Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: gel filtration

Macromolecule Content

• Total Structure Weight: 29.77 kDa 
• Atom Count: 2565 
• Modelled Residue Count: 254 
• Deposited Residue Count: 262 
• Unique protein chains: 1

6UBQ

Crystal Structure of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to 4-Androstenedione at 100 K

• PDB DOI: 10.2210/pdb6UBQ/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-12 Released: 2020-09-23 
• Deposition Author(s): Yabukarski, F., Herschlag, D.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.170 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 

Literature

Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles.

Yabukarski, F., Biel, J.T., Pinney, M.M., Doukov, T., Powers, A.S., Fraser, J.S., Herschlag, D.

(2020) Proc Natl Acad Sci U S A 117: 33204-33215

• PubMed: 33376217 
• DOI: 10.1073/pnas.2011350117
• Primary Citation of Related Structures:  
  6TZD, 6U1Z, 6U4I, 6UBQ, 6UCN, 6UCW, 6UCY


• PubMed Abstract: 
  

How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes position catalytic and reactant groups in active sites, physics requires that atoms undergo constant motion. Numerous proposals have invoked positioning or motions as central for enzyme function, but a scarcity of experimental data has limited our understanding of positioning and motion, their relative importance, and their changes through the enzyme's reaction cycle. To examine positioning and motions and test catalytic proposals, we collected "room temperature" X-ray crystallography data for Pseudomonas putida ketosteroid isomerase (KSI), and we obtained conformational ensembles for this and a homologous KSI from multiple PDB crystal structures. Ensemble analyses indicated limited change through KSI's reaction cycle. Active site positioning was on the 1- to 1.5-Å scale, and was not exceptional compared to noncatalytic groups. The KSI ensembles provided evidence against catalytic proposals invoking oxyanion hole geometric discrimination between the ground state and transition state or highly precise general base positioning. Instead, increasing or decreasing positioning of KSI's general base reduced catalysis, suggesting optimized Ångstrom-scale conformational heterogeneity that allows KSI to efficiently catalyze multiple reaction steps. Ensemble analyses of surrounding groups for WT and mutant KSIs provided insights into the forces and interactions that allow and limit active-site motions. Most generally, this ensemble perspective extends traditional structure-function relationships, providing the basis for a new era of "ensemble-function" interrogation of enzymes.

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Organizational Affiliation: 

Department of Chemical Engineering, Stanford University, Stanford, CA 94305.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroid Delta-isomerase	A, B	131	Pseudomonas putida	Mutation(s): 0  Gene Names: ksi EC: 5.3.3.1
UniProt
Find proteins for P07445 (Pseudomonas putida) Explore P07445  Go to UniProtKB:  P07445

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASD (Subject of Investigation/LOI)	C [auth A], E [auth B]	4-ANDROSTENE-3-17-DIONE C19 H26 O2 AEMFNILZOJDQLW-QAGGRKNESA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.170 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.209	α = 90
b = 74.316	β = 90
c = 95.562	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-09-12 
• Released Date: 2020-09-23 
Deposition Author(s): Yabukarski, F., Herschlag, D.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1714723

Revision History  

• Version 1.0: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2021-03-17
  Changes: Database references