2XEC | pdb_00002xec

Nocardia farcinica maleate cis-trans isomerase bound to TRIS

• PDB DOI: https://doi.org/10.2210/pdb2XEC/pdb

• Classification: ISOMERASE
• Organism(s): Nocardia farcinica IFM 10152
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-13 Released: 2010-08-18 
• Deposition Author(s): Fisch, F., Martinez-Fleites, C., Baudendistel, N., Hauer, B., Turkenburg, J.P., Hart, S., Bruce, N.C., Grogan, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.288 (Depositor), 0.303 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

A Covalent Succinylcysteine-Like Intermediate in the Enzyme-Catalyzed Transformation of Maleate to Fumarate by Maleate Isomerase.

Fisch, F., Fleites, C.M., Delenne, M., Baudendistel, N., Hauer, B., Turkenburg, J.P., Hart, S., Bruce, N.C., Grogan, G.

(2010) J Am Chem Soc 132: 11455

• PubMed: 20677745 
• DOI: https://doi.org/10.1021/ja1053576
• Primary Citation Related Structures: 
  2XEC, 2XED


• PubMed Abstract: 
  

  Maleate isomerase (MI), a member of the Asp/Glu racemase superfamily, catalyzes cis-trans isomerization of the C2-C3 double bond in maleate to yield fumarate. Mutational studies, in conjunction with the structure of the C194A mutant of Nocardia farcinica MI cocrystallized with maleate, have revealed an unprecedented mode of catalysis for the superfamily in which the isomerization reaction is initiated by nucleophilic attack of cysteine at the double bond, yielding a covalent succinylcysteine-like intermediate.

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Organizational Affiliation: 
• York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 115.76 kDa 
• Atom Count: 7,377 
• Modeled Residue Count: 979 
• Deposited Residue Count: 1,092 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE MALEATE ISOMERASE	A, B, C, D	273	Nocardia farcinica IFM 10152	Mutation(s): 0  EC: 5.2.1.1
UniProt
Find proteins for Q5YXQ1 (Nocardia farcinica (strain IFM 10152)) Explore Q5YXQ1  Go to UniProtKB:  Q5YXQ1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth A], G [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CA	F [auth B], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.288 (Depositor), 0.303 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.16	α = 90
b = 84.51	β = 90
c = 238.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Fisch, F., Martinez-Fleites, C., Baudendistel, N., Hauer, B., Turkenburg, J.P., Hart, S., Bruce, N.C., Grogan, G.

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2012-10-03
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description