5ETJ

Crystal structure of purine nucleoside phosphorylase (E258D, L261A) mutant from human complexed with DADMe-ImmG and phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics.

Zoi, I.Suarez, J.Antoniou, D.Cameron, S.A.Schramm, V.L.Schwartz, S.D.

(2016) J Am Chem Soc 138: 3403-3409

  • DOI: https://doi.org/10.1021/jacs.5b12551
  • Primary Citation of Related Structures:  
    5ETJ

  • PubMed Abstract: 

    The relevance of sub-picosecond protein motions to the catalytic event remains a topic of debate. Heavy enzymes (isotopically substituted) provide an experimental tool for bond-vibrational links to enzyme catalysis. A recent transition path sampling study with heavy purine nucleoside phosphorylase (PNP) characterized the experimentally observed mass-dependent slowing of barrier crossing (Antoniou, D.; Ge, X.; Schramm, V. L.; Schwartz, S. D. J. Phys. Chem. Lett. 2012, 3, 3538). Here we computationally identify second-sphere amino acid residues predicted to influence the freedom of the catalytic site vibrational modes linked to heavy enzyme effects in PNP. We mutated heavy and light PNPs to increase the catalytic site vibrational freedom. Enzymatic barrier-crossing rates were converted from mass-dependent to mass-independent as a result of the mutations. The mutagenic uncoupling of femtosecond motions between catalytic site groups and reactants decreased transition state barrier crossing by 2 orders of magnitude, an indication of the femtosecond dynamic contributions to catalysis.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Blvd, Tucson, Arizona 85721, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase
A, B, C, D, E
A, B, C, D, E, F
324Homo sapiensMutation(s): 2 
Gene Names: PNPNP
EC: 2.4.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00491 (Homo sapiens)
Explore P00491 
Go to UniProtKB:  P00491
PHAROS:  P00491
GTEx:  ENSG00000198805 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00491
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IM5
Query on IM5

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
M [auth C]
P [auth D]
S [auth E]
G [auth A],
J [auth B],
M [auth C],
P [auth D],
S [auth E],
V [auth F]
2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
C12 H17 N5 O3
GSPTUGDLYPMLCQ-SFYZADRCSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
K [auth B]
L [auth B]
N [auth C]
H [auth A],
I [auth A],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
Q [auth D],
R [auth D],
T [auth E],
U [auth F],
W [auth F],
X [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Binding Affinity Annotations 
IDSourceBinding Affinity
IM5 BindingDB:  5ETJ Ki: min: 7.00e-3, max: 0.16 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 268.808α = 90
b = 58.845β = 112.92
c = 173.155γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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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 StatesGM068036

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description