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Escherichia coli K-12 substr. MG1655 Enzyme: RNA 3'-terminal phosphate cyclase



Gene: rtcA Accession Numbers: G7750 (EcoCyc), b4475, ECK3406

Synonyms: yhgJ, yhgK, b3420 (obsolete), b3419 (obsolete)

Regulation Summary Diagram: ?

Summary:
RNA 3'-terminal phosphate cyclase (RtcA) converts the 3'-terminal phosphate of various RNA substrates into the 2',3'-cyclic phosphodiester in an ATP-dependent reaction [Genschik97, Genschik98]. The physiological role of the enzyme is unknown. Recently, it was shown that the enzyme also has a novel polynucleotide 5' adenylylation activity [Chakravarty11], which raises additional possibilities for its physiological function. RtcA can also act on RNA substrates with 2'-terminal phosphate ends, albeit at a dramatically lower rate. RtcA is proposed to be part of an RNA repair pathway, converting RNA 2'-phosphates, which are not substrates of RtcB, to 2',3'-cyclic phosphates that can be sealed [Das13].

The reaction mechanism of RtcA has been studied [Genschik97, Genschik98]. Cyclization occurs by a three-step mechanism involving formation of a covalent protein-nucleoside monophosphate intermediate [Genschik98]. In E. coli, the site of adenylation was shown to be the His308 residue [Billy99].

Crystal structures of the apoenzyme and several enzyme-substrate and enzyme-product complexes have been solved [Palm00, Tanaka10, Chakravarty11a]. The enzyme consists of two identifiable domains [Palm00]. A crystal structure of the RtcA-adenylate intermediate at 1.7 Å resolution and site-directed mutagenesis of residues in the adenylate-binding pocket revealed a potential mechanism for nucleotidyl transfer [Tanaka10], which was further investigated with the help of crystal structures of additional reaction intermediates [Chakravarty11a].

The rtcA gene is not essential for growth in E. coli [Genschik98].

Review: [Filipowicz98]

Locations: cytosol

Map Position: [3,553,855 <- 3,554,871] (76.6 centisomes)
Length: 1017 bp / 338 aa

Molecular Weight of Polypeptide: 35.903 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0174104 , EchoBASE:EB2773 , EcoGene:EG12938 , EcoliWiki:b4475 , ModBase:P46849 , OU-Microarray:b3420 , PortEco:rtcA , Pride:P46849 , Protein Model Portal:P46849 , RefSeq:YP_026219 , RegulonDB:G7750 , SMR:P46849 , String:511145.b4475 , UniProt:P46849

Relationship Links: InterPro:IN-FAMILY:IPR000228 , InterPro:IN-FAMILY:IPR013791 , InterPro:IN-FAMILY:IPR013792 , InterPro:IN-FAMILY:IPR017770 , InterPro:IN-FAMILY:IPR020719 , InterPro:IN-FAMILY:IPR023797 , Panther:IN-FAMILY:PTHR11096 , PDB:Structure:1QMH , PDB:Structure:1QMI , PDB:Structure:3KGD , PDB:Structure:3TUT , PDB:Structure:3TUX , PDB:Structure:3TV1 , PDB:Structure:3TW3 , Pfam:IN-FAMILY:PF01137 , Pfam:IN-FAMILY:PF05189 , Prosite:IN-FAMILY:PS01287

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006396 - RNA processing Inferred by computational analysis [GOA01a]
Molecular Function: GO:0003963 - RNA-3'-phosphate cyclase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Genschik98]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rtcA 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 ? 21-Nov-2013 by Keseler I , SRI International


Enzymatic reaction of: RNA 3'-terminal phosphate cyclase

Synonyms: RNA-3'-phosphate cyclase, RNA cyclase

EC Number: 6.5.1.4

an RNA 3'-terminal-phosphate + ATP <=> an RNA terminal-2',3'-cyclic-phosphate + AMP + diphosphate

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 [Genschik98 ]

Cofactors or Prosthetic Groups: Mn2+ [Genschik98]

Kinetic Parameters:

Substrate
Km (μM)
Citations
ATP
20.0
[Genschik98]

pH(opt): 8-8.5 [Genschik98]


Enzymatic reaction of: polynucleotide 5' adenylyl transferase (RNA 3'-terminal phosphate cyclase)

a 5'-phosphopolynucleotide + ATP <=> a 5' adenylylated polynucleotide + diphosphate

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.

Summary:
Both DNA and RNA can serve as substrates [Chakravarty11].


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 103
[Tanaka10, UniProt11]
Alternate sequence: Q → A; UniProt: No effect on RNA cyclase activity and RtcA adenylation.
Amino-Acid-Sites-That-Bind 103
[UniProt10b]
UniProt: ATP;
Mutagenesis-Variant 128
[Tanaka10, UniProt11]
Alternate sequence: S → A; UniProt: No effect on RNA cyclase activity and RtcA adenylation.
Mutagenesis-Variant 130
[Tanaka10, UniProt11]
Alternate sequence: P → G; UniProt: 33% of wild-type RNA cyclase activity and 13% of wild-type RtcA adenylation.
Mutagenesis-Variant 134
[Tanaka10, UniProt11]
Alternate sequence: F → A; UniProt: 3% of wild-type RNA cyclase activity and 2% of wild-type RtcA adenylation.
Mutagenesis-Variant 250
[Tanaka10, UniProt11]
Alternate sequence: F → A; UniProt: 28% of wild-type RNA cyclase activity and 38% of wild-type RtcA adenylation.
Mutagenesis-Variant 269
[Tanaka10, UniProt11]
Alternate sequence: E → A; UniProt: Nearly no effect on RNA cyclase activity and 2-fold decrease in RtcA adenylation.
Mutagenesis-Variant 283
[Tanaka10, UniProt11]
Alternate sequence: Y → A; UniProt: 12% of wild-type RNA cyclase activity and 2% of wild-type RtcA adenylation.
Nucleotide-Phosphate-Binding-Region 283 -> 287
[UniProt10b]
UniProt: ATP;
Mutagenesis-Variant 286
[Tanaka10, UniProt11]
Alternate sequence: D → A; UniProt: Loss of RNA cyclase activity and RtcA adenylation.
Mutagenesis-Variant 287
[Tanaka10, UniProt11]
Alternate sequence: Q → A; UniProt: Loss of RNA cyclase activity and RtcA adenylation.
Mutagenesis-Variant 308
[Tanaka10, UniProt11]
Alternate sequence: H → G; UniProt: Loss of RNA cyclase activity and RtcA adenylation.
Alternate sequence: H → A; UniProt: Loss of RNA cyclase activity and RtcA adenylation.
Active-Site 308
[Tanaka10, UniProt11]
UniProt: Tele-AMP-histidine intermediate.
Amino-Acid-Sites-That-Bind 308
His308 is the adenylation site of the E. coli enzyme [Billy99].


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/21/2004 (paley) Merged genes G7749/b3419 into G7750/rtcA
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.
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

Billy99: Billy E, Hess D, Hofsteenge J, Filipowicz W (1999). "Characterization of the adenylation site in the RNA 3'-terminal phosphate cyclase from Escherichia coli." J Biol Chem 274(49);34955-60. PMID: 10574971

Chakravarty11: Chakravarty AK, Shuman S (2011). "RNA 3'-phosphate cyclase (RtcA) catalyzes ligase-like adenylylation of DNA and RNA 5'-monophosphate ends." J Biol Chem 286(6);4117-22. PMID: 21098490

Chakravarty11a: Chakravarty AK, Smith P, Shuman S (2011). "Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis." Proc Natl Acad Sci U S A 108(52);21034-9. PMID: 22167800

Das13: Das U, Shuman S (2013). "2'-Phosphate cyclase activity of RtcA: a potential rationale for the operon organization of RtcA with an RNA repair ligase RtcB in Escherichia coli and other bacterial taxa." RNA 19(10);1355-62. PMID: 23945037

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Filipowicz98: Filipowicz W, Billy E, Drabikowski K, Genschik P (1998). "Cyclases of the 3'-terminal phosphate in RNA: a new family of RNA processing enzymes conserved in eucarya, bacteria and archaea." Acta Biochim Pol 45(4);895-906. PMID: 10397337

Genschik97: Genschik P, Billy E, Swianiewicz M, Filipowicz W (1997). "The human RNA 3'-terminal phosphate cyclase is a member of a new family of proteins conserved in Eucarya, Bacteria and Archaea." EMBO J 16(10);2955-67. PMID: 9184239

Genschik98: Genschik P, Drabikowski K, Filipowicz W (1998). "Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon." J Biol Chem 273(39);25516-26. PMID: 9738023

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, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: 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."

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

Palm00: Palm GJ, Billy E, Filipowicz W, Wlodawer A (2000). "Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology." Structure 8(1);13-23. PMID: 10673421

Tanaka10: Tanaka N, Smith P, Shuman S (2010). "Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer." Structure 18(4);449-57. PMID: 20399182

UniProt10b: UniProt Consortium (2010). "UniProt version 2010-12 released on 2010-12-01 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 the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords 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 Fri Nov 21, 2014, BIOCYC14A.