1QMH

Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

Starting Model: experimental
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Literature

Crystal Structure of RNA 3'-Terminal Phosphate Cyclase, a Ubiquitous Enzyme with Unusual Topology

Palm, G.J.Billy, E.Filipowicz, W.Wlodawer, A.

(2000) Structure 8: 13

  • DOI: https://doi.org/10.1016/s0969-2126(00)00076-9
  • Primary Citation of Related Structures:  
    1QMH, 1QMI

  • PubMed Abstract: 

    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. 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. 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.


  • Organizational Affiliation

    Program in Structural Biology, Macromolecular Crystallography Laboratory, National Cancer Institute-FCRDC, Frederick, MD 21702, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-TERMINAL PHOSPHATE CYCLASE
A, B
347Escherichia coli K-12Mutation(s): 0 
Gene Names: RTCA
EC: 6.5.1.4
UniProt
Find proteins for P46849 (Escherichia coli (strain K12))
Explore P46849 
Go to UniProtKB:  P46849
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46849
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.8α = 90
b = 133.5β = 90
c = 51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-01-11
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description