6NI4

Pseudomonas fluorescens isocyanide hydratase at 277 K G150T mutant

• PDB DOI:  https://doi.org/10.2210/pdb6NI4/pdb

• Classification: LYASE
• Organism(s): Pseudomonas protegens Pf-5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-12-26 Released: 2019-11-20 
• Deposition Author(s): Wilson, M.A., Dasgupta, M., van den Bedem, H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.128 
• R-Value Work: 0.110 
• R-Value Observed: 0.111 

Literature

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.

Dasgupta, M., Budday, D., de Oliveira, S.H.P., Madzelan, P., Marchany-Rivera, D., Seravalli, J., Hayes, B., Sierra, R.G., Boutet, S., Hunter, M.S., Alonso-Mori, R., Batyuk, A., Wierman, J., Lyubimov, A., Brewster, A.S., Sauter, N.K., Applegate, G.A., Tiwari, V.K., Berkowitz, D.B., Thompson, M.C., Cohen, A.E., Fraser, J.S., Wall, M.E., van den Bedem, H., Wilson, M.A.

(2019) Proc Natl Acad Sci U S A 116: 25634-25640

• PubMed: 31801874 
• DOI: https://doi.org/10.1073/pnas.1901864116
• Primary Citation of Related Structures:  
  6NI4, 6NI5, 6NI6, 6NI7, 6NI9, 6NIA, 6NPQ, 6UND, 6UNF


• PubMed Abstract: 
  

How changes in enzyme structure and dynamics facilitate passage along the reaction coordinate is a fundamental unanswered question. Here, we use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL), ambient-temperature X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent catalysis modulates isocyanide hydratase (ICH) conformational dynamics throughout its catalytic cycle. We visualize this previously hypothetical reaction mechanism, directly observing formation of a thioimidate covalent intermediate in ICH microcrystals during catalysis. ICH exhibits a concerted helical displacement upon active-site cysteine modification that is gated by changes in hydrogen bond strength between the cysteine thiolate and the backbone amide of the highly strained Ile152 residue. These catalysis-activated motions permit water entry into the ICH active site for intermediate hydrolysis. Mutations at a Gly residue (Gly150) that modulate helical mobility reduce ICH catalytic turnover and alter its pre-steady-state kinetic behavior, establishing that helical mobility is important for ICH catalytic efficiency. These results demonstrate that MISC can capture otherwise elusive aspects of enzyme mechanism and dynamics in microcrystalline samples, resolving long-standing questions about the connection between nonequilibrium protein motions and enzyme catalysis.

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Organizational Affiliation: 

Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, NE 68588; [e-mail] [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 24.22 kDa 
• Atom Count: 2,017 
• Modelled Residue Count: 226 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isonitrile hydratase InhA	A	231	Pseudomonas protegens Pf-5	Mutation(s): 1  Gene Names: inhA, PFL_4109
UniProt
Find proteins for Q4K977 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4K977  Go to UniProtKB:  Q4K977

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.128 
• R-Value Work: 0.110 
• R-Value Observed: 0.111 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.11	α = 90
b = 59.744	β = 115.86
c = 56.125	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Wilson, M.A., Dasgupta, M., van den Bedem, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM123159

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence, Database references