1ELU | pdb_00001elu

COMPLEX BETWEEN THE CYSTINE C-S LYASE C-DES AND ITS REACTION PRODUCT CYSTEINE PERSULFIDE.

• PDB DOI: https://doi.org/10.2210/pdb1ELU/pdb

• Classification: LYASE
• Organism(s): Synechocystis sp. PCC 6714
• Expression System: Bacteria
• Mutation(s): Yes 


• Deposited: 2000-03-14 Released: 2000-04-19 
• Deposition Author(s): Clausen, T., Kaiser, J.T., Steegborn, C., Huber, R., Kessler, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Crystal structure of the cystine C-S lyase from Synechocystis: stabilization of cysteine persulfide for FeS cluster biosynthesis.

Clausen, T., Kaiser, J.T., Steegborn, C., Huber, R., Kessler, D.

(2000) Proc Natl Acad Sci U S A 97: 3856-3861

• PubMed: 10760256 
• DOI: https://doi.org/10.1073/pnas.97.8.3856
• Primary Citation Related Structures: 
  1ELQ, 1ELU


• PubMed Abstract: 
  

  FeS clusters are versatile cofactors of a variety of proteins, but the mechanisms of their biosynthesis are still unknown. The cystine C-S lyase from Synechocystis has been identified as a participant in ferredoxin FeS cluster formation. Herein, we report on the crystal structure of the lyase and of a complex with the reaction products of cystine cleavage at 1.8- and 1.55-A resolution, respectively. The sulfur-containing product was unequivocally identified as cysteine persulfide. The reactive persulfide group is fixed by a hydrogen bond to His-114 in the center of a hydrophobic pocket and is thereby shielded from the solvent. Binding and stabilization of the cysteine persulfide represent an alternative to the generation of a protein-bound persulfide by NifS-like proteins and point to the general importance of persulfidic compounds for FeS cluster assembly.

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Organizational Affiliation: 
• Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany. [e-mail]

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: 86.57 kDa 
• Atom Count: 6,680 
• Modeled Residue Count: 762 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-CYSTEINE/L-CYSTINE C-S LYASE	A, B	390	Synechocystis sp. PCC 6714	Mutation(s): 8
UniProt
Find proteins for A0ACD6B834 (Synechocystis sp. (strain PCC 6714)) Explore A0ACD6B834  Go to UniProtKB:  A0ACD6B834

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PDA	D [auth A], G [auth B]	2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID C11 H17 N2 O7 P WACJCHFWJNNBPR-ZETCQYMHSA-N
CSS	E [auth A]	S-MERCAPTOCYSTEINE C3 H7 N O2 S2 XBKONSCREBSMCS-REOHCLBHSA-N
K	C [auth A], F [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.448	α = 90
b = 65.386	β = 90
c = 170.532	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-04-19 
Deposition Author(s): Clausen, T., Kaiser, J.T., Steegborn, C., Huber, R., Kessler, D.

Revision History  

• Version 1.0: 2000-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-11-03
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-02-07
  Changes: Data collection