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- PDB-8ry3: CryoEM structure of M. smegmatis GMP reductase in complex with GM... -

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Basic information

Entry
Database: PDB / ID: 8ry3
TitleCryoEM structure of M. smegmatis GMP reductase in complex with GMP and GTP at pH 6.6, extended conformation I.
ComponentsGMP reductase
KeywordsOXIDOREDUCTASE / GMP reductase / GuaB1 / CBS domain / Mycobacterium smegmatis
Function / homology
Function and homology information


GMP reductase / GMP reductase activity / IMP salvage / IMP dehydrogenase activity / purine ribonucleoside salvage / cytosol
Similarity search - Function
GMP reductase-like / : / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / GMP reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsDolezal, M. / Kouba, T. / Pichova, I.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: To Be Published
Title: Structural basis for allosteric regulation of mycobacterial guanosine 5'-monophosphate reductase with ATP and GTP.
Authors: Dolezal, M. / Knejzlik, Z. / Kouba, T. / Filimonenko, A. / Svachova, H. / Klima, M. / Pichova, I.
History
DepositionFeb 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)421,35124
Polymers414,2598
Non-polymers7,09116
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain C
d_2ens_1chain B
d_3ens_1chain A
d_4ens_1chain D
d_5ens_1chain E
d_6ens_1chain F
d_7ens_1chain G
d_8ens_1chain H

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11VALVALALAALACC2 - 4812 - 481
d_125GP5GP5GP5GPCM501
d_13GTPGTPGTPGTPCN502
d_21VALVALALAALABB2 - 4812 - 481
d_225GP5GP5GP5GPBK501
d_23GTPGTPGTPGTPBL502
d_31VALVALALAALAAA2 - 4812 - 481
d_325GP5GP5GP5GPAI501
d_33GTPGTPGTPGTPAJ502
d_41VALVALALAALADD2 - 4812 - 481
d_425GP5GP5GP5GPDO501
d_43GTPGTPGTPGTPDP502
d_51VALVALALAALAEE2 - 4812 - 481
d_525GP5GP5GP5GPEQ501
d_53GTPGTPGTPGTPER502
d_61VALVALALAALAFF2 - 4812 - 481
d_625GP5GP5GP5GPFS501
d_63GTPGTPGTPGTPFT502
d_71VALVALALAALAGG2 - 4812 - 481
d_725GP5GP5GP5GPGU501
d_73GTPGTPGTPGTPGV502
d_81VALVALALAALAHH2 - 4812 - 481
d_825GP5GP5GP5GPHW501
d_83GTPGTPGTPGTPHX502

NCS oper:
IDCodeMatrixVector
1given(-6.50889939359E-5, -0.999999825341, 0.000587436775472), (0.999999942882, -6.48941488621E-5, 0.000331699850091), (-0.000331661670947, 0.000587458331928, 0.999999772447)385.760760183, -0.0202371653483, -0.0117281380202
2given(-0.999997926088, 0.00162743329767, 0.00122445147144), (-0.0016262245236, -0.999998190072, 0.000987545209187), (0.00122605641923, 0.000985551928094, 0.999998762736)385.383556198, 386.047605205, -0.423974479922
3given(0.000190687668772, 0.999999722043, -0.000720799628245), (-0.99999990082, 0.000190397488451, -0.000402628301961), (-0.000402490951609, 0.000720876333008, 0.999999659169)0.0755698097604, 385.859511633, -0.0195658471406
4given(-0.999808374248, -0.0195527767234, -0.000950634288708), (-0.0195514911802, 0.999807948936, -0.00134329341799), (0.000976716834657, -0.00132444969047, -0.999998645928)389.736277575, 4.00592541236, 385.815529533
5given(0.02028401138, -0.999793097503, 0.00152350510799), (-0.999794181626, -0.0202845829683, -0.00036066805637), (0.000391497099014, -0.00151587574769, -0.999998774425)381.637880396, 389.783739996, 385.960197077
6given(0.999810544573, 0.0194423092743, 0.000933579848172), (0.0194410144667, -0.999810058019, 0.0013765320593), (0.000960165484189, -0.00135812152849, -0.999998616793)-3.86627181301, 381.860216159, 385.82339241
7given(-0.0204089257243, 0.999790535247, -0.00153667860941), (0.999791635512, 0.0204095174115, 0.000370349373998), (0.000401634667693, -0.00152879998729, -0.999998750729)4.24322571083, -3.95472825252, 385.959425392

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Components

#1: Protein
GMP reductase / Guanosine 5'-monophosphate reductase / GMPR


Mass: 51782.434 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Guanosine 5'-monophosphate reductase / Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: guaB1, MSMEG_3634, MSMEI_3548 / Plasmid: pTriex / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QYE8, GMP reductase
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Msm GMPR with GMP and GTP at pH 6.6 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pTriex
Buffer solutionpH: 6.6
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acidHEPES1
2100 mMPotassium chlorideKCl1
32 mMMagnesium chlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 20 mg/ml Msm GMPR with 2 mM GMP and 2 mM GTP in the storage buffer (50 mM Tris, pH 8.0, 2.5 mM TCEP) was diluted with the cryoEM buffer (50 mM HEPES, pH 6.6, 100 mM KCl, 2 mM MgCl2).
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
7MOLREP11.9.02model fitting
8UCSF ChimeraX1.5model fitting
13RELION43D reconstruction
20PHENIX1.21rc1_4985model refinement
21Coot0.9.8.1 ELmodel refinement
22ISOLDE1.5model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72987 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Details: The initial structure was obtained by fitting an appropriate model into the cryo-EM map using MolRep and ChimeraX. The structure was then refined by iterative manual rebuilding in Coot and ...Details: The initial structure was obtained by fitting an appropriate model into the cryo-EM map using MolRep and ChimeraX. The structure was then refined by iterative manual rebuilding in Coot and Isolde, and automatic refinement in phenix.real_space_refine.
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 58.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002929016
ELECTRON MICROSCOPYf_angle_d0.5639696
ELECTRON MICROSCOPYf_chiral_restr0.04184648
ELECTRON MICROSCOPYf_plane_restr0.00365272
ELECTRON MICROSCOPYf_dihedral_angle_d4.4034656
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DDELECTRON MICROSCOPYNCS constraints2.1915097925E-10
ens_1d_3DDELECTRON MICROSCOPYNCS constraints7.92517318638E-11
ens_1d_4DDELECTRON MICROSCOPYNCS constraints9.30125419339E-14
ens_1d_5DDELECTRON MICROSCOPYNCS constraints3.97640866641E-11
ens_1d_6DDELECTRON MICROSCOPYNCS constraints3.35652980622E-13
ens_1d_7DDELECTRON MICROSCOPYNCS constraints8.29469720956E-13
ens_1d_8DDELECTRON MICROSCOPYNCS constraints4.0926995458E-13

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