3IVZ | pdb_00003ivz

Crystal structure of hyperthermophilic nitrilase

• PDB DOI: https://doi.org/10.2210/pdb3IVZ/pdb

• Classification: HYDROLASE
• Organism(s): Pyrococcus abyssi GE5
• Expression System: Escherichia coli
• Mutation(s): No 


• 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 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.132 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1016/j.jsb.2010.11.017
• Primary Citation Related Structures: 
  3IVZ, 3IW3, 3KI8, 3KLC


• 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.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 59.57 kDa 
• Atom Count: 4,314 
• Modeled Residue Count: 522 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrilase	A, B	262	Pyrococcus abyssi GE5	Mutation(s): 0  Gene Names: nit-30, PAB1449, PYRAB13990 EC: 3.5.1.6 (PDB Primary Data), 3.5.5.1 (UniProt)
UniProt
Find proteins for Q9UYV8 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9UYV8  Go to UniProtKB:  Q9UYV8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth 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 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.132 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.174	α = 90
b = 59.174	β = 90
c = 127.22	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description