5EUN | pdb_00005eun

The Crystal Structure of Human Kynurenine Aminotransferase II, PLP-bound form, at 1.83 A

• PDB DOI: https://doi.org/10.2210/pdb5EUN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-18 Released: 2015-12-16 
• Deposition Author(s): Nematollahi, A., Sun, G., Kwan, A., Jeffries, C.M., Harrop, S.J., Hanrahan, J.R., Nadvi, N.A., Church, W.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Structure of the PLP-Form of the Human Kynurenine Aminotransferase II in a Novel Spacegroup at 1.83 angstrom Resolution.

Nematollahi, A., Sun, G., Harrop, S.J., Hanrahan, J.R., Church, W.B.

(2016) Int J Mol Sci 17: 446-446

• PubMed: 27023527 
• DOI: https://doi.org/10.3390/ijms17040446
• Primary Citation Related Structures: 
  5EUN


• PubMed Abstract: 
  

  Kynurenine aminotransferase II (KAT-II) is a 47 kDa pyridoxal phosphate (PLP)-dependent enzyme, active as a homodimer, which catalyses the transamination of the amino acids kynurenine (KYN) and 3-hydroxykynurenine (3-HK) in the tryptophan pathway, and is responsible for producing metabolites that lead to kynurenic acid (KYNA), which is implicated in several neurological diseases such as schizophrenia. In order to fully describe the role of KAT-II in the pathobiology of schizophrenia and other brain disorders, the crystal structure of full-length PLP-form hKAT-II was determined at 1.83 Å resolution, the highest available. The electron density of the active site reveals an aldimine linkage between PLP and Lys263, as well as the active site residues, which characterize the fold-type I PLP-dependent enzymes.

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Organizational Affiliation: 
• Group in Biomolecular Structure and Informatics, Faculty of Pharmacy, University of Sydney, Sydney, NSW 2006, Australia. [e-mail].
Group in Biomolecular Structure and Informatics, Faculty of Pharmacy, University of Sydney, Sydney, NSW 2006, Australia. [e-mail].
MX Beamlines, Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia. [e-mail].
Faculty of Pharmacy, University of Sydney, Sydney, NSW 2006, Australia. [e-mail].
Group in Biomolecular Structure and Informatics, Faculty of Pharmacy, University of Sydney, Sydney, NSW 2006, Australia. [e-mail].

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: 47.63 kDa 
• Atom Count: 3,785 
• Modeled Residue Count: 425 
• Deposited Residue Count: 425 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial	A	425	Homo sapiens	Mutation(s): 0  Gene Names: AADAT, KAT2 EC: 2.6.1.39 (PDB Primary Data), 2.6.1.7 (PDB Primary Data), 2.6.1.4 (UniProt), 2.6.1.63 (UniProt), 2.6.1.73 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N5Z0 (Homo sapiens) Explore Q8N5Z0  Go to UniProtKB:  Q8N5Z0
PHAROS:  Q8N5Z0 GTEx:  ENSG00000109576

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.455	α = 90
b = 102.455	β = 90
c = 86.236	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-16 
Deposition Author(s): Nematollahi, A., Sun, G., Kwan, A., Jeffries, C.M., Harrop, S.J., Hanrahan, J.R., Nadvi, N.A., Church, W.B.

Revision History  

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2016-03-02
  Changes: Data collection
• Version 1.2: 2016-04-13
  Changes: Database references
• Version 1.3: 2016-08-10
  Changes: Database references
• Version 1.4: 2025-04-02
  Changes: Data collection, Database references, Derived calculations, Structure summary