7CIF

Crystal structure of L-methionine decarboxylase from Streptomyces sp.590 (internal aldimine form).

• PDB DOI: https://doi.org/10.2210/pdb7CIF/pdb

• Classification: LYASE
• Organism(s): Streptomyces sp. 590 KI-2014
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-07 Released: 2021-01-27 
• Deposition Author(s): Okawa, A., Shiba, T., Hayashi, M., Onoue, Y., Murota, M., Sato, D., Inagaki, J., Tamura, T., Harada, S., Inagaki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Structural basis for substrate specificity of l-methionine decarboxylase.

Okawa, A., Shiba, T., Hayashi, M., Onoue, Y., Murota, M., Sato, D., Inagaki, J., Tamura, T., Harada, S., Inagaki, K.

(2021) Protein Sci 30: 663-677

• PubMed: 33452696 
• DOI: https://doi.org/10.1002/pro.4027
• Primary Citation of Related Structures:  
  7CIF, 7CIG, 7CII, 7CIJ, 7CIM


• PubMed Abstract: 
  

  l -Methionine decarboxylase (MetDC) from Streptomyces sp. 590 is a vitamin B ₆ -dependent enzyme and catalyzes the non-oxidative decarboxylation of l -methionine to produce 3-methylthiopropylamine and carbon dioxide. We present here the crystal structures of the ligand-free form of MetDC and of several enzymatic reaction intermediates. Group II amino acid decarboxylases have many residues in common around the active site but the residues surrounding the side chain of the substrate differ. Based on information obtained from the crystal structure, and mutational and biochemical experiments, we propose a key role for Gln64 in determining the substrate specificity of MetDC, and for Tyr421 as the acid catalyst that participates in protonation after the decarboxylation reaction.

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Organizational Affiliation: 

Department of Biofunctional Chemistry, Okayama University, Okayama, Japan.

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: 123.41 kDa 
• Atom Count: 8,502 
• Modelled Residue Count: 1,045 
• Deposited Residue Count: 1,114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-methionine decarboxylase	A, B	557	Streptomyces sp. 590 KI-2014	Mutation(s): 0  EC: 4.1.1.57
UniProt
Find proteins for A0A0G4DBU7 (Streptomyces sp. 590 KI-2014) Explore A0A0G4DBU7  Go to UniProtKB:  A0A0G4DBU7

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.631	α = 90
b = 147.499	β = 99.87
c = 53.904	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
CRANK2	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Okawa, A., Shiba, T., Hayashi, M., Onoue, Y., Murota, M., Sato, D., Inagaki, J., Tamura, T., Harada, S., Inagaki, K.

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2021-03-03
  Changes: Database references