Enzymol.

59

190-203

441361

8419334

The tRNA-(m5U54)-methyltransferase of Escherichia coli is present in two forms in vivo, one of which is present as bound to tRNA and to a 3-end fragment of 16S rRNA

1993

Gustafsson, C.; Björk, G.R.

J. Biol. Chem.

268

1326-1331

441362

343812

Kinetic studies of Escherichia coli transfer RNA (uracil-5-)-methyltransferase

1978

Shugart, L.

Biochemistry

17

1068-1072

441363

3327525

Catalytic mechanism and inhibition of tRNA (uracil-5-)methyltransferase: Evidence for covalent catalysis

1987

Santi, D.V.; Hardy, L.W.

Biochemistry

26

8599-8606

441364

2007136

The T-arm of tRNA is a substrate for tRNA (m5U54)-methyltransferase

1991

Gu, X.; Santi, D.V.

Biochemistry

30

2999-3002

441365

2461858

Purification of transfer RNA (m5U54)-methyltransferase from Escherichia coli. Association with RNA

1988

Ny, T.; Lindström, P.H.R.; Hagervall, T.G.; Björk, G.R.

Eur. J. Biochem.

177

467-475

441366

1754383

Stereochemistry of methyl transfer catalyzed by tRNA (m5U54)-methyltransferase--evidence for a single displacement mechanism

1991

Kealey, J.T.; Lee, S.; Floss, H.G.; Santi, D.V.

Nucleic Acids Res.

19

6465-6468

441367

345244

Selective inhibition of uracil tRNA methylases of E. coli by ethionine

1978

Tscherne, J.S.; Wainfan, E.

Nucleic Acids Res.

5

451-461

441372

7748948

Enzymatic mechanism of tRNA (m5U54)methyltransferase

1994

Kealey, J.T.; Gu, X.; Santi, D.V.

Biochimie

76

1133-1142

441373

8054847

High-level expression and rapid purification of tRNA (m5U54)-methyltransferase

1994

Kealey, J.T.; Santi, D.V.

Protein Expr. Purif.

5

149-152

441374

8604339

Interaction of tRNA (uracil-5-)-methyltransferase with NO2Ura-tRNA

1996

Gu, X.; Matsuda, A.; Ivanetich, K.M.; Santi, D.V.

Nucleic Acids Res.

24

1059-1064

441375

7532997

Stereochemistry of tRNA(m5U54)-methyltransferase catalysis: 19F NMR spectroscopy of an enzyme-FUraRNA covalent complex

1995

Kealey, J.T.; Santi, D.V.

Biochemistry

34

2441-2446

441376

8117682

In vitro methylation of Escherichia coli 16S rRNA by tRNA (m5U54)-methyltransferase

1994

Gu, X.; Ofengand, J.; Santi, D.V.

Biochemistry

33

2255-2261

441377

7748949

Aminoacyl-tRNA synthetase and U54 methyltransferase recognize conformations of the yeast tRNAPhe anticodon and T stem/loop domain

1994

Guenther, R.H.; Bakal, R.S.; Forrest, B.; Chen, Y.; Sengupta, R.; Nawrot, B.; Sochacka, E.; Jankowska, J.; Kraszewski, A.; Malkiewicz, A.; Agris, P.F.

Biochimie

76

1143-1151

441378

10684932

Modified constructs of the tRNA TPsiC domain to probe substrate conformational requirements of m1A58 and m5U54 tRNA methyltransferases

2000

Sengupta, R.; Vainauskas, S.; Yarian, C.; Sochacka, E.; Malkiewicz, A.; Guenther, R.H.; Koshlap, K.M.; Agris, P.F.

Nucleic Acids Res.

28

1374-1380

441379

8794745

Recognition of the T-arm of tRNA by tRNA (m5U54)-methyltransferase is not sequence specific

1996

Gu, X.; Ivanetich, K.M.; Santi, D.V.

Biochemistry

35

11652-11659

441380

10864043

Identification of the TRM2 gene encoding the tRNA(m5U54)methyltransferase of Saccharomyces cerevisiae

2000

Nordlund, M.E.; Johansson, J.O.M.; von Pawel-Rammingen, U.; Byström, A.S.

RNA

6

844-860

441381

12003492

Dual function of the tRNA(m5U54)methyltransferase in tRNA maturation

2002

Johansson, M.J.O.; Byström, A.S.

RNA

8

324-335

485581

826533

Biosynthesis of ribothymidine in the transfer RNA of Streptococcus faecalis and Bacillus subtilis. A methylation of RNA involving 5,10-methylenetetrahydrofolate

1976

Delk, A.S.; Romeo, J.M.; Nagle, D.P.; Rabinowitz, J.C.

J. Biol. Chem.

251

7649-7656

485582

106850

The methylenetetrahydrofolate-mediated biosynthesis of ribothymidine in the transfer-RNA of Streptococcus faecalis: incorporation of hydrogen from solvent into the methyl moiety

1979

Delk, A.S.; Nagle, D.P.; Rabinowitz, J.C.

Biochem. Biophys. Res. Commun.

86

244-251

485583

6768721

Methylenetetrahydrofolate-dependent biosynthesis of ribothymidine in transfer RNA of Streptococcus faecalis. Evidence for reduction of the 1-carbon unit by FADH2

1980

Delk, A.S.; Nagle, D.P.; Rabinowitz, J.C.

J. Biol. Chem.

255

4387-4390

671555

17216455

Thymidyl biosynthesis enzymes as antibiotic targets

2007

Chernyshev, A.; Fleischmann, T.; Kohen, A.

Appl. Microbiol. Biotechnol.

74

282-289

676202

16027442

Identification of a novel gene encoding a flavin-dependent tRNA:m5U methyltransferase in bacteria -evolutionary implications

2005

Urbonavicius, J.; Skouloubris, S.; Myllykallio, H.; Grosjean, H.

Nucleic Acids Res.

33

3955-3964

689248

17459887

Amino acid residues of the Escherichia coli tRNA(m5U54)methyltransferase (TrmA) critical for stability, covalent binding of tRNA and enzymatic activity

2007

Urbonavicius, J.; Jaeger, G.; Bjoerk, G.R.

Nucleic Acids Res.

35

3297-3305

689809

18451029

Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases

2008

Alian, A.; Lee, T.T.; Griner, S.L.; Stroud, R.M.; Finer-Moore, J.

Proc. Natl. Acad. Sci. USA

105

6876-6881

695108

18952823

Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA

2008

Gurha, P.; Gupta, R.

RNA

14

2521-2527

701488

18323606

Crystallization and preliminary X-ray crystallographic characterization of TrmFO, a folate-dependent tRNA methyltransferase from Thermotoga maritima

2008

Cicmil, N.

Acta Crystallogr. Sect. F

64

193-195

705768

18069966

Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer

2008

Urbonavicius, J.; Auxilien, S.; Walbott, H.; Trachana, K.; Golinelli-Pimpaneau, B.; Brochier-Armanet, C.; Grosjean, H.

Mol. Microbiol.

67

323-335

705962

18653523

The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity

2008

Walbott, H.; Leulliot, N.; Grosjean, H.; Golinelli-Pimpaneau, B.

Nucleic Acids Res.

36

4929-4940

706541

19416846

Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase

2009

Nishimasu, H.; Ishitani, R.; Yamashita, K.; Iwashita, C.; Hirata, A.; Hori, H.; Nureki, O.

Proc. Natl. Acad. Sci. USA

106

8180-8185

716902

21628430

Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii

2011

Blaby, I.K.; Majumder, M.; Chatterjee, K.; Jana, S.; Grosjean, H.; de Crecy-Lagard, V.; Gupta, R.

RNA

17

1367-1380

718903

21561081

A catalytic intermediate and several flavin redox states stabilized by folate-dependent tRNA methyltransferase from Bacillus subtilis

2011

Hamdane, D.; Guerineau, V.; Un, S.; Golinelli-Pimpaneau, B.

Biochemistry

50

5208-5219

719972

21846722

Insights into folate/FAD-dependent tRNA methyltransferase mechanism: role of two highly conserved cysteines in catalysis

2011

Hamdane, D.; Argentini, M.; Cornu, D.; Myllykallio, H.; Skouloubris, S.; Hui-Bon-Hoa, G.; Golinelli-Pimpaneau, B.

J. Biol. Chem.

286

36268-36280

720967

20412857

Expression and purification of untagged and histidine-tagged folate-dependent tRNA:m5U54 methyltransferase from Bacillus subtilis

2010

Hamdane, D.; Skouloubris, S.; Myllykallio, H.; Golinelli-Pimpaneau, B.

Protein Expr. Purif.

73

83-89

721041

22274953

The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA

2012

Chatterjee, K.; Blaby, I.K.; Thiaville, P.C.; Majumder, M.; Grosjean, H.; Yuan, Y.A.; Gupta, R.; de Crecy-Lagard, V.

RNA

18

421-433

728787

23898217

Role of forefinger and thumb loops in production of Psi54 and Psi55 in tRNAs by archaeal Pus10

2013

Joardar, A.; Jana, S.; Fitzek, E.; Gurha, P.; Majumder, M.; Chatterjee K, Geisler M, Gupta R.

RNA

19

1279-1294

748425

29349599

Evolution of eukaryal and archaeal pseudouridine synthase Pus10

2018

Fitzek, E.; Joardar, A.; Gupta, R.; Geisler, M.

J. Mol. Evol.

86

77-89

Links to other databases for tRNA UpsiC

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Show Links (1 entry)