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- PDB-2jky: SACCHAROMYCES CEREVISIAE HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANS... -

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Basic information

Entry
Database: PDB / ID: 2jky
TitleSACCHAROMYCES CEREVISIAE HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH GMP (GUANOSINE 5'- MONOPHOSPHATE) (TETRAGONAL CRYSTAL FORM)
ComponentsHYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / NUCLEUS / MAGNESIUM / GMP COMPLEX / FLIP PEPTIDE-PLANE / GLYCOSYLTRANSFERASE / METAL-BINDING / PURINE SALVAGE
Function / homology
Function and homology information


XMP salvage / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / metal ion binding ...XMP salvage / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsMoynie, L. / Giraud, M.F. / Breton, A. / Boissier, F. / Daignan-Fornier, B. / Dautant, A.
Citation
Journal: Protein Sci. / Year: 2012
Title: Functional Significance of Four Successive Glycine Residues in the Pyrophosphate Binding Loop of Fungal 6-Oxopurine Phosphoribosyltransferases.
Authors: Moynie, L. / Giraud, M.F. / Breton, A. / Boissier, F. / Daignan-Fornier, B. / Dautant, A.
#1: Journal: Genetics / Year: 2008
Title: Lethal Accumulation of Guanylic Nucleotides in Saccharomyces Cerevisiae Hpt1-Deregulated Mutants.
Authors: Breton, A. / Pinson, B. / Coulpier, F. / Giraud, M. / Dautant, A. / Daignan-Fornier, B.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: Structures of Free and Complexed Forms of Escherichia Coli Xanthine-Guanine Phosphoribosyltransferase.
Authors: Vos, S. / Parry, R.J. / Burns, M.R. / De Jersey, J. / Martin, J.L.
#3: Journal: Biochemistry / Year: 1997
Title: Crystal Structure of Escherichia Coli Xanthine Phosphoribosyltransferase.
Authors: Vos, S. / De Jersey, J. / Martin, J.L.
History
DepositionSep 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 19, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.5Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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.status_code_sf / _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.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.value / _struct_conn.pdbx_dist_value / _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.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_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)49,3707
Polymers48,4272
Non-polymers9435
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-75.2 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.443, 128.443, 56.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE / HGPRTASE / HGPRT / BYPASS OF REPRESSION BY ADENINE PROTEIN 6


Mass: 24213.590 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: Y1846 / Plasmid: PET-21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q04178, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.6
Details: 0.2 M AMMONIUM ACETATE, 30% PEG 4000, 0.1 M TRI-SODIUM CITRATE PH 5.6, IN MICROBATCH UNDER OIL, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 26, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) SINGLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 20429 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 57.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.94
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.92 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.3→30.27 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 15.449 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.375 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1048 5.1 %RANDOM
Rwork0.203 ---
obs0.204 19355 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2---0.99 Å20 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 59 95 3446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223429
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.9834649
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.025405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00824.81158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50115615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7471517
X-RAY DIFFRACTIONr_chiral_restr0.0690.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022543
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1770.21514
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22287
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2169
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2981.52107
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.47723314
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.65631535
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0294.51335
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 76
Rwork0.263 1405
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0326-0.868-0.51863.8870.33881.5630.082-0.4030.55210.2701-0.0637-0.52230.1784-0.0669-0.0183-0.2992-0.0245-0.0593-0.3145-0.1057-0.205815.77418.3250.143
25.6799-4.2471-0.125414.6116-1.41172.65240.49390.69371.7185-1.3041-0.7416-1.6855-0.1637-0.10780.2477-0.19240.13110.1856-0.21030.27460.311715.29735.936-17.787
318.1043.3525.84326.81562.8933.3245-0.39460.51322.34320.24820.1494-0.7338-0.33890.11950.2452-0.1647-0.0229-0.1236-0.263-0.15190.224618.29129.4574.459
412.6873-0.89161.274810.6031-2.78456.7453-0.20610.43831.85160.72120.87510.8918-0.4609-1.682-0.669-0.34430.19850.1361-0.04880.27770.41760.8140.773-10.823
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 65
2X-RAY DIFFRACTION1A110 - 214
3X-RAY DIFFRACTION2B5 - 65
4X-RAY DIFFRACTION2B110 - 214
5X-RAY DIFFRACTION3A66 - 109
6X-RAY DIFFRACTION4B66 - 109

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