4K6N | pdb_00004k6n

Crystal structure of yeast 4-amino-4-deoxychorismate lyase

• PDB DOI: https://doi.org/10.2210/pdb4K6N/pdb

• Classification: LYASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-16 Released: 2013-07-10 
• Deposition Author(s): Dai, Y.-N., Chi, C.-B., Zhou, K., Cheng, W., Jiang, Y.-L., Ren, Y.-M., Chen, Y., Zhou, C.-Z.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Structure and catalytic mechanism of yeast 4-amino-4-deoxychorismate lyase

Dai, Y.-N., Chi, C.-B., Zhou, K., Cheng, W., Jiang, Y.-L., Ren, Y.-M., Ruan, K., Chen, Y., Zhou, C.-Z.

(2013) J Biological Chem 288: 22985-22992

• PubMed: 23818518 
• DOI: https://doi.org/10.1074/jbc.M113.480335
• Primary Citation Related Structures: 
  4K6N


• PubMed Abstract: 
  

  Saccharomyces cerevisiae Abz2 is a pyridoxal 5'-phosphate (PLP)-dependent lyase that converts 4-amino-4-deoxychorismate (ADC) to para-aminobenzoate and pyruvate. To investigate the catalytic mechanism, we determined the 1.9 Å resolution crystal structure of Abz2 complexed with PLP, representing the first eukaryotic ADC lyase structure. Unlike Escherichia coli ADC lyase, whose dimerization is critical to the formation of the active site, the overall structure of Abz2 displays as a monomer of two domains. At the interdomain cleft, a molecule of cofactor PLP forms a Schiff base with residue Lys-251. Computational simulations defined a basic clamp to orientate the substrate ADC in a proper pose, which was validated by site-directed mutageneses combined with enzymatic activity assays. Altogether, we propose a putative catalytic mechanism of a unique class of monomeric ADC lyases led by yeast Abz2.

---

Organizational Affiliation: 
• Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 44.08 kDa 
• Atom Count: 3,090 
• Modeled Residue Count: 352 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminodeoxychorismate lyase	A	383	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: ABZ2, YMR289W EC: 4.1.3.38
UniProt
Find proteins for Q03266 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q03266  Go to UniProtKB:  Q03266

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.966	α = 90
b = 113.893	β = 90
c = 86.004	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-10 
Deposition Author(s): Dai, Y.-N., Chi, C.-B., Zhou, K., Cheng, W., Jiang, Y.-L., Ren, Y.-M., Chen, Y., Zhou, C.-Z.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2013-10-16
  Changes: Database references
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary