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- PDB-4rhy: Crystal structures of Mycobacterium tuberculosis 6-oxopurine phos... -

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Basic information

Entry
Database: PDB / ID: 4rhy
TitleCrystal structures of Mycobacterium tuberculosis 6-oxopurine phosphoribosyltransferase which is a potential target for drug development against this disease
ComponentsHypoxanthine-guanine phosphoribosyltransferase
Keywordstransferase/transferase inhibitor / 6-oxopurine phosphoribosyltransferase / Cytoplasmic / transferase-transferase inhibitor complex
Function / homology
Function and homology information


IMP biosynthetic process / purine-containing compound salvage / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / GMP biosynthetic process ...IMP biosynthetic process / purine-containing compound salvage / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / GMP biosynthetic process / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / metal ion 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-3QG / Hypoxanthine phosphoribosyltransferase / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3196 Å
AuthorsEng, W.S. / Hockova, D. / Spacek, P. / West, N.P. / Woods, K. / Naesens, L.M.J. / Keough, D.T. / Guddat, L.W.
CitationJournal: J.Med.Chem. / Year: 2015
Title: First Crystal Structures of Mycobacterium tuberculosis 6-Oxopurine Phosphoribosyltransferase: Complexes with GMP and Pyrophosphate and with Acyclic Nucleoside Phosphonates Whose Prodrugs Have ...Title: First Crystal Structures of Mycobacterium tuberculosis 6-Oxopurine Phosphoribosyltransferase: Complexes with GMP and Pyrophosphate and with Acyclic Nucleoside Phosphonates Whose Prodrugs Have Antituberculosis Activity.
Authors: Eng, W.S. / Hockova, D. / Spacek, P. / Janeba, Z. / West, N.P. / Woods, K. / Naesens, L.M. / Keough, D.T. / Guddat, L.W.
History
DepositionOct 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,94316
Polymers88,5644
Non-polymers2,38012
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4728
Polymers44,2822
Non-polymers1,1906
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-44 kcal/mol
Surface area15450 Å2
MethodPISA
3
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4728
Polymers44,2822
Non-polymers1,1906
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-41 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.179, 85.525, 152.727
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hypoxanthine-guanine phosphoribosyltransferase


Mass: 22140.918 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: This sequence occurs naturally in Mycobacterium tuberculosis
Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: A5U8U8, UniProt: P9WHQ9*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-3QG / [2-({2-[bis(2-phosphonoethyl)amino]ethyl}[2-(6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl]amino)ethyl]phosphonic acid


Mass: 546.346 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H29N6O10P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG8000, 0.1 M Tris-HCl pH8.5, 0.2 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 25, 2014
RadiationMonochromator: None / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.3196→46.366 Å / Num. all: 32001 / Num. obs: 32001 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3196→46.366 Å / SU ML: 0.34 / σ(F): 1.36 / Phase error: 26.94 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 1997 6.25 %Random
Rwork0.1898 ---
all0.1927 31931 --
obs0.1935 31931 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3196→46.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5491 0 144 237 5872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075765
X-RAY DIFFRACTIONf_angle_d0.777791
X-RAY DIFFRACTIONf_dihedral_angle_d13.0042087
X-RAY DIFFRACTIONf_chiral_restr0.029907
X-RAY DIFFRACTIONf_plane_restr0.004977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3196-2.37760.34411330.27751981X-RAY DIFFRACTION94
2.3776-2.44180.35731400.2552106X-RAY DIFFRACTION100
2.4418-2.51370.31691420.2342130X-RAY DIFFRACTION100
2.5137-2.59480.27651410.23362103X-RAY DIFFRACTION100
2.5948-2.68750.31851420.23652126X-RAY DIFFRACTION100
2.6875-2.79510.34111420.24282121X-RAY DIFFRACTION100
2.7951-2.92230.32921420.22232130X-RAY DIFFRACTION100
2.9223-3.07640.28091430.21572137X-RAY DIFFRACTION100
3.0764-3.26910.25791430.20362132X-RAY DIFFRACTION100
3.2691-3.52140.22521410.17892145X-RAY DIFFRACTION100
3.5214-3.87560.23011440.16692161X-RAY DIFFRACTION100
3.8756-4.4360.18261440.1522157X-RAY DIFFRACTION100
4.436-5.58740.22231480.14342220X-RAY DIFFRACTION100
5.5874-46.37560.211520.18442285X-RAY DIFFRACTION99
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)
16.04811.8566-2.09424.0409-1.18842.9963-0.11371.0142-0.7724-0.9287-0.00561.3562-0.123-0.47190.05740.3611-0.0688-0.21370.4835-0.01860.6588-42.06349.5941-38.2202
25.94451.47575.95294.56070.96716.47750.06961.23730.1597-0.59360.0666-0.6914-0.48370.9186-0.14290.5123-0.02770.11410.32020.01380.2634-18.623511.6826-39.8682
36.6688-1.91713.49334.92211.3946.92810.12060.0259-0.2853-0.28150.2353-0.3897-0.05290.1081-0.26280.2474-0.03580.02860.1312-0.02120.3079-17.91615.4726-29.7538
45.08190.416-4.1821.2642-0.01857.9578-0.2125-0.311-0.18950.3204-0.0589-0.1769-0.0699-0.01850.25810.4159-0.0049-0.05940.3006-0.06310.3648-18.18475.5049-18.9704
55.3809-0.90272.69573.3327-1.54793.838-0.0452-0.47970.24110.20370.2095-0.2267-0.3856-0.0241-0.17960.3634-0.0366-0.03040.1869-0.03970.2938-20.241617.4566-24.1853
67.74911.5081-2.21893.9054-1.01157.07330.251-0.0187-0.19730.4152-0.12850.4619-0.3969-0.7328-0.09770.36630.0307-0.07410.24020.03860.352-37.023610.7489-30.8442
76.14985.4674-6.3038.7525-5.30466.54570.3563-0.50650.89090.43520.68081.6414-1.8396-0.9347-0.9940.54050.12520.07710.59980.10310.4967-44.993314.1512-31.786
81.41051.53342.28975.40112.53363.68920.10241.04620.0148-0.61760.8029-1.9566-0.33721.3552-0.56680.359-0.04270.28410.4914-0.12810.6684-9.3465-8.5782-39.4777
98.179-2.06-6.60672.44040.3846.3883-0.19650.7205-0.7492-0.8499-0.05550.78310.2716-0.66280.35490.5674-0.0141-0.15090.2699-0.07960.3354-33.1659-11.0984-39.6213
108.19570.34714.91156.7902-0.49019.9459-0.0030.50930.5605-0.049-0.01631.1444-0.0621-0.15210.04620.2854-0.0597-0.01690.25210.06290.4998-39.1301-5.8068-26.9505
113.49160.62590.54781.34351.26995.065-0.0063-0.321-0.21930.14340.08550.3659-0.13240.0476-0.06260.35150.06130.01190.16390.02040.4093-30.7012-5.194-22.2173
126.2814-0.4469-1.98482.19651.04894.44840.1428-0.5561-0.50240.3587-0.09990.50510.41580.136-0.03510.4293-0.0631-0.00170.20570.01030.3939-30.5631-17.114-24.329
139.44591.82920.60367.68420.44458.71710.317-0.4818-0.23110.3376-0.3003-0.79580.80060.3436-0.02570.26230.02230.0130.3102-0.09690.3252-13.9689-11.0437-30.6324
144.72912.46671.60031.31711.23755.92320.29640.6328-0.0027-0.27430.3211-2.12440.60871.1896-0.35570.35790.01230.07980.473-0.23680.8634-8.6635-11.42-34.8086
156.4243-2.6713-1.08426.13520.51084.25640.0046-1.1401-0.39170.36070.0352-0.1692-0.01140.1731-0.04660.2342-0.080.00550.53660.08350.398-31.8632-6.703916.1031
160.89291.2532-1.33185.2671.49895.9535-0.117-0.2183-0.3247-0.354-0.042-0.0519-0.10780.00350.05890.19520.0619-0.00820.35180.04090.3863-27.1889-7.91913.146
173.2659-0.1742-1.25393.48131.342.842-0.0416-0.025-0.40280.0634-0.22330.67470.0865-0.530.25030.23980.0289-0.02320.42330.02140.4689-39.1859-5.31318.1637
185.593-2.91891.44098.3155-2.1183.3026-0.4161-1.22690.22141.37130.0999-0.4911-0.31530.10070.20090.3805-0.0109-0.08050.6517-0.0140.3446-14.46093.710819.9713
198.1881-2.4906-1.42337.95092.20694.78430.3661-0.44840.2863-0.2843-0.12670.1658-0.3512-0.3273-0.21460.2669-0.027-0.02840.34150.02120.3405-24.52259.35858.6811
206.6191-4.6865-4.85783.51724.34858.8806-0.10330.18070.33990.19920.2102-0.3432-0.11240.1728-0.06970.3665-0.0288-0.05120.30190.00430.32-20.76938.8067-4.9913
216.1686-1.43921.93883.7429-1.26935.5224-0.072-0.13470.9446-0.1149-0.0147-0.7894-0.6320.74790.12480.31-0.0727-0.02330.3722-0.04370.4934-12.571313.10264.821
223.2071-0.23360.9993.70571.55243.062-0.4374-0.2426-0.29230.14060.5164-0.5355-0.04780.2797-0.06110.28070.0914-0.08650.49010.12180.6183-8.2437-5.997712.481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 78 )
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 116 )
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 169 )
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 192 )
7X-RAY DIFFRACTION7chain 'A' and (resid 193 through 201 )
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 29 )
9X-RAY DIFFRACTION9chain 'B' and (resid 30 through 48 )
10X-RAY DIFFRACTION10chain 'B' and (resid 49 through 64 )
11X-RAY DIFFRACTION11chain 'B' and (resid 65 through 116 )
12X-RAY DIFFRACTION12chain 'B' and (resid 117 through 169 )
13X-RAY DIFFRACTION13chain 'B' and (resid 170 through 189 )
14X-RAY DIFFRACTION14chain 'B' and (resid 190 through 201 )
15X-RAY DIFFRACTION15chain 'C' and (resid 17 through 68 )
16X-RAY DIFFRACTION16chain 'C' and (resid 69 through 116 )
17X-RAY DIFFRACTION17chain 'C' and (resid 117 through 202 )
18X-RAY DIFFRACTION18chain 'D' and (resid 18 through 48 )
19X-RAY DIFFRACTION19chain 'D' and (resid 49 through 92 )
20X-RAY DIFFRACTION20chain 'D' and (resid 93 through 116 )
21X-RAY DIFFRACTION21chain 'D' and (resid 117 through 167 )
22X-RAY DIFFRACTION22chain 'D' and (resid 168 through 202 )

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