6NZC | pdb_00006nzc

Crystal structure of E. coli fumarase C N326A variant with closed SS Loop at 1.40 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6NZC/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-02-13 Released: 2019-09-25 
• Deposition Author(s): Weaver, T.M., May, J.F., Bhattacharyya, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.161 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Closed fumarase C active-site structures reveal SS Loop residue contribution in catalysis.

Stuttgen, G.M., Grosskopf, J.D., Berger, C.R., May, J.F., Bhattacharyya, B., Weaver, T.M.

(2020) FEBS Lett 594: 337-357

• PubMed: 31514245 
• DOI: https://doi.org/10.1002/1873-3468.13603
• Primary Citation Related Structures: 
  6NZ9, 6NZA, 6NZB, 6NZC


• PubMed Abstract: 
  

  Fumarase C (FumC) catalyzes the reversible conversion of fumarate to S-malate. Previous structural investigations within the superfamily have reported a dynamic structural segment, termed the SS Loop. To date, active-site asymmetry has raised the question of how SS Loop placement affects participation of key residues during the reaction. Herein, we report structural and kinetic analyses from Escherichia coli FumC variants to understand the contribution of SS Loop residues S318, K324, and N326. High-resolution X-ray crystallographic results reveal three distinct FumC active-site conformations; disordered-open, ordered-open, and the newly discovered ordered-closed. Surprisingly, each SS Loop variant has unaffected Michaelis constants coupled to reductions in turnover number. Based upon our structural and functional analyses, we propose structural and catalytic roles for each of the aforementioned residues.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University Wisconsin - La Crosse, WI, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 102.78 kDa 
• Atom Count: 8,117 
• Modeled Residue Count: 920 
• Deposited Residue Count: 944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fumarate hydratase class II	A, B	472	Escherichia coli K-12	Mutation(s): 1  Gene Names: fumC, b1611, JW1603 EC: 4.2.1.2
UniProt
Find proteins for P05042 (Escherichia coli (strain K12)) Explore P05042  Go to UniProtKB:  P05042

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], D [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.161 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.819	α = 90
b = 217.389	β = 90
c = 86.109	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Weaver, T.M., May, J.F., Bhattacharyya, B.

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2020-02-12
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description