Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 95.40 kDa 
• Atom Count: 6463 
• Modelled Residue Count: 788 
• Deposited Residue Count: 864 
• Unique protein chains: 1

3A9X

Crystal structure of rat selenocysteine lyase

• PDB DOI: 10.2210/pdb3A9X/pdb

• Classification: LYASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-08 Released: 2010-03-16 
• Deposition Author(s): Omi, R., Hirotsu, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.197 

Literature

Reaction mechanism and molecular basis for selenium/sulfur discrimination of selenocysteine lyase.

Omi, R., Kurokawa, S., Mihara, H., Hayashi, H., Goto, M., Miyahara, I., Kurihara, T., Hirotsu, K., Esaki, N.

(2010) J Biol Chem 285: 12133-12139

• PubMed: 20164179 
• DOI: 10.1074/jbc.M109.084475
• Primary Citation of Related Structures:  
  3A9X, 3A9Y, 3A9Z


• PubMed Abstract: 
  

Selenocysteine lyase (SCL) catalyzes the pyridoxal 5'-phosphate-dependent removal of selenium from l-selenocysteine to yield l-alanine. The enzyme is proposed to function in the recycling of the micronutrient selenium from degraded selenoproteins containing selenocysteine residue as an essential component. The enzyme exhibits strict substrate specificity toward l-selenocysteine and no activity to its cognate l-cysteine. However, it remains unclear how the enzyme distinguishes between selenocysteine and cysteine. Here, we present mechanistic studies of selenocysteine lyase from rat. ESI-MS analysis of wild-type and C375A mutant SCL revealed that the catalytic reaction proceeds via the formation of an enzyme-bound selenopersulfide intermediate on the catalytically essential Cys-375 residue. UV-visible spectrum analysis and the crystal structure of SCL complexed with l-cysteine demonstrated that the enzyme reversibly forms a nonproductive adduct with l-cysteine. Cys-375 on the flexible loop directed l-selenocysteine, but not l-cysteine, to the correct position and orientation in the active site to initiate the catalytic reaction. These findings provide, for the first time, the basis for understanding how trace amounts of a selenium-containing substrate is distinguished from excessive amounts of its cognate sulfur-containing compound in a biological system.

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Organizational Affiliation: 

Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Selenocysteine lyase	A, B	432	Rattus norvegicus	Mutation(s): 0  Gene Names: Scly EC: 4.4.1.16
UniProt
Find proteins for Q68FT9 (Rattus norvegicus) Explore Q68FT9  Go to UniProtKB:  Q68FT9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PO4	E [auth B], F [auth B], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.445	α = 90
b = 102.771	β = 90
c = 197.753	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-11-08 
• Released Date: 2010-03-16 
Deposition Author(s): Omi, R., Hirotsu, K.

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-10-30
  Changes: Database references