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PDBsum entry 2hzp

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protein ligands links
Hydrolase PDB id
2hzp
Jmol
Contents
Protein chain
447 a.a. *
Ligands
PLP
Waters ×540
* Residue conservation analysis
PDB id:
2hzp
Name: Hydrolase
Title: Crystal structure of homo sapiens kynureninase
Structure: Kynureninase. Chain: a. Synonym: l-kynurenine hydrolase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: kynu. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.152     R-free:   0.195
Authors: S.Lima,R.Khristoforov,C.Momany,R.S.Phillips
Key ref: S.Lima et al. (2007). Crystal structure of Homo sapiens kynureninase. Biochemistry, 46, 2735-2744. PubMed id: 17300176 DOI: 10.1021/bi0616697
Date:
09-Aug-06     Release date:   07-Nov-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q16719  (KYNU_HUMAN) -  Kynureninase
Seq:
Struc:
465 a.a.
447 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.7.1.3  - Kynureninase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Tryptophan Catabolism
      Reaction: L-kynurenine + H2O = anthranilate + L-alanine
L-kynurenine
+ H(2)O
= anthranilate
+ L-alanine
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   4 terms 
  Biological process     metabolic process   14 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi0616697 Biochemistry 46:2735-2744 (2007)
PubMed id: 17300176  
 
 
Crystal structure of Homo sapiens kynureninase.
S.Lima, R.Khristoforov, C.Momany, R.S.Phillips.
 
  ABSTRACT  
 
Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19170761 Y.Meng, S.Katsuma, K.Mita, and T.Shimada (2009).
Abnormal red body coloration of the silkworm, Bombyx mori, is caused by a mutation in a novel kynureninase.
  Genes Cells, 14, 129-140.  
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