Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.32 kDa 
• Atom Count: 2127 
• Modelled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

1NLI

Complex of [E160A-E189A] trichosanthin and adenine

• DOI: 10.2210/pdb1NLI/pdb

• Classification: HYDROLASE
• Organism(s): Trichosanthes kirilowii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-01-07 Released: 2003-01-21 
• Deposition Author(s): Shaw, P.C., Wong, K.B., Chan, D.S.B., Williams, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.208 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Literature

Structural basis for the interaction of [E160A-E189A]-trichosanthin with adenine.

Shaw, P.C., Wong, K.B., Chan, D.S., Williams, R.L.

(2003) Toxicon 41: 575-581

• PubMed: 12676436 
• DOI: 10.1016/s0041-0101(02)00387-2
• Primary Citation of Related Structures:  
  1NLI


• PubMed Abstract: 
  

Trichosanthin is a ribosome-inactivating protein that cleaves specifically the N-glycosidic bond of A-4324 of 28S rRNA. Trichosanthin and its variant [E160A-E189A]-trichosanthin were found to bind an adenine base with a K(d) value of approximately 0.2mM. To determine how this doubly mutated variant of trichosanthin interacts with adenine, the co-crystal structure of [E160A-E189A]-trichosanthin and adenine was resolved to 0.193nm which revealed that the active site conformation of the doubly mutated variant is isomorphous to wild-type trichosanthin. Water molecules were found at locations corresponding to the eliminated side chain of Glu-160 and Glu-189. On the other hand, the adenine base interacted with [E160A-E189A]-trichosanthin in a manner similar to that in wild-type trichosanthin. Our structural analysis illustrates that Glu-160 and Glu-189 in trichosanthin do not play an important role in maintaining the active site conformation and binding adenine, an essential step for substrate-enzyme interaction. On the other hand, removal of two glutamate residues changed a large patch of negatively charged surface to a positive charge, which may account for the destabilization of the oxocarbenium-like transition-state and the significant decrease in ribosome-inactivating activity in [E160A-E189A]-trichosanthin.

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Organizational Affiliation: 

Department of Biochemistry, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, People's Republic of China. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-inactivating protein alpha-trichosanthin	A	248	Trichosanthes kirilowii	Mutation(s): 2  Gene Names: Trichosanthin EC: 3.2.2.22
Find proteins for P09989 (Trichosanthes kirilowii) Explore P09989  Go to UniProtKB:  P09989

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	A	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ADE	Kd:  260000   nM  Binding MOAD
ADE	Kd :  260000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.208 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.928	α = 90
b = 75.299	β = 90
c = 78.65	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
TRUNCATE	data reduction
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-07 
• Released Date: 2003-01-21 
Deposition Author(s): Shaw, P.C., Wong, K.B., Chan, D.S.B., Williams, R.L.

Revision History  

• Version 1.0: 2003-01-21
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance