4WLH

High resolution crystal structure of human kynurenine aminotransferase-I bound to PLP cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

High resolution crystal structures of human kynurenine aminotransferase-I bound to PLP cofactor, and in complex with aminooxyacetate.

Nadvi, N.A.Salam, N.K.Park, J.Akladios, F.N.Kapoor, V.Collyer, C.A.Gorrell, M.D.Church, W.B.

(2017) Protein Sci 26: 727-736

  • DOI: 10.1002/pro.3119
  • Primary Citation of Related Structures:  
    4WLH, 4WLJ

  • PubMed Abstract: 
  • In this study, we report two high-resolution structures of the pyridoxal 5' phosphate (PLP)-dependent enzyme kynurenine aminotransferase-I (KAT-I). One is the native structure with the cofactor in the PLP form bound to Lys247 with the highest resolut ...

    In this study, we report two high-resolution structures of the pyridoxal 5' phosphate (PLP)-dependent enzyme kynurenine aminotransferase-I (KAT-I). One is the native structure with the cofactor in the PLP form bound to Lys247 with the highest resolution yet available for KAT-I at 1.28 Å resolution, and the other with the general PLP-dependent aminotransferase inhibitor, aminooxyacetate (AOAA) covalently bound to the cofactor at 1.54 Å. Only small conformational differences are observed in the vicinity of the aldimine (oxime) linkage with which the PLP forms the Schiff base with Lys247 in the 1.28 Å resolution native structure, in comparison to other native PLP-bound structures. We also report the inhibition of KAT-1 by AOAA and aminooxy-phenylpropionic acid (AOPP), with IC50s of 13.1 and 5.7 μM, respectively. The crystal structure of the enzyme in complex with the inhibitor AOAA revealed that the cofactor is the PLP form with the external aldimine linkage. The location of this oxime with the PLP, which forms in place of the native internal aldimine linkage of PLP of the native KAT-I, is away from the position of the native internal aldimine, with the free Lys247 substantially retaining the orientation of the native structure. Tyr101, at the active site, was observed in two conformations in both structures.


    Organizational Affiliation

    Group in Biomolecular Structure and Informatics, Faculty of Pharmacy, University of Sydney, Sydney, New South Wales, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kynurenine--oxoglutarate transaminase 1AB422Homo sapiensMutation(s): 0 
Gene Names: KYAT1CCBL1
EC: 2.6.1.7 (PDB Primary Data), 4.4.1.13 (PDB Primary Data), 2.6.1.64 (PDB Primary Data)
Find proteins for Q16773 (Homo sapiens)
Explore Q16773 
Go to UniProtKB:  Q16773
NIH Common Fund Data Resources
PHAROS  Q16773
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A,BL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.44α = 90
b = 107.56β = 112.64
c = 81.53γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Other
  • Version 1.2: 2017-05-03
    Changes: Non-polymer description
  • Version 1.3: 2017-05-10
    Changes: Structure summary
  • Version 1.4: 2017-05-31
    Changes: Database references