3TY4

Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe

• PDB DOI: https://doi.org/10.2210/pdb3TY4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Schizosaccharomyces pombe 972h-
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-23 Released: 2011-11-09 
• Deposition Author(s): Bulfer, S.L., Hendershot, J.M., Trievel, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.215 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Literature

Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe.

Bulfer, S.L., Hendershot, J.M., Trievel, R.C.

(2012) Proteins 80: 661-666

• PubMed: 22105743 
• DOI: https://doi.org/10.1002/prot.23231
• Primary Citation of Related Structures:  
  3TY3, 3TY4


• PubMed Abstract: 
  

  Homoisocitrate dehydrogenase (HICDH) catalyzes the conversion of homoisocitrate to 2-oxoadipate, the third enzymatic step in the α-aminoadipate pathway by which lysine is synthesized in fungi and certain archaebacteria. This enzyme represents a potential target for anti-fungal drug design. Here, we describe the first crystal structures of a fungal HICDH, including structures of an apoenzyme and a binary complex with a glycine tri-peptide. The structures illustrate the homology of HICDH with other β-hydroxyacid oxidative decarboxylases and reveal key differences with the active site of Thermus thermophilus HICDH that provide insights into the differences in substrate specificity of these enzymes.

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Organizational Affiliation: 

Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109.

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: 80.21 kDa 
• Atom Count: 6,084 
• Modelled Residue Count: 713 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable homoisocitrate dehydrogenase	A, B	366	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: lys12, SPAC31G5.04 EC: 1.1.1.87
UniProt
Find proteins for O14104 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O14104  Go to UniProtKB:  O14104

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.215 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.851	α = 90
b = 94.452	β = 106.63
c = 76.076	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Bulfer, S.L., Hendershot, J.M., Trievel, R.C.

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2011-12-14
  Changes: Database references
• Version 1.2: 2013-11-27
  Changes: Database references
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description