Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: tRNAMet cytidine acetyltransferase



Gene: tmcA Accession Numbers: G7297 (EcoCyc), b2474, ECK2470

Synonyms: ypfI

Regulation Summary Diagram: ?

Summary:
tRNAMet cytidine acetyltransferase acetylates the wobble base C34 of the elongation-specific tRNAMet. TmcA specifically recognizes the anticodon stem of tRNAMet, thus distinguishing between tRNAMet and tRNAIle2, which is structurally similar and has the same anticodon loop [Ikeuchi08, Chimnaronk09].

A crystal structure of the enzyme complexed with acetyl-CoA and ADP has been solved at 2.35 Å resolution. A modified DEAD-box RNA helicase module is formed by the peripheral N-terminal and the DUF699 PFAM domains. The authors propose that the RNA helicase motor delivers the wobble base substrate of the tRNA to the enzyme active site [Chimnaronk09].

The presence of acetyl-CoA is essential for the formation of a stable complex between TmcA and tRNAMet and also activates the intrinsic ATPase activity of TmcA. The substrate tRNA may be transiently rearranged during ATP hydrolysis [Chimnaronk09].

In vitro, it was observed that the N4-acetylcytidine (ac4C) modification at wobble position of tRNAMet is important for preventing misreading of the AUA codon [Stern78]. RNA isolated from a tmcA deletion strain lacks the ac4C modification; however, the strain does not show a growth defect. Thus, this modification does not appear to be required for faithful translation in an otherwise wild-type strain. A tmcA dusC double deletion strain has a severe cold-sensitive growth defect [Ikeuchi08]. Residues essential for either the ATPase or tRNA binding activities were identified by site-directed mutagenesis [Chimnaronk09].

TmcA: "tRNAMet cytidine acetyltransferase" [Ikeuchi08]

Locations: cytosol

Map Position: [2,591,866 <- 2,593,881] (55.86 centisomes)
Length: 2016 bp / 671 aa

Molecular Weight of Polypeptide: 74.892 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008150 , DIP:DIP-12825N , EchoBASE:EB3948 , EcoGene:EG14196 , EcoliWiki:b2474 , OU-Microarray:b2474 , PortEco:tmcA , Pride:P76562 , Protein Model Portal:P76562 , RefSeq:NP_416969 , RegulonDB:G7297 , SMR:P76562 , String:511145.b2474 , UniProt:P76562

Relationship Links: InterPro:IN-FAMILY:IPR000182 , InterPro:IN-FAMILY:IPR007807 , InterPro:IN-FAMILY:IPR013562 , InterPro:IN-FAMILY:IPR016181 , InterPro:IN-FAMILY:IPR024914 , InterPro:IN-FAMILY:IPR027417 , InterPro:IN-FAMILY:IPR027992 , PDB:Structure:2ZPA , Pfam:IN-FAMILY:PF05127 , Pfam:IN-FAMILY:PF08351 , Pfam:IN-FAMILY:PF13718 , Pfam:IN-FAMILY:PF13725 , Prosite:IN-FAMILY:PS51186

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0002101 - tRNA wobble cytosine modification Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Ikeuchi08]
GO:0051391 - tRNA acetylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Ikeuchi08]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0000049 - tRNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Chimnaronk09]
GO:0051392 - tRNA N-acetyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Ikeuchi08]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0008080 - N-acetyltransferase activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016746 - transferase activity, transferring acyl groups Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for tmcA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Last-Curated ? 30-Mar-2009 by Keseler I , SRI International


Enzymatic reaction of: tRNAMet cytidine acetyltransferase

EC Number: 2.3.1.193

a cytidine34 in tRNAmet + ATP + acetyl-CoA + H2O <=> [elongator tRNAmet]-N4-acetylcytidine34 + ADP + coenzyme A + phosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for ATP: GTP [Ikeuchi08 ]

Summary:
The ATP/GTP hydrolase activity of the enzyme is stimulated by the presence of acetyl-CoA and tRNAMet [Ikeuchi08].

Kinetic Parameters:

Substrate
Km (μM)
Citations
ATP
4.16
[Ikeuchi08]


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 174 -> 175
[UniProt11]
UniProt: ATP.
Amino-Acid-Sites-That-Bind 180
[UniProt11]
UniProt: ATP.
Nucleotide-Phosphate-Binding-Region 202 -> 211
[UniProt11]
UniProt: ATP.
Mutagenesis-Variant 287
[Chimnaronk09, UniProt11]
Alternate sequence: T → A; UniProt: Loss of ATPase activity, but no change in tRNA-binding.
Mutagenesis-Variant 291
[Chimnaronk09, UniProt11]
Alternate sequence: Y → A; UniProt: Loss of ATPase activity, but no change in tRNA-binding.
Mutagenesis-Variant 292
[Chimnaronk09, UniProt11]
Alternate sequence: E → A; UniProt: Loss of ATPase activity, but no change in tRNA-binding.
Mutagenesis-Variant 296
[Chimnaronk09, UniProt11]
Alternate sequence: R → A; UniProt: Decrease in ATPase activity and loss of tRNA-binding.
Mutagenesis-Variant 301
[Chimnaronk09, UniProt11]
Alternate sequence: K → A; UniProt: Decrease in ATPase activity and loss of tRNA-binding.
Mutagenesis-Variant 319
[Chimnaronk09, UniProt11]
Alternate sequence: R → A; UniProt: Loss of ATPase activity, but no change in tRNA-binding.
Amino-Acid-Sites-That-Bind 319
[UniProt11]
UniProt: ATP.
Mutagenesis-Variant 327
[Chimnaronk09, UniProt11]
Alternate sequence: E → A; UniProt: Loss of ATPase activity, but no change in tRNA-binding.
Conserved-Region 356 -> 531
[UniProt09]
UniProt: N-acetyltransferase;
Mutagenesis-Variant 377
[Chimnaronk09, UniProt11]
Alternate sequence: H → A; UniProt: Decrease in ATPase activity and loss of tRNA-binding.
Mutagenesis-Variant 387
[Chimnaronk09, UniProt11]
Alternate sequence: R → A; UniProt: Abolishes the tRNA-binding capacity, but no loss of activity.
Mutagenesis-Variant 460
[Chimnaronk09, UniProt11]
Alternate sequence: R → A; UniProt: Loss of tRNA-binding.
Protein-Segment 461 -> 463
[UniProt11]
UniProt: Acetyl-CoA binding; Sequence Annotation Type: region of interest.
Protein-Segment 468 -> 474
[UniProt11]
UniProt: Acetyl-CoA binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 499
[UniProt11]
UniProt: Acetyl-CoA.
Amino-Acid-Sites-That-Bind 506
[UniProt11]
UniProt: Acetyl-CoA.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Chimnaronk09: Chimnaronk S, Suzuki T, Manita T, Ikeuchi Y, Yao M, Suzuki T, Tanaka I (2009). "RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon." EMBO J 28(9):1362-73. PMID: 19322199

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Ikeuchi08: Ikeuchi Y, Kitahara K, Suzuki T (2008). "The RNA acetyltransferase driven by ATP hydrolysis synthesizes N(4)-acetylcytidine of tRNA anticodon." EMBO J 27(16):2194-203. PMID: 18668122

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Stern78: Stern L, Schulman LH (1978). "The role of the minor base N4-acetylcytidine in the function of the Escherichia coli noninitiator methionine transfer RNA." J Biol Chem 253(17);6132-9. PMID: 355249

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Nov 24, 2014, biocyc13.