3TY3 | pdb_00003ty3

Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe bound to glycyl-glycyl-glycine

• PDB DOI: https://doi.org/10.2210/pdb3TY3/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: 1.85 Å
• R-Value Free: 
  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

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 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: 80.03 kDa 
• Atom Count: 5,761 
• Modeled Residue Count: 710 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GGG	C [auth A], G [auth B]	glycylglycylglycine C6 H11 N3 O4 XKUKSGPZAADMRA-UHFFFAOYSA-N
GOL	D [auth A], E [auth A], F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.243	α = 90
b = 92.854	β = 106.71
c = 75.474	γ = 90

Software Package:

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

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