4O8J | pdb_00004o8j

Crystal structure of RtcA, the RNA 3'-terminal phosphate cyclase from Pyrococcus horikoshii, in complex with rACAAA3'phosphate and adenine.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.198 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4O8J

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 

Literature

Structure of RNA 3'-phosphate cyclase bound to substrate RNA.

Desai, K.K., Bingman, C.A., Cheng, C.L., Phillips Jr., G.N., Raines, R.T.

(2014) RNA 20: 1560-1566

  • DOI: https://doi.org/10.1261/rna.045823.114
  • Primary Citation Related Structures: 
    4O89, 4O8J

  • PubMed Abstract: 

    RNA 3'-phosphate cyclase (RtcA) catalyzes the ATP-dependent cyclization of a 3'-phosphate to form a 2',3'-cyclic phosphate at RNA termini. Cyclization proceeds through RtcA-AMP and RNA(3')pp(5')A covalent intermediates, which are analogous to intermediates formed during catalysis by the tRNA ligase RtcB. Here we present a crystal structure of Pyrococcus horikoshii RtcA in complex with a 3'-phosphate terminated RNA and adenosine in the AMP-binding pocket. Our data reveal that RtcA recognizes substrate RNA by ensuring that the terminal 3'-phosphate makes a large contribution to RNA binding. Furthermore, the RNA 3'-phosphate is poised for in-line attack on the P-N bond that links the phosphorous atom of AMP to N(ε) of His307. Thus, we provide the first insights into RNA 3'-phosphate termini recognition and the mechanism of 3'-phosphate activation by an Rtc enzyme.

    • Organizational Affiliation: 
    • Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

Macromolecule Content 

  • Total Structure Weight: 79.03 kDa 
  • Atom Count: 6,148 
  • Modeled Residue Count: 694 
  • Deposited Residue Count: 694 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase
A, B
341Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: PH1529, PHCV028, rtcA
EC: 6.5.1.4
UniProt
Find proteins for O59198 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O59198 
Go to UniProtKB:  O59198
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO59198
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNAC [auth D],
D [auth E]		6N/A
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.198 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.921α = 90
b = 110.261β = 90
c = 127.648γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-11-29
    Changes: Database references
  • Version 1.3: 2020-09-23
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary