Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59574.75 
• Atom Count: 4188 
• Residue Count: 524 
• Unique protein chains: 1

3IVZ

Crystal structure of hyperthermophilic nitrilase

• DOI: 10.2210/pdb3IVZ/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus abyssi (strain GE5 / Orsay)
• Expression System: Escherichia coli


• Deposited: 2009-09-02 Released: 2010-09-22 
• Deposition Author(s): Raczynska, J., Vorgias, C., Antranikian, G., Rypniewski, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.176 
• R-Value Work: 0.131 

Literature

Crystallographic analysis of a thermoactive nitrilase.

Raczynska, J.E., Vorgias, C.E., Antranikian, G., Rypniewski, W.

(2010) J.Struct.Biol. 173: 294-302

• PubMed: 21095228 
• DOI: 10.1016/j.jsb.2010.11.017
• Primary Citation of Related Structures:  
  3KLC, 3KI8, 3IW3


• PubMed Abstract: 
  

The nitrilase superfamily is a large and diverse superfamily of enzymes that catalyse the cleavage of various types of carbon-nitrogen bonds using a Cys-Glu-Lys catalytic triad. Thermoactive nitrilase from Pyrococcus abyssi (PaNit) hydrolyses small aliphatic nitriles like fumaro- and malononitryl. Yet, the biological role of this enzyme is unknown. We have analysed several crystal structures of PaNit: without ligands, with an acetate ion bound in the active site and with a bromide ion in the active site. In addition, docking calculations have been performed for fumaro- and malononitriles. The structures provide a proof for specific binding of the carboxylate ion and a general affinity for negatively changed ligands. The role of residues in the active site is considered and an enzymatic reaction mechanism is proposed in which Cys146 acts as the nucleophile, Glu42 as the general base, Lys113/Glu42 as the general acid, WatA as the hydrolytic water and Nζ_Lys113 and N_Phe147 form the oxyanion hole.

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Organizational Affiliation: 

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Nitrilase	A, B	262	Pyrococcus abyssi (strain GE5 / Orsay)	Mutation(s): 0  EC: 3.5.5.1
Find proteins for Q9UYV8 (Pyrococcus abyssi (strain GE5 / Orsay)) Go to UniProtKB:  Q9UYV8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.176 
• R-Value Work: 0.131 
• Space Group: P 4₁

Unit Cell:

Length (Å)	Angle (°)
a = 59.174	α = 90.00
b = 59.174	β = 90.00
c = 127.220	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
SCALEPACK	data scaling
ADSC	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-02 
• Released Date: 2010-09-22 
• Deposition Author(s): Raczynska, J., Vorgias, C., Antranikian, G., Rypniewski, W.

Revision History 

• Version 1.0: 2010-09-22
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Source and taxonomy, Version format compliance