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)

Biological Assembly 2  

 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 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 336.62 kDa 
• Atom Count: 24441 
• Modelled Residue Count: 2939 
• Deposited Residue Count: 3112 
• Unique protein chains: 1

4U1T

The crystal structure of holo CalE6, a methionine gamma lyase from Micromonospora echinospora

• PDB DOI: 10.2210/pdb4U1T/pdb

• Classification: LYASE
• Organism(s): Micromonospora echinospora
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-16 Released: 2015-01-14 
• Deposition Author(s): Song, H.G., Guo, Z.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.184 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 

Literature

Identification and Characterization of a Methionine gamma-Lyase in the Calicheamicin Biosynthetic Cluster of Micromonospora echinospora

Song, H., Xu, R., Guo, Z.

(2015) Chembiochem 16: 100-109

• PubMed: 25404066 
• DOI: 10.1002/cbic.201402489
• Primary Citation of Related Structures:  
  4U1T, 4U2H


• PubMed Abstract: 
  

CalE6 is a previously uncharacterized protein involved in the biosynthesis of calicheamicins in Micromonospora echinospora. It is a pyridoxal-5'-phosphate-dependent enzyme and exhibits high sequence homology to cystathionine γ-lyases and cystathionine γ-synthases. However, it was found to be active towards methionine and to convert this amino acid into α-ketobutyrate, ammonium, and methanethiol. The crystal structure of the cofactor-bound holoenzyme was resolved at 2.0 Å; it contains two active site residues, Gly105 and Val322, specific for methionine γ-lyases. Modeling of methionine into the active site allows identification of the active site residues responsible for substrate recognition and catalysis. These findings support that CalE6 is a putative methionine γ-lyase producing methanethiol as a building block in biosynthesis of calicheamicins.

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Organizational Affiliation: 

Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong).

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CalE6	A, B, C, D, E, F, G, H	389	Micromonospora echinospora	Mutation(s): 0  Gene Names: calE6 EC: 4.4.1.11
UniProt
Find proteins for Q8KNG3 (Micromonospora echinospora) Explore Q8KNG3  Go to UniProtKB:  Q8KNG3

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.184 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.17	α = 90
b = 146.22	β = 90
c = 348.091	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
iMOSFLM	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-07-16 
• Released Date: 2015-01-14 
Deposition Author(s): Song, H.G., Guo, Z.H.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release