1OBT

STRUCTURE OF RICIN A CHAIN MUTANT, COMPLEX WITH AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and activity of an active site substitution of ricin A chain.

Day, P.J.Ernst, S.R.Frankel, A.E.Monzingo, A.F.Pascal, J.M.Molina-Svinth, M.C.Robertus, J.D.

(1996) Biochemistry 35: 11098-11103

  • DOI: 10.1021/bi960880n
  • Primary Citation of Related Structures:  1OBS

  • PubMed Abstract: 
  • The A chain of ricin (RTA) is an N-glycosidase which inactivates ribosomes by removing a single adenine base from a conserved region of rRNA. X-ray structures and site-directed mutagenesis revealed that Arg 180 interacts with the target adenine hydro ...

    The A chain of ricin (RTA) is an N-glycosidase which inactivates ribosomes by removing a single adenine base from a conserved region of rRNA. X-ray structures and site-directed mutagenesis revealed that Arg 180 interacts with the target adenine hydrogen bonding with N3. It may fully or partially protonate that atom as part of the hydrolysis mechanism. Arg 180 was previously converted to His (R180H) and shown to greatly reduce activity. Here R180H is shown to reduce overall activity 500-fold against Artemia salina ribosomes. A 2.2 A crystal structure reveals the mutation causes a rearrangement of the active site cleft, with Tyr 80 moving to block access to the adenine recognition site. His 180 forms a strong aromatic interaction with Trp 211, Tyr 80, and Tyr 123. A complex is formed with 250 mM AMP. The nucleotide binds in the active site region, but in an apparently nonproductive orientation. His 180 cannot bond to N3 and is screened from the substrate analog by the intervening Tyr 80. It may be that natural polynucleotide substrates, using additional interactions, can displace Tyr 80 and effect a productive binding.


    Related Citations: 
    • X-Ray Structure of Recombinant Ricin A-Chain at 1.8 A Resolution
      Weston, S.A.,Tucker, A.D.,Thatcher, D.R.,Derbyshire, D.J.,Pauptit, R.A.
      (1994) J.Mol.Biol. 244: 410
    • Structure of Recombinant Ricin a Chain at 2.3 A
      Mlsna, D.,Monzingo, A.F.,Katzin, B.J.,Ernst, S.,Robertus, J.D.
      (1993) Protein Sci. 2: 429


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas, Austin 78712, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RICIN A CHAIN
A
267Ricinus communisEC: 3.2.2.22
Find proteins for P02879 (Ricinus communis)
Go to UniProtKB:  P02879
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.650α = 90.00
b = 68.650β = 90.00
c = 141.100γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
SDMSdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-06-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance