8DKG

Structure of PYCR1 Thr171Met variant complexed with NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Functional Impact of a Cancer-Related Variant in Human Delta 1 -Pyrroline-5-Carboxylate Reductase 1.

Daudu, O.I.Meeks, K.R.Zhang, L.Seravalli, J.Tanner, J.J.Becker, D.F.

(2023) ACS Omega 8: 3509-3519

  • DOI: https://doi.org/10.1021/acsomega.2c07788
  • Primary Citation of Related Structures:  
    8DKG

  • PubMed Abstract: 

    Pyrroline-5-carboxylate reductase (PYCR) is a proline biosynthetic enzyme that catalyzes the NAD(P)H-dependent reduction of Δ 1 -pyrroline-5-carboxylate (P5C) to proline. Humans have three PYCR isoforms, with PYCR1 often upregulated in different types of cancers. Here, we studied the biochemical and structural properties of the Thr171Met variant of PYCR1, which is found in patients with malignant melanoma and lung adenocarcinoma. Although PYCR1 is strongly associated with cancer progression, characterization of a PYCR1 variant in cancer patients has not yet been reported. Thr171 is conserved in all three PYCR isozymes and is located near the P5C substrate binding site. We found that the amino acid replacement does not affect thermostability but has a profound effect on PYCR1 catalytic activity. The k cat of the PYCR1 variant T171M is 100- to 200-fold lower than wild-type PYCR1 when P5C is the variable substrate, and 10- to 25-fold lower when NAD(P)H is varied. A 1.84 Å resolution X-ray crystal structure of T171M reveals that the Met side chain invades the P5C substrate binding site, suggesting that the catalytic defect is due to steric clash preventing P5C from achieving the optimal pose for hydride transfer from NAD(P)H. These results suggest that any impact on PYCR1 function associated with T171M in cancer does not derive from increased catalytic activity.


  • Organizational Affiliation

    Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
A, B, C, D, E
322Homo sapiensMutation(s): 1 
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
PHAROS:  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
NAI
Query on NAI

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
L [auth C],
M [auth D],
Q [auth E]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
K [auth B]
N [auth D]
G [auth A],
H [auth A],
I [auth A],
K [auth B],
N [auth D],
O [auth D],
P [auth D],
R [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.603α = 90
b = 179.929β = 107.01
c = 88.304γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description