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- PDB-2c6q: Crystal structure of human guanosine monophosphate reductase 2 GM... -

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Basic information

Entry
Database: PDB / ID: 2c6q
TitleCrystal structure of human guanosine monophosphate reductase 2 GMPR2 in complex with IMP and NADPH
ComponentsGMP REDUCTASE 2
KeywordsOXIDOREDUCTASE / TIM BARREL / METAL-BINDING / NADP / POTASSIUM
Function / homology
Function and homology information


GMP reductase / GMP reductase complex / GMP reductase activity / GMP metabolic process / Purine salvage / purine nucleobase metabolic process / metal ion binding / cytosol
Similarity search - Function
GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / Chem-NDP / GMP reductase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKursula, P. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Kotenyova, T. ...Kursula, P. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Kotenyova, T. / Nilsson-Ehle, P. / Ogg, D. / Persson, C. / Sagemark, J. / Schuler, H. / Sundstrom, M. / Thorsell, A. / Weigelt, J. / Nordlund, P.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Cofactor Mobility Determines Reaction Outcome in the Impdh and Gmpr (Beta-Alpha)(8) Barrel Enzymes.
Authors: Patton, G.C. / Stenmark, P. / Gollapalli, D.R. / Sevastik, R. / Kursula, P. / Flodin, S. / Schuler, H. / Swales, C.T. / Eklund, H. / Himo, F. / Nordlund, P. / Hedstrom, L.
History
DepositionNov 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 30, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GMP REDUCTASE 2
B: GMP REDUCTASE 2
C: GMP REDUCTASE 2
D: GMP REDUCTASE 2
E: GMP REDUCTASE 2
F: GMP REDUCTASE 2
G: GMP REDUCTASE 2
H: GMP REDUCTASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,26423
Polymers305,2608
Non-polymers8,00415
Water46,2812569
1
A: GMP REDUCTASE 2
B: GMP REDUCTASE 2
C: GMP REDUCTASE 2
D: GMP REDUCTASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,00512
Polymers152,6304
Non-polymers4,3758
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18690 Å2
ΔGint-46.5 kcal/mol
Surface area45250 Å2
MethodPISA
2
E: GMP REDUCTASE 2
F: GMP REDUCTASE 2
G: GMP REDUCTASE 2
H: GMP REDUCTASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,25911
Polymers152,6304
Non-polymers3,6297
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16670 Å2
ΔGint-50.4 kcal/mol
Surface area45580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.676, 141.366, 164.318
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
GMP REDUCTASE 2 / / GUANOSINE MONOPHOSPHATE REDUCTASE 2 / GUANOSINE 5'-MONOPHOSPHATE OXIDOREDUCTASE 2


Mass: 38157.543 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9P2T1, GMP reductase
#2: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2569 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES THE IRREVERSIBLE NADPH-DEPENDENT DEAMINATION OF GMP TO IMP

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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: 2.37 Å3/Da / Density % sol: 47.68 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. obs: 332307 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BZN

2bzn


Resolution: 1.7→10 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.771 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 16714 5 %RANDOM
Rwork0.163 ---
obs0.165 315592 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.64 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19909 0 520 2569 22998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02220897
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218808
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9928211
X-RAY DIFFRACTIONr_angle_other_deg0.8892.99743883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40352625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35123.589822
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.082153621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.29515120
X-RAY DIFFRACTIONr_chiral_restr0.1030.23126
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024173
X-RAY DIFFRACTIONr_nbd_refined0.2150.24259
X-RAY DIFFRACTIONr_nbd_other0.1950.219787
X-RAY DIFFRACTIONr_nbtor_refined0.1820.210208
X-RAY DIFFRACTIONr_nbtor_other0.0880.212084
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.22171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.155216529
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.453320679
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.22149240
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.47157532
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 1193
Rwork0.26 22617
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)
11.1010.06140.15050.77570.1131.16790.0172-0.1154-0.05590.1179-0.0348-0.02990.03990.12230.0176-0.1286-0.0188-0.0378-0.07010.0127-0.129722.147-4.66623.325
20.8808-0.07450.19781.1012-0.17980.9754-0.0045-0.09320.11020.14710.03770.0489-0.1705-0.0501-0.0332-0.0623-0.03310.0134-0.1214-0.0234-0.103-4.58627.43421.395
31.0456-0.1126-0.16040.75670.02420.59810.0521-0.0523-0.019-0.0348-0.0236-0.07220.03470.0585-0.0285-0.1399-0.00650.0168-0.12020.0129-0.142426.768-3.241-18.304
40.95390.0319-0.29631.22740.03250.81740.03780.14850.0754-0.18-0.03590.0487-0.1053-0.0302-0.0019-0.0948-0.00630.0035-0.1330.0291-0.1018-0.09628.799-20.187
50.95650.0448-0.11670.9664-0.09930.69240.0059-0.17120.0280.0963-0.0097-0.04880.03860.05350.0038-0.1413-0.01220.0067-0.1395-0.0124-0.1475-24.504-21.69525.972
60.7478-0.0009-0.06310.77280.0690.97480.01850.0626-0.0953-0.0113-0.0136-0.02610.15270.0706-0.005-0.10110.0366-0.0067-0.1667-0.0061-0.1165-4.385-39.482-6.218
70.95240.0997-0.11930.6523-0.08781.34210.03610.01420.08060.0297-0.01010.0871-0.1798-0.1654-0.026-0.13510.0428-0.0058-0.14780.0074-0.0788-43.1855.069-1.59
80.8716-0.09410.2380.7869-0.01540.9384-0.01140.10690.0612-0.11760.01350.02150.0014-0.001-0.0021-0.13060.0021-0.0137-0.12970.0056-0.144-23.061-13.157-32.718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 336
2X-RAY DIFFRACTION2B9 - 337
3X-RAY DIFFRACTION3C9 - 336
4X-RAY DIFFRACTION4D9 - 336
5X-RAY DIFFRACTION5E9 - 336
6X-RAY DIFFRACTION6F9 - 336
7X-RAY DIFFRACTION7G9 - 337
8X-RAY DIFFRACTION8H9 - 336

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