RNA-3'-phosphate cyclase

 

The enzyme converts the 3'-terminal phosphate of various RNA substrates into the 2',3'-cyclic phosphodiester in an ATP-dependent reaction. The enzyme also has a polynucleotide 5' adenylylation activity [PMID:21098490 ]. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing.

 

Reference Protein and Structure

Sequence
P46849 UniProt (6.5.1.4) IPR017770 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1qmh - Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology (2.1 Å) PDBe PDBsum 1qmh
Catalytic CATH Domains
3.65.10.20 CATHdb (see all for 1qmh)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:6.5.1.4)

3'-end ribonucleotide 3'-phosphate(3-) residue
CHEBI:83062ChEBI
+
ATP(4-)
CHEBI:30616ChEBI
→
adenosine 5'-monophosphate(2-)
CHEBI:456215ChEBI
+
3'-end ribonucleotide 2',3'-cyclic phosphate(2-) residue
CHEBI:83064ChEBI
+
diphosphate(3-)
CHEBI:33019ChEBI
Alternative enzyme names: RNA cyclase, RNA-3'-phosphate cyclase, RtcA (gene name),

Enzyme Mechanism

Introduction

Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP, forming a phosphoramide bond between adenylate and a histidine (His309, activated by Glu14) residue [PMID:10574971, PMID:19690099]. The adenylate group is then transferred to the 3'-phosphate terminus of the substrate, forming the capped structure [RNA]-3'-(5'-diphosphoadenosine). Finally, the enzyme catalyses an attack of the vicinal O-2' on the 3'-phosphorus, which results in formation of cyclic phosphate and release of the adenylate. As with other ATP-dependent enzymes, it is thought that the magnesium ion is bound directly to the phosphate groups of ATP.

Catalytic Residues Roles

UniProt PDB* (1qmh)
Glu13 Glu14A Helps activate the histidine. It could either do this thought electrostatic interactions or by acting as a general acid/base. modifies pKa
His308 His309A Acts as a nucleophile. covalent catalysis
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Palm GJ et al. (2000), Structure, 8, 13-23. Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology. PMID:10673421.
  2. Chakravarty AK et al. (2011), Proc Natl Acad Sci U S A, 108, 21034-21039. Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis. DOI:10.1073/pnas.1115560108. PMID:22167800.
  3. Chakravarty AK et al. (2011), J Biol Chem, 286, 4117-4122. RNA 3'-phosphate cyclase (RtcA) catalyzes ligase-like adenylylation of DNA and RNA 5'-monophosphate ends. DOI:10.1074/jbc.M110.196766. PMID:21098490.
  4. Tanaka N et al. (2010), Structure, 18, 449-457. Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer. DOI:10.1016/j.str.2010.01.016. PMID:20399182.
  5. Tanaka N et al. (2009), RNA, 15, 1865-1874. Structure-activity relationships in human RNA 3'-phosphate cyclase. DOI:10.1261/rna.1771509. PMID:19690099.
  6. Billy E et al. (1999), J Biol Chem, 274, 34955-34960. Characterization of the adenylation site in the RNA 3'-terminal phosphate cyclase from Escherichia coli. PMID:10574971.
  7. Genschik P et al. (1998), J Biol Chem, 273, 25516-25526. Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon. PMID:9738023.
  8. Genschik P et al. (1997), EMBO J, 16, 2955-2967. The human RNA 3'-terminal phosphate cyclase is a member of a new family of proteins conserved in Eucarya, Bacteria and Archaea. DOI:10.1093/emboj/16.10.2955. PMID:9184239.

Step 1.

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Catalytic Residues Roles

Residue Roles
Glu14A modifies pKa
His309A covalent catalysis

Chemical Components

Step 1.

Contributors

Alex Gutteridge, Craig Porter, Gemma L. Holliday