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- PDB-3gep: Human hypoxanthine guanine phosphoribosyltranserfase in complex w... -

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Basic information

Entry
Database: PDB / ID: 3gep
TitleHuman hypoxanthine guanine phosphoribosyltranserfase in complex with (S)-9-(3-hydroxy-2-phosphonylmethoxypropyl)guanine
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / phosphoribosyltransferase / acyclic nucleoside phosphonate / purine salvage pathway / malarial chemotherapeutic / Acetylation / Cytoplasm / Disease mutation / Glycosyltransferase / Gout / Magnesium / Metal-binding / Purine salvage
Function / homology
Function and homology information


Defective HPRT1 disrupts guanine and hypoxanthine salvage / positive regulation of dopamine metabolic process / GMP catabolic process / adenine metabolic process / cerebral cortex neuron differentiation / hypoxanthine salvage / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process ...Defective HPRT1 disrupts guanine and hypoxanthine salvage / positive regulation of dopamine metabolic process / GMP catabolic process / adenine metabolic process / cerebral cortex neuron differentiation / hypoxanthine salvage / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / IMP metabolic process / hypoxanthine phosphoribosyltransferase activity / lymphocyte proliferation / Purine salvage / GMP salvage / grooming behavior / IMP salvage / striatum development / AMP salvage / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / Azathioprine ADME / purine ribonucleoside salvage / dendrite morphogenesis / central nervous system neuron development / dopamine metabolic process / response to amphetamine / locomotory behavior / T cell mediated cytotoxicity / protein homotetramerization / nucleotide binding / magnesium ion binding / extracellular exosome / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-24H / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGuddat, L.W. / Keough, D.T. / Jersey, J.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Inhibition of hypoxanthine-guanine phosphoribosyltransferase by acyclic nucleoside phosphonates: a new class of antimalarial therapeutics.
Authors: Keough, D.T. / Hockova, D. / Holy, A. / Naesens, L.M. / Skinner-Adams, T.S. / Jersey, J. / Guddat, L.W.
History
DepositionFeb 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6014
Polymers48,9622
Non-polymers6382
Water3,027168
1
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules

A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2028
Polymers97,9254
Non-polymers1,2774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area9300 Å2
ΔGint-29 kcal/mol
Surface area35120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.122, 72.590, 51.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hypoxanthine-guanine phosphoribosyltransferase / HGPRTase / HGPRT


Mass: 24481.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPRT, HPRT1, HPT / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): Sphi606
References: UniProt: P00492, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-24H / {[(1S)-2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-1-(hydroxymethyl)ethoxy]methyl}phosphonic acid


Mass: 319.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M citrate, 10% isopropanol, 29% PEG 4000, 3.9mM (RS)- HPMPG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 5, 2007 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→29.63 Å / Num. all: 13343 / Num. obs: 13343 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 9.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1334 / Rsym value: 0.179 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z7G

1z7g


Resolution: 2.6→29.63 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2983 666 5.1 %RANDOM
Rwork0.24725 ---
obs0.24984 12298 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.15 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 42 168 3493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223394
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9934601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2875422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40223.732142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.2815583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5931521
X-RAY DIFFRACTIONr_chiral_restr0.2340.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022521
X-RAY DIFFRACTIONr_nbd_refined0.2070.21521
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22247
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2185
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.221
X-RAY DIFFRACTIONr_mcbond_it3.7711.52102
X-RAY DIFFRACTIONr_mcangle_it5.52123389
X-RAY DIFFRACTIONr_scbond_it1.74931292
X-RAY DIFFRACTIONr_scangle_it2.8894.51210
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5 48 -
Rwork0.333 871 -
obs--99.14 %

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