3MVE

Crystal structure of a novel pyruvate decarboxylase

• PDB DOI: https://doi.org/10.2210/pdb3MVE/pdb

• Classification: LYASE
• Organism(s): Vibrio vulnificus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-04 Released: 2011-05-18 
• Deposition Author(s): Cha, S.S., Jeong, C.S., An, Y.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.229 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

Literature

FrsA functions as a cofactor-independent decarboxylase to control metabolic flux.

Lee, K.J., Jeong, C.S., An, Y.J., Lee, H.J., Park, S.J., Seok, Y.J., Kim, P., Lee, J.H., Lee, K.H., Cha, S.S.

(2011) Nat Chem Biol 7: 434-436

• PubMed: 21623357 
• DOI: https://doi.org/10.1038/nchembio.589
• Primary Citation of Related Structures:  
  3MVE, 3OUR


• PubMed Abstract: 
  

  The interaction between fermentation-respiration switch (FrsA) protein and glucose-specific enzyme IIA(Glc) increases glucose fermentation under oxygen-limited conditions. We show that FrsA converts pyruvate to acetaldehyde and carbon dioxide in a cofactor-independent manner and that its pyruvate decarboxylation activity is enhanced by the dephosphorylated form of IIA(Glc) (d-IIA(Glc)). Crystal structures of FrsA and its complex with d-IIA(Glc) revealed residues required for catalysis as well as the structural basis for the activation by d-IIA(Glc).

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Organizational Affiliation: 

Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, Republic of Korea.

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)

Macromolecule Content

• Total Structure Weight: 95.25 kDa 
• Atom Count: 6,505 
• Modelled Residue Count: 791 
• Deposited Residue Count: 830 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0255 protein VV1_0328	A, B	415	Vibrio vulnificus	Mutation(s): 0  Gene Names: frsA, VV1_0328
UniProt
Find proteins for Q8DF91 (Vibrio vulnificus (strain CMCP6)) Explore Q8DF91  Go to UniProtKB:  Q8DF91

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], P [auth B], Q [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.229 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.834	α = 90
b = 88.201	β = 106.62
c = 79.629	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-18 
Deposition Author(s): Cha, S.S., Jeong, C.S., An, Y.J.

Revision History  

• Version 1.0: 2011-05-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-12-17
  Changes: Experimental preparation
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations