Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1

J Biol Chem. 2017 Apr 28;292(17):7233-7243. doi: 10.1074/jbc.M117.780288. Epub 2017 Mar 3.

Abstract

Pyrroline-5-carboxylate reductase (PYCR) is the final enzyme in proline biosynthesis, catalyzing the NAD(P)H-dependent reduction of Δ1-pyrroline-5-carboxylate (P5C) to proline. Mutations in the PYCR1 gene alter mitochondrial function and cause the connective tissue disorder cutis laxa. Furthermore, PYCR1 is overexpressed in multiple cancers, and the PYCR1 knock-out suppresses tumorigenic growth, suggesting that PYCR1 is a potential cancer target. However, inhibitor development has been stymied by limited mechanistic details for the enzyme, particularly in light of a previous crystallographic study that placed the cofactor-binding site in the C-terminal domain rather than the anticipated Rossmann fold of the N-terminal domain. To fill this gap, we report crystallographic, sedimentation-velocity, and kinetics data for human PYCR1. Structures of binary complexes of PYCR1 with NADPH or proline determined at 1.9 Å resolution provide insight into cofactor and substrate recognition. We see NADPH bound to the Rossmann fold, over 25 Å from the previously proposed site. The 1.85 Å resolution structure of a ternary complex containing NADPH and a P5C/proline analog provides a model of the Michaelis complex formed during hydride transfer. Sedimentation velocity shows that PYCR1 forms a concentration-dependent decamer in solution, consistent with the pentamer-of-dimers assembly seen crystallographically. Kinetic and mutational analysis confirmed several features seen in the crystal structure, including the importance of a hydrogen bond between Thr-238 and the substrate as well as limited cofactor discrimination.

Keywords: NAD(P)H-dependent reductase; Rossmann fold; X-ray crystallography; analytical ultracentrifugation; enzyme kinetics; nicotinamide adenine dinucleotide (NADH); reductase; site-directed mutagenesis; substrate specificity.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Binding Sites
  • Catalytic Domain
  • Crystallography, X-Ray
  • Humans
  • Kinetics
  • Ligands
  • Mutation
  • NADP / chemistry
  • Proline / chemistry*
  • Protein Binding
  • Protein Multimerization
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • Pyrroline Carboxylate Reductases / chemistry*
  • Substrate Specificity
  • Ultracentrifugation
  • delta-1-Pyrroline-5-Carboxylate Reductase

Substances

  • Ligands
  • NADP
  • Proline
  • Pyrroline Carboxylate Reductases

Associated data

  • PDB/5UAT
  • PDB/5UAU
  • PDB/5UAV
  • PDB/5UAW
  • PDB/5UAX
  • PDB/2GER
  • PDB/2GR9
  • PDB/2GRA
  • PDB/2IZZ
  • PDB/3qd1
  • PDB/4i8e