Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.26 kDa 
• Atom Count: 2137 
• Residue Count: 258 
• Unique protein chains: 1

1OBT

STRUCTURE OF RICIN A CHAIN MUTANT, COMPLEX WITH AMP

• DOI: 10.2210/pdb1OBT/pdb

• Classification: GLYCOSIDASE
• Organism(s): Ricinus communis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1996-06-22 Released: 1997-06-16 
• Deposition Author(s): Day, P.J., Ernst, S.R., Frankel, A.E., Monzingo, A.F., Pascal, J.M., Svinth, M., Robertus, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

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

• PubMed: 8780513 
• DOI: 10.1021/bi960880n
• Primary Citation of Related Structures:  
  1OBT, 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RICIN A CHAIN	A	267	Ricinus communis	Mutation(s): 1  EC: 3.2.2.22
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	A	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.65	α = 90
b = 68.65	β = 90
c = 141.1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
SDMS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-06-22 
• Released Date: 1997-06-16 
Deposition Author(s): Day, P.J., Ernst, S.R., Frankel, A.E., Monzingo, A.F., Pascal, J.M., Svinth, M., Robertus, J.D.

Revision History 

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