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- PDB-1bzy: HUMAN HGPRTASE WITH TRANSITION STATE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1bzy
TitleHUMAN HGPRTASE WITH TRANSITION STATE INHIBITOR
ComponentsHYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
KeywordsPHOSPHORIBOSYLTRANSFERASE / IMMUCILLIN / LESCH-NYHAN / HGPRT / TRANSITION STATE / MAGNESIUM / PYROPHOSPHATE / OXOCARBENIUM ION / NEIGHBORING GROUP PARTICIPATION
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-IMU / PYROPHOSPHATE 2- / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShi, W. / Li, C. / Tyler, P.C. / Furneaux, R.H. / Grubmeyer, C. / Schramm, V.L. / Almo, S.C.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: The 2.0 A structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with a transition-state analog inhibitor.
Authors: Shi, W. / Li, C.M. / Tyler, P.C. / Furneaux, R.H. / Grubmeyer, C. / Schramm, V.L. / Almo, S.C.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1994
Title: The Crystal Structure of Human Hypoxanthine-Guanine Phosphoribosyltransferase with Bound Gmp
Authors: Eads, J.C. / Scapin, G. / Xu, Y. / Grubmeyer, C. / Sacchettini, J.C.
History
DepositionNov 5, 1998Processing site: BNL
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
B: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
C: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
D: HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,26820
Polymers97,9254
Non-polymers2,34316
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15770 Å2
ΔGint-138 kcal/mol
Surface area29290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.960, 102.010, 144.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.98169, -0.00764, -0.19031), (-0.01344, -0.99392, 0.10924), (-0.18999, 0.1098, 0.97563)21.46923, 196.16934, -8.75712
2given(-0.92377, -0.38044, 0.04371), (-0.38238, 0.9102, -0.15915), (0.02076, -0.16374, -0.98629)43.98996, 21.11449, 144.92862
3given(0.90602, 0.38961, 0.16533), (0.38917, -0.92045, 0.03639), (0.16636, 0.03137, -0.98557)-50.00994, 191.68289, 124.52213

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Components

#1: Protein
HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE


Mass: 24481.217 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P00492, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-IMU / PHOSPHORIC ACID MONO-[5-(2-AMINO-4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-3,4-DIHYDROXY-PYRROLIDIN-2-YLMETHYL] ESTER / MODIFIED QUANOSINE-5-PHOSPHATE


Mass: 361.248 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H16N5O7P
#4: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113-15 mg/mlprotein1drop
2100 mMsodium acetate1reservoir
320 %mPEG20001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. obs: 44301 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.045 / Net I/σ(I): 13.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 8.3 / Rsym value: 0.2 / % possible all: 81
Reflection
*PLUS
Num. measured all: 232173 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 81 % / Rmerge(I) obs: 0.2

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DBR

1dbr


Resolution: 2→10 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2097 5 %RANDOM
Rwork0.19 ---
obs0.19 41998 79 %-
Displacement parametersBiso mean: 16.9 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6780 0 140 297 7217
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.64
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.284 239 5 %
Rwork0.218 4398 -
obs--71 %

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