5FAV | pdb_00005fav

E491Q mutant of choline TMA-lyase

• PDB DOI: https://doi.org/10.2210/pdb5FAV/pdb

• Classification: LYASE
• Organism(s): Oleidesulfovibrio alaskensis G20
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-12-12 Released: 2016-09-28 
• Deposition Author(s): Funk, M.A., Drennan, C.L.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.178 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Molecular Basis of C-N Bond Cleavage by the Glycyl Radical Enzyme Choline Trimethylamine-Lyase.

Bodea, S., Funk, M.A., Balskus, E.P., Drennan, C.L.

(2016) Cell Chem Biol 23: 1206-1216

• PubMed: 27642068 
• DOI: https://doi.org/10.1016/j.chembiol.2016.07.020
• Primary Citation Related Structures: 
  5FAU, 5FAV, 5FAW, 5FAY, 5KDP


• PubMed Abstract: 
  

  Deamination of choline catalyzed by the glycyl radical enzyme choline trimethylamine-lyase (CutC) has emerged as an important route for the production of trimethylamine, a microbial metabolite associated with both human disease and biological methane production. Here, we have determined five high-resolution X-ray structures of wild-type CutC and mechanistically informative mutants in the presence of choline. Within an unexpectedly polar active site, CutC orients choline through hydrogen bonding with a putative general base, and through close interactions between phenolic and carboxylate oxygen atoms of the protein scaffold and the polarized methyl groups of the trimethylammonium moiety. These structural data, along with biochemical analysis of active site mutants, support a mechanism that involves direct elimination of trimethylamine. This work broadens our understanding of radical-based enzyme catalysis and will aid in the rational design of inhibitors of bacterial trimethylamine production.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts, Avenue 68-680, Cambridge, MA 02139, USA.
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA. Electronic address: [e-mail].
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts, Avenue 68-680, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: [e-mail].

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 184.16 kDa 
• Atom Count: 15,213 
• Modeled Residue Count: 1,609 
• Deposited Residue Count: 1,630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline trimethylamine-lyase	A, B	815	Oleidesulfovibrio alaskensis G20	Mutation(s): 1  Gene Names: Dde_3282 EC: 4.3.99.4
UniProt
Find proteins for Q30W70 (Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20)) Explore Q30W70  Go to UniProtKB:  Q30W70

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
NA	C [auth A], I [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.178 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 228.922	α = 90
b = 228.922	β = 90
c = 78.924	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-28 
Deposition Author(s): Funk, M.A., Drennan, C.L.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	0645960

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2016-11-02
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2017-11-01
  Changes: Author supporting evidence
• Version 1.4: 2019-11-27
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description