3QXE

Crystal Structure of Co-type Nitrile Hydratase from Pseudomonas putida.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evidence of the Participation of Remote Residues in the Catalytic Activity of Co-Type Nitrile Hydratase from Pseudomonas putida.

Brodkin, H.R.Novak, W.R.Milne, A.C.D'Aquino, J.A.Karabacak, N.M.Goldberg, I.G.Agar, J.N.Payne, M.S.Petsko, G.A.Ondrechen, M.J.Ringe, D.

(2011) Biochemistry 50: 4923-4935

  • DOI: 10.1021/bi101761e
  • Primary Citation of Related Structures:  
    3QXE, 3QZ5, 3QZ9, 3QYG, 3QYH

  • PubMed Abstract: 
  • Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell and these in turn interact with residues in a third shell. These residues in the second and t ...

    Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell and these in turn interact with residues in a third shell. These residues in the second and third layers may have distinct roles in maintaining the essential chemical properties of the first-shell catalytic residues, particularly their spatial arrangement relative to the substrate binding pocket, and their electrostatic and dynamic properties. The extent to which these remote residues participate in catalysis and precisely how they affect first-shell residues remains unexplored. To improve our understanding of the roles of second- and third-shell residues in catalysis, we used THEMATICS to identify residues in the second and third shells of the Co-type nitrile hydratase from Pseudomonas putida (ppNHase) that may be important for catalysis. Five of these predicted residues, and three additional, conserved residues that were not predicted, have been conservatively mutated, and their effects have been studied both kinetically and structurally. The eight residues have no direct contact with the active site metal ion or bound substrate. These results demonstrate that three of the predicted second-shell residues (α-Asp164, β-Glu56, and β-His147) and one predicted third-shell residue (β-His71) have significant effects on the catalytic efficiency of the enzyme. One of the predicted residues (α-Glu168) and the three residues not predicted (α-Arg170, α-Tyr171, and β-Tyr215) do not have any significant effects on the catalytic efficiency of the enzyme.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology and Institute for Complex Scientific Software, Northeastern University, Boston, Massachusetts 02115, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Co-type Nitrile Hydratase alpha subunitACEG226Pseudomonas putidaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Co-type Nitrile Hydratase beta subunitBDFH219Pseudomonas putidaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, B, C, D, E, F, G, H
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
3CO
Query on 3CO

Download CCD File 
A, C, E, G
COBALT (III) ION
Co
JAWGVVJVYSANRY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A,C,E,GL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.202α = 90
b = 137.428β = 92.32
c = 85.384γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
PHENIXrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description