2OC4

Crystal structure of human purine nucleoside phosphorylase mutant H257D with Imm-H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Neighboring Group Participation in the Transition State of Human Purine Nucleoside Phosphorylase

Murkin, A.S.Birck, M.R.Rinaldo-Matthis, A.Shi, W.Taylor, E.A.Almo, S.C.Schramm, V.L.

(2007) Biochemistry 46: 5038-5049

  • DOI: https://doi.org/10.1021/bi700147b
  • Primary Citation of Related Structures:  
    2A0W, 2A0X, 2A0Y, 2OC4, 2OC9, 2ON6

  • PubMed Abstract: 

    The X-ray crystal structures of human purine nucleoside phosphorylase (PNP) with bound inosine or transition-state analogues show His257 within hydrogen bonding distance of the 5'-hydroxyl. The mutants His257Phe, His257Gly, and His257Asp exhibited greatly decreased affinity for Immucillin-H (ImmH), binding this mimic of an early transition state as much as 370-fold (Km/Ki) less tightly than native PNP. In contrast, these mutants bound DADMe-ImmH, a mimic of a late transition state, nearly as well as the native enzyme. These results indicate that His257 serves an important role in the early stages of transition-state formation. Whereas mutation of His257 resulted in little variation in the PNP x DADMe-ImmH x SO4 structures, His257Phe x ImmH x PO4 showed distortion at the 5'-hydroxyl, indicating the importance of H-bonding in positioning this group during progression to the transition state. Binding isotope effect (BIE) and kinetic isotope effect (KIE) studies of the remote 5'-(3)H for the arsenolysis of inosine with native PNP revealed a BIE of 1.5% and an unexpectedly large intrinsic KIE of 4.6%. This result is interpreted as a moderate electronic distortion toward the transition state in the Michaelis complex with continued development of a similar distortion at the transition state. The mutants His257Phe, His257Gly, and His257Asp altered the 5'-(3)H intrinsic KIE to -3, -14, and 7%, respectively, while the BIEs contributed 2, 2, and -2%, respectively. These surprising results establish that forces in the Michaelis complex, reported by the BIEs, can be reversed or enhanced at the transition state.


  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase289Homo sapiensMutation(s): 2 
Gene Names: NPPNP
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
IMH
Query on IMH

Download Ideal Coordinates CCD File 
C [auth A]1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL
C11 H14 N4 O4
IWKXDMQDITUYRK-KUBHLMPHSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Binding Affinity Annotations 
IDSourceBinding Affinity
IMH BindingDB:  2OC4 Ki: min: 0.06, max: 72 (nM) from 6 assay(s)
Kd: min: 0.02, max: 0.06 (nM) from 3 assay(s)
IC50: min: 0.06, max: 100 (nM) from 3 assay(s)
ΔH: -3.50e+1 (kJ/mol) from 1 assay(s)
ΔG: -4.56e+1 (kJ/mol) from 1 assay(s)
PDBBind:  2OC4 Ki: 86 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.974α = 90
b = 142.974β = 90
c = 168.55γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-02-01
    Changes: Structure summary
  • Version 1.4: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 2.0: 2022-10-05
    Changes: Atomic model, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Refinement description