5UAU

Structure of human PYCR-1 complexed with proline

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

  • Deposited: 2016-12-20 Released: 2017-03-15 
  • Deposition Author(s): Tanner, J.J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

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

Christensen, E.M.Patel, S.M.Korasick, D.A.Campbell, A.C.Krause, K.L.Becker, D.F.Tanner, J.J.

(2017) J Biol Chem 292: 7233-7243

  • DOI: https://doi.org/10.1074/jbc.M117.780288
  • Primary Citation of Related Structures:  
    5UAT, 5UAU, 5UAV, 5UAW, 5UAX

  • PubMed Abstract: 

    Pyrroline-5-carboxylate reductase (PYCR) is the final enzyme in proline biosynthesis, catalyzing the NAD(P)H-dependent reduction of Δ 1 -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.


  • Organizational Affiliation

    From the Departments of Chemistry and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrroline-5-carboxylate reductase 1, mitochondrial
A, B, C, D, E
322Homo sapiensMutation(s): 0 
Gene Names: PYCR1
EC: 1.5.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for P32322 (Homo sapiens)
Explore P32322 
Go to UniProtKB:  P32322
GTEx:  ENSG00000183010 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32322
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PRO
Query on PRO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth B]
I [auth B]
K [auth C]
F [auth A],
G [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
N [auth D],
O [auth D],
Q [auth E],
R [auth E]
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth B],
M [auth C],
P [auth D],
S [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.13α = 90
b = 87.75β = 90
c = 117.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2017-03-15 
  • Deposition Author(s): Tanner, J.J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM065546

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-05-10
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description