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- PDB-5ugf: Crystal structure of human purine nucleoside phosphorylase (F159Y... -

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Basic information

Entry
Database: PDB / ID: 5ugf
TitleCrystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with DADMe-ImmG and phosphate
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / phosphorylase / inhibitor / transition state analogue / purine salvage pathway / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / nucleotide biosynthetic process / deoxyadenosine catabolic process / dAMP catabolic process / inosine catabolic process / urate biosynthetic process ...nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / nucleotide biosynthetic process / deoxyadenosine catabolic process / dAMP catabolic process / inosine catabolic process / urate biosynthetic process / IMP catabolic process / Ribavirin ADME / guanosine phosphorylase activity / nucleoside binding / Purine salvage / Purine catabolism / allantoin metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / positive regulation of alpha-beta T cell differentiation / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / phosphate ion binding / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / secretory granule lumen / ficolin-1-rich granule lumen / immune response / response to xenobiotic stimulus / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IM5 / PHOSPHATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHarijan, R.K. / Cameron, S.A. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM068036 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Catalytic-site design for inverse heavy-enzyme isotope effects in human purine nucleoside phosphorylase.
Authors: Harijan, R.K. / Zoi, I. / Antoniou, D. / Schwartz, S.D. / Schramm, V.L.
History
DepositionJan 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,82041
Polymers214,3906
Non-polymers4,43035
Water12,845713
1
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,55222
Polymers107,1953
Non-polymers2,35719
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-133 kcal/mol
Surface area29850 Å2
MethodPISA
2
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,26719
Polymers107,1953
Non-polymers2,07316
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-122 kcal/mol
Surface area29370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.960, 124.270, 136.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPROAA1 - 28532 - 316
21METMETPROPROBB1 - 28532 - 316
12METMETPROPROAA1 - 28532 - 316
22METMETPROPROCC1 - 28532 - 316
13METMETASPASPAA1 - 28632 - 317
23METMETASPASPDD1 - 28632 - 317
14METMETPROPROAA1 - 28532 - 316
24METMETPROPROEE1 - 28532 - 316
15METMETPROPROAA1 - 28532 - 316
25METMETPROPROFF1 - 28532 - 316
16LEULEUPROPROBB0 - 28531 - 316
26LEULEUPROPROCC0 - 28531 - 316
17METMETPROPROBB1 - 28532 - 316
27METMETPROPRODD1 - 28532 - 316
18LEULEUASPASPBB0 - 28631 - 317
28LEULEUASPASPEE0 - 28631 - 317
19LEULEUASPASPBB0 - 28631 - 317
29LEULEUASPASPFF0 - 28631 - 317
110METMETPROPROCC1 - 28532 - 316
210METMETPROPRODD1 - 28532 - 316
111LEULEUPROPROCC0 - 28531 - 316
211LEULEUPROPROEE0 - 28531 - 316
112LEULEUPROPROCC0 - 28531 - 316
212LEULEUPROPROFF0 - 28531 - 316
113METMETPROPRODD1 - 28532 - 316
213METMETPROPROEE1 - 28532 - 316
114METMETPROPRODD1 - 28532 - 316
214METMETPROPROFF1 - 28532 - 316
115LEULEUASPASPEE0 - 28631 - 317
215LEULEUASPASPFF0 - 28631 - 317

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Purine nucleoside phosphorylase / PNP / Inosine phosphorylase / Inosine-guanosine phosphorylase


Mass: 35731.652 Da / Num. of mol.: 6 / Mutation: F159Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNP, NP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P00491, purine-nucleoside phosphorylase
#2: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-IM5 / 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one / DADMe-ImmG


Mass: 279.295 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H17N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 0.2 M lithium sulfate, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 18, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.2→69.26 Å / Num. obs: 91303 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.71 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3PHB

3phb


Resolution: 2.2→69.26 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.822 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23809 4492 4.9 %RANDOM
Rwork0.21382 ---
obs0.21503 86719 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.993 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å20 Å20 Å2
2---1.13 Å20 Å2
3----1.59 Å2
Refinement stepCycle: 1 / Resolution: 2.2→69.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13348 0 265 713 14326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01913957
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212632
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.97418955
X-RAY DIFFRACTIONr_angle_other_deg0.931329231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17851725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53723.649633
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.746152225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0321596
X-RAY DIFFRACTIONr_chiral_restr0.0750.22043
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022925
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.783.5586903
X-RAY DIFFRACTIONr_mcbond_other1.783.5576902
X-RAY DIFFRACTIONr_mcangle_it3.1955.3268627
X-RAY DIFFRACTIONr_mcangle_other3.1955.3278628
X-RAY DIFFRACTIONr_scbond_it1.4293.6797054
X-RAY DIFFRACTIONr_scbond_other1.4293.6797055
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5265.4710329
X-RAY DIFFRACTIONr_long_range_B_refined6.50140.51115367
X-RAY DIFFRACTIONr_long_range_B_other6.50140.51115368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A178760.07
12B178760.07
21A177840.08
22C177840.08
31A179400.07
32D179400.07
41A178220.07
42E178220.07
51A175400.09
52F175400.09
61B179000.07
62C179000.07
71B179220.06
72D179220.06
81B180120.05
82E180120.05
91B176420.08
92F176420.08
101C177060.07
102D177060.07
111C176860.07
112E176860.07
121C177820.06
122F177820.06
131D179340.05
132E179340.05
141D175560.07
142F175560.07
151E177060.07
152F177060.07
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 341 -
Rwork0.3 6338 -
obs--100 %

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