1KQ7 | pdb_00001kq7

E315Q Mutant Form of Fumarase C from E.coli

• PDB DOI: https://doi.org/10.2210/pdb1KQ7/pdb

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


• Deposited: 2002-01-04 Released: 2002-08-23 
• Deposition Author(s): Weaver, T.M., Estevez, M., Skarda, J., Spencer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.251 (Depositor) 
• R-Value Work: 
  0.179 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

X-ray crystallographic and kinetic correlation of a clinically observed human fumarase mutation.

Estevez, M., Skarda, J., Spencer, J., Banaszak, L., Weaver, T.M.

(2002) Protein Sci 11: 1552-1557

• PubMed: 12021453 
• DOI: https://doi.org/10.1110/ps.0201502
• Primary Citation Related Structures: 
  1KQ7


• PubMed Abstract: 
  

  Fumarase catalyzes the reversible conversion of fumarate to S- malate during the operation of the ubiquitous Kreb's cycle. Previous studies have shown that the active site includes side chains from three of the four subunits within the tetrameric enzyme. We used a clinically observed human mutation to narrow our search for potential catalytic groups within the fumarase active site. Offspring homozygous for the missense mutation, a G-955-C transversion in the fumarase gene, results in the substitution of a glutamine at amino acid 319 for the normal glutamic acid. To more fully understand the implications of this mutation, a single-step site-directed mutagenesis method was used to generate the homologous substitution at position 315 within fumarase C from Escherichia coli. Subsequent kinetic and X-ray crystal structure analyses show changes in the turnover number and the cocrystal structure with bound citrate.

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Organizational Affiliation: 
• Johns Hopkins University, School of Medicine, Department of Neuroscience, Baltimore, Maryland 21205, 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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 101.61 kDa 
• Atom Count: 6,960 
• Modeled Residue Count: 911 
• Deposited Residue Count: 934 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUMARATE HYDRATASE CLASS II	A, B	467	Escherichia coli	Mutation(s): 1  Gene Names: fumc EC: 4.2.1.2
UniProt
Find proteins for P05042 (Escherichia coli (strain K12)) Explore P05042  Go to UniProtKB:  P05042

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D [auth A], E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
MLT	C [auth A]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.251 (Depositor) 
• R-Value Work:  0.179 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.02	α = 90
b = 220	β = 90
c = 86.23	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-GEN	data reduction
X-GEN	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-23 
Deposition Author(s): Weaver, T.M., Estevez, M., Skarda, J., Spencer, J.

Revision History  

• Version 1.0: 2002-08-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-16
  Changes: Data collection, Refinement description