PDBsum entry 1qmh

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Ligase PDB id
Protein chains
334 a.a. *
CIT ×2
Waters ×424
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology
Structure: RNA 3'-terminal phosphate cyclase. Chain: a, b. Synonym: RNA cyclase, RNA-3'-phosphate cyclase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k-12. Cellular_location: cytoplasm. Gene: rtca. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PQS)
2.10Å     R-factor:   0.207     R-free:   0.276
Authors: G.J.Palm,E.Billy,W.Filipowicz,A.Wlodawer
Key ref:
G.J.Palm et al. (2000). Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology. Structure, 8, 13-23. PubMed id: 10673421 DOI: 10.1016/S0969-2126(00)00076-9
28-Sep-99     Release date:   11-Jan-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P46849  (RTCA_ECOLI) -  RNA 3'-terminal phosphate cyclase
338 a.a.
334 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Rna 3'-terminal-phosphate cyclase (ATP).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal- 2',3'-cyclic-phosphate
+ RNA 3'-terminal-phosphate
+ diphosphate
+ RNA terminal- 2',3'-cyclic-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     RNA processing   1 term 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1016/S0969-2126(00)00076-9 Structure 8:13-23 (2000)
PubMed id: 10673421  
Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology.
G.J.Palm, E.Billy, W.Filipowicz, A.Wlodawer.
BACKGROUND: RNA cyclases are a family of RNA-modifying enzymes that are conserved in eucarya, bacteria and archaea. They catalyze the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate. These enzymes might be responsible for production of the cyclic phosphate RNA ends that are known to be required by many RNA ligases in both prokaryotes and eukaryotes. RESULTS: The high-resolution structure of the Escherichia coli RNA 3'-terminal phosphate cyclase was determined using multiwavelength anomalous diffraction. Two orthorhombic crystal forms of E. coli cyclase (space group P2(1)2(1)2(1) and P2(1)2(1)2) were used to solve and refine the structure to 2.1 A resolution (R factor 20.4%; R(free) 27.6%). Each molecule of RNA cyclase consists of two domains. The larger domain contains three repeats of a folding unit comprising two parallel alpha helices and a four-stranded beta sheet; this fold was previously identified in translation initiation factor 3 (IF3). The large domain is similar to one of the two domains of 5-enolpyruvylshikimate-3-phosphate synthase and UDP-N-acetylglucosamine enolpyruvyl transferase. The smaller domain uses a similar secondary structure element with different topology, observed in many other proteins such as thioredoxin. CONCLUSIONS: The fold of RNA cyclase consists of known elements connected in a new and unique manner. Although the active site of this enzyme could not be unambiguously assigned, it can be mapped to a region surrounding His309, an adenylate acceptor, in which a number of amino acids are highly conserved in the enzyme from different sources. The structure of E. coli cyclase will be useful for interpretation of structural and mechanistic features of this and other related enzymes.
  Selected figure(s)  
Figure 3.
Figure 3. Stereo diagrams of the backbone of RNA cyclase. (a) Ribbon representation of the crystal structure of a single cyclase molecule and the atomic surface of the protein. The chain corresponding to the large domain is shown in blue and the small domain is shown in pink. The sidechain of His309 is shown in red. (b) A noncrystallographic dimer of RNA cyclase, with two molecules shown in green and gold. Sidechains of His309 are rendered in atomic colors and the citrate molecules are shown in space-filling representation.
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 13-23) copyright 2000.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18996897 A.L.Cuff, I.Sillitoe, T.Lewis, O.C.Redfern, R.Garratt, J.Thornton, and C.A.Orengo (2009).
The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.
  Nucleic Acids Res, 37, D310-D314.  
16677078 S.Mkrtchian, and T.Sandalova (2006).
ERp29, an unusual redox-inactive member of the thioredoxin family.
  Antioxid Redox Signal, 8, 325-337.  
16307926 K.Karbstein, S.Jonas, and J.A.Doudna (2005).
An essential GTPase promotes assembly of preribosomal RNA processing complexes.
  Mol Cell, 20, 633-643.  
15558583 Y.Qi, and N.V.Grishin (2005).
Structural classification of thioredoxin-like fold proteins.
  Proteins, 58, 376-388.  
15112237 E.Staub, P.Fiziev, A.Rosenthal, and B.Hinzmann (2004).
Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire.
  Bioessays, 26, 567-581.  
12377789 J.Phan, A.Zdanov, A.G.Evdokimov, J.E.Tropea, H.K.Peters, R.B.Kapust, M.Li, A.Wlodawer, and D.S.Waugh (2002).
Structural basis for the substrate specificity of tobacco etch virus protease.
  J Biol Chem, 277, 50564-50572.
PDB codes: 1lvb 1lvm
11565748 T.Wegierski, E.Billy, F.Nasr, and W.Filipowicz (2001).
Bms1p, a G-domain-containing protein, associates with Rcl1p and is required for 18S rRNA biogenesis in yeast.
  RNA, 7, 1254-1267.  
10790377 E.Billy, T.Wegierski, F.Nasr, and W.Filipowicz (2000).
Rcl1p, the yeast protein similar to the RNA 3'-phosphate cyclase, associates with U3 snoRNP and is required for 18S rRNA biogenesis.
  EMBO J, 19, 2115-2126.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.