Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 61.38 kDa 
• Atom Count: 4044 
• Modelled Residue Count: 497 
• Deposited Residue Count: 562 
• Unique protein chains: 1

4FQ5

Crystal structure of the maleate isomerase Iso(C200A) from Pseudomonas putida S16 with maleate

• PDB DOI: 10.2210/pdb4FQ5/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas putida S16
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-06-25 Released: 2013-07-24 
• Deposition Author(s): Lu, Y., Chen, D., Zhang, Z., Li, Q., Wu, G., Xu, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.241 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Structural and computational studies of the maleate isomerase from Pseudomonas putida S16 reveal a breathing motion wrapping the substrate inside.

Chen, D., Tang, H., Lu, Y., Zhang, Z., Shen, K., Lin, K., Zhao, Y.L., Wu, G., Xu, P.

(2013) Mol Microbiol 87: 1237-1244

• PubMed: 23347155 
• DOI: 10.1111/mmi.12163
• Primary Citation of Related Structures:  
  4FQ5, 4FQ7


• PubMed Abstract: 
  

Nicotine is an environmental toxicant in tobacco waste, imposing a serious hazard for human health. Some bacteria including Pseudomonas spp. strains are able to metabolize nicotine to non-toxic compounds. The pyrrolidine pathway of nicotine degradation in Pseudomonas putida S16 has recently been revealed. The maleate isomerase (Pp-Iso) catalyses the last step in nicotine degradation of P. putida S16, the cis-trans isomerization of maleate to fumarate. In this study, we determined the crystal structures of both wild type isomerase by itself and its C200A point mutant in complex with its substrate maleate, to resolutions of 2.95 Å and 2.10 Å respectively. Our structures reveal that Asn17 and Asn169 play critical roles in recognizing the maleate by site-directed mutants' analysis. Surprisingly, our structure shows that the maleate is completely wrapped inside the isomerase. Examination of the structure prompted us to hypothesize that the β2-α2 loop and the β6-α7 loop have a breathing motion that regulates substrate/solvent entry and product departure. Our results of molecular dynamics simulation and enzymatic activity assay are fully consistent with this hypothesis. The isomerase probably uses this breathing motion to prevent the solvent from entering the active site and prohibit unproductive side reactions from happening.

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Organizational Affiliation: 

State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maleate cis-trans isomerase	B [auth A], A [auth B]	281	Pseudomonas putida S16	Mutation(s): 1  Gene Names: PPS_4060, maiA EC: 5.2.1.1
UniProt
Find proteins for F8G0M3 (Pseudomonas putida (strain S16)) Explore F8G0M3  Go to UniProtKB:  F8G0M3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAE	C [auth B], D [auth A]	MALEIC ACID C4 H4 O4 VZCYOOQTPOCHFL-UPHRSURJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.241 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.725	α = 90
b = 66.725	β = 90
c = 421.606	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-25 
• Released Date: 2013-07-24 
Deposition Author(s): Lu, Y., Chen, D., Zhang, Z., Li, Q., Wu, G., Xu, P.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description