4Q31 | pdb_00004q31

The crystal structure of cystathione gamma lyase (CalE6) from Micromonospora echinospora

• PDB DOI: https://doi.org/10.2210/pdb4Q31/pdb

• Classification: LYASE
• Organism(s): Micromonospora echinospora
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-04-10 Released: 2014-05-07 
• Deposition Author(s): Tan, K., Bigelow, L., Jedrzejczak, R., Babnigg, G., Bingman, C.A., Yennamalli, R.M., Singh, S., Kharel, M.K., Thorson, J.S., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

Structural dynamics of a methionine gamma-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate.

Cao, H., Tan, K., Wang, F., Bigelow, L., Yennamalli, R.M., Jedrzejczak, R., Babnigg, G., Bingman, C.A., Joachimiak, A., Kharel, M.K., Singh, S., Thorson, J.S., Phillips, G.N.

(2016) Struct Dyn 3: 034702-034702

• PubMed: 27191010 
• DOI: https://doi.org/10.1063/1.4948539
• Primary Citation Related Structures: 
  4Q31


• PubMed Abstract: 
  

  CalE6 from Micromonospora echinospora is a (pyridoxal 5' phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. We report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.

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Organizational Affiliation: 
• Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA.
Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA.
Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, USA.
Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 335.29 kDa 
• Atom Count: 24,719 
• Modeled Residue Count: 3,018 
• Deposited Residue Count: 3,072 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cystathione gamma lyase CalE6	A, B, C, D, E, F, G, H	384	Micromonospora echinospora	Mutation(s): 1  Gene Names: calE6 EC: 4.4.1.2
UniProt
Find proteins for Q8KNG3 (Micromonospora echinospora) Explore Q8KNG3  Go to UniProtKB:  Q8KNG3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	DA [auth D], EB [auth H], I [auth A], KA [auth E], Q [auth B], QA [auth F], WA [auth G], Y [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	AB [auth G], BA [auth C], BB [auth G], CB [auth G], GA [auth D], HA [auth D], HB [auth H], IA [auth D], JA [auth D], L [auth A], M [auth A], MA [auth E], N [auth A], NA [auth E], O [auth A], OA [auth E], PA [auth E], S [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth F], V [auth B], W [auth B], X [auth B], YA [auth G], ZA [auth G]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	CA [auth C], DB [auth G], IB [auth H], P [auth A], VA [auth F]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	AA [auth C], EA [auth D], FA [auth D], FB [auth H], GB [auth H], J [auth A], K [auth A], LA [auth E], R [auth B], RA [auth F], XA [auth G], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 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
MSE	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.855	α = 90
b = 146.981	β = 90
c = 349.905	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-07 
Deposition Author(s): Tan, K., Bigelow, L., Jedrzejczak, R., Babnigg, G., Bingman, C.A., Yennamalli, R.M., Singh, S., Kharel, M.K., Thorson, J.S., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Revision History  

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2017-03-08
  Changes: Database references
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary