Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.88 kDa 
• Atom Count: 4237 
• Modelled Residue Count: 446 
• Deposited Residue Count: 465 
• Unique protein chains: 1

3E9K

Crystal structure of Homo sapiens kynureninase-3-hydroxyhippuric acid inhibitor complex

• PDB DOI: 10.2210/pdb3E9K/pdb

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


• Deposited: 2008-08-22 Released: 2008-12-09 
• Deposition Author(s): Lima, S., Kumar, S., Gawandi, V., Momany, C., Phillips, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.191 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Literature

Crystal structure of the Homo sapiens kynureninase-3-hydroxyhippuric acid inhibitor complex: insights into the molecular basis of kynureninase substrate specificity.

Lima, S., Kumar, S., Gawandi, V., Momany, C., Phillips, R.S.

(2009) J Med Chem 52: 389-396

• PubMed: 19143568 
• DOI: 10.1021/jm8010806
• Primary Citation of Related Structures:  
  3E9K


• PubMed Abstract: 
  

Homo sapiens kynureninase is a pyridoxal-5'-phosphate dependent enzyme that catalyzes the hydrolytic cleavage of 3-hydroxykynurenine to yield 3-hydroxyanthranilate and L-alanine as part of the tryptophan catabolic pathway leading to the de novo biosynthesis of NAD(+). This pathway results in quinolinate, an excitotoxin that is an NMDA receptor agonist. High levels of quinolinate have been correlated with the etiology of neurodegenerative disorders such as AIDS-related dementia and Alzheimer's disease. We have synthesized a novel kynureninase inhibitor, 3-hydroxyhippurate, cocrystallized it with human kynureninase, and solved the atomic structure. On the basis of an analysis of the complex, we designed a series of His-102, Ser-332, and Asn-333 mutants. The H102W/N333T and H102W/S332G/N333T mutants showed complete reversal of substrate specificity between 3-hydroxykynurenine and L-kynurenine, thus defining the primary residues contributing to substrate specificity in kynureninases.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kynureninase	A	465	Homo sapiens	Mutation(s): 0  Gene Names: KYNU EC: 3.7.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q16719 (Homo sapiens) Explore Q16719  Go to UniProtKB:  Q16719
PHAROS:  Q16719

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
3XH	C [auth A]	3-Hydroxyhippuric acid C9 H9 N O4 XDOFWFNMYJRHEW-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
3XH	Binding MOAD:  3E9K	Ki: 6.00e+4 (nM) from 1 assay(s)
	BindingDB:  3E9K	Ki: 6.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.191 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.444	α = 90
b = 77.124	β = 109.35
c = 94.558	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-08-22 
• Released Date: 2008-12-09 
Deposition Author(s): Lima, S., Kumar, S., Gawandi, V., Momany, C., Phillips, R.S.

Revision History  

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance