4EB8 | pdb_00004eb8

Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with DADMe-ImmG and phosphate

PDB DOI: https://doi.org/10.2210/pdb4EB8/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-03-23 Released: 2013-02-06
Deposition Author(s): Ho, M.C., Haapalainen, A.M., Suarez, J.J., Almo, S.C., Schramm, V.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.228 (Depositor), 0.227 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Catalytic Site Conformations in Human PNP by (19)F-NMR and Crystallography.

Suarez, J., Haapalainen, A.M., Cahill, S.M., Ho, M.C., Yan, F., Almo, S.C., Schramm, V.L.

(2013) Chem Biol 20: 212-222

PubMed: 23438750 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.chembiol.2013.01.009
Primary Citation Related Structures:
4EAR, 4EB8, 4ECE, 4GKA

PubMed Abstract:
Purine nucleoside phosphorylase (PNP) is a target for leukemia, gout, and autoimmune disorders. Dynamic motion of catalytic site loops has been implicated in catalysis, but experimental evidence was lacking. We replaced catalytic site groups His257 or His64 with 6-fluoro-tryptophan (6FW) as site-specific NMR probes. Conformational adjustments in the 6FW-His257-helical and His64-6FW-loop regions were characterized in PNP phosphate-bound enzyme and in complexes with catalytic site ligands, including transition state analogs. Chemical shift and line-shape changes associated with these complexes revealed dynamic coexistence of several conformational states in these regions in phosphate-bound enzyme and altered or single conformations in other complexes. These conformations were also characterized by X-ray crystallography. Specific (19)F-Trp labels and X-ray crystallography provide multidimensional characterization of conformational states for free, catalytic, and inhibited complexes of human PNP.

Organizational Affiliation

Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA.

Macromolecule Content

Total Structure Weight: 109.63 kDa
Atom Count: 7,126
Modeled Residue Count: 859
Deposited Residue Count: 972
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A, B, C	324	Homo sapiens	Mutation(s): 5 Gene Names: NP, PNP, X00737.1 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00491
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IM5 Query on IM5 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C]	E [auth A], G [auth B], J [auth C]	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		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth C] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth C] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth C] mmCIF format, chain F [auth B]	D [auth A], F [auth B], I [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain I [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B]	H [auth B], K [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain H [auth B] Focus chain K [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
IM5	BindingDB: 4EB8	Ki: min: 7.00e-3, max: 7 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.228 (Depositor), 0.227 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.752	α = 90
b = 131.035	β = 90
c = 137.503	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-02-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-02-06
Type: Initial release
Version 1.1: 2013-03-06
Changes: Database references
Version 1.2: 2013-03-13
Changes: Database references
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations