5CEF

Cystal structure of aspartate semialdehyde dehydrogenase from Cryptococcus neoformans

• PDB DOI: https://doi.org/10.2210/pdb5CEF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cryptococcus neoformans var. neoformans JEC21
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-06 Released: 2015-11-18 
• Deposition Author(s): Dahal, G.P., Viola, R.E.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.220 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Structure of a fungal form of aspartate semialdehyde dehydrogenase from Cryptococcus neoformans.

Dahal, G., Viola, R.E.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1365-1371

• PubMed: 26527262 
• DOI: https://doi.org/10.1107/S2053230X15017495
• Primary Citation of Related Structures:  
  5CEF


• PubMed Abstract: 
  

  Aspartate semialdehyde dehydrogenase (ASADH) functions at a critical junction in the aspartate-biosynthetic pathway and represents a valid target for antimicrobial drug design. This enzyme catalyzes the NADPH-dependent reductive dephosphorylation of β-aspartyl phosphate to produce the key intermediate aspartate semialdehyde. Production of this intermediate represents the first committed step in the biosynthesis of the essential amino acids methionine, isoleucine and threonine in fungi, and also the amino acid lysine in bacteria. The structure of a new fungal form of ASADH from Cryptococcus neoformans has been determined to 2.6 Å resolution. The overall structure of CnASADH is similar to those of its bacterial orthologs, but with some critical differences both in biological assembly and in secondary-structural features that can potentially be exploited for the development of species-selective drugs.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, 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)

Macromolecule Content

• Total Structure Weight: 161.33 kDa 
• Atom Count: 11,419 
• Modelled Residue Count: 1,436 
• Deposited Residue Count: 1,500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate-semialdehyde dehydrogenase	A, B, C, D	375	Cryptococcus neoformans var. neoformans JEC21	Mutation(s): 0  Gene Names: CNA02450 EC: 1.2.1.11
UniProt
Find proteins for Q5KPK7 (Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565)) Explore Q5KPK7  Go to UniProtKB:  Q5KPK7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.220 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.59	α = 90
b = 130.96	β = 92.87
c = 91.94	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
iMOSFLM	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Dahal, G.P., Viola, R.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI077720

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description