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- PDB-8ry8: CryoEM structure of M. smegmatis GMP reductase apoform at pH 7.8,... -

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Basic information

Entry
Database: PDB / ID: 8ry8
TitleCryoEM structure of M. smegmatis GMP reductase apoform at pH 7.8, 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
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsDolezal, M. / Kouba, T. / Svachova, H. / Pichova, I.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for allosteric regulation of mycobacterial guanosine 5´-monophosphate reductase by ATP and GTP.
Authors: Michal Doležal / Zdeněk Knejzlík / Tomáš Kouba / Anatolij Filimoněnko / Hana Šváchová / Matteo Dedola / Martin Klíma / Iva Pichová /
Abstract: Guanosine 5'-monophosphate reductase (GMPR) is a crucial enzyme in the purine salvage pathway that catalyses the NADPH-dependent conversion of GMP to IMP, thereby contributing to purine nucleotide ...Guanosine 5'-monophosphate reductase (GMPR) is a crucial enzyme in the purine salvage pathway that catalyses the NADPH-dependent conversion of GMP to IMP, thereby contributing to purine nucleotide homeostasis. Mycobacterium smegmatis GMPR (MsmGMPR) contains a regulatory cystathionine β-synthase (CBS) domain, which mediates allosteric modulation by ATP and GTP. However, MsmGMPR exhibits an atypical tertiary structure that is incompatible with the acknowledged regulatory mechanisms of IMPDH/GMPR family enzymes. Here, we combine X-ray crystallography, cryogenic electron microscopy, and biochemical binding assays to elucidate the molecular basis of MsmGMPR regulation by ATP and GTP. We show that ATP stabilises a compressed conformation that inhibits the enzyme by restricting access to the active site and preventing NADPH binding. In contrast, GTP counteracts ATP binding, promoting an active conformation that enables catalysis. Our results provide insight into how MsmGMPR senses and responds to the purine nucleotide balance, revealing a distinct utilisation of the CBS domain compared with its typical role in IMPDH/GMPR enzymes.
History
DepositionFeb 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)414,2598
Polymers414,2598
Non-polymers00
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 (eV)
d_1ens_1chain C
d_2ens_1chain A
d_1ens_2chain B
d_2ens_2chain D
d_1ens_3chain G
d_2ens_3chain E
d_1ens_4chain H
d_2ens_4chain F
d_1ens_5chain H
d_2ens_5chain B
d_3ens_5chain C
d_4ens_5chain D
d_5ens_5chain E
d_6ens_5chain F
d_7ens_5chain G
d_8ens_5chain A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 2 - 470 / Label seq-ID: 2 - 470

Dom-IDEns-IDAuth asym-IDLabel asym-ID
d_1ens_1CC
d_2ens_1AA
d_1ens_2BB
d_2ens_2DD
d_1ens_3GG
d_2ens_3EE
d_1ens_4HH
d_2ens_4FF
d_1ens_5HH
d_2ens_5BB
d_3ens_5CC
d_4ens_5DD
d_5ens_5EE
d_6ens_5FF
d_7ens_5GG
d_8ens_5AA

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(-0.999986916794, 0.00187157332122, 0.00476061484891), (-0.00187278573516, -0.999998215027, -0.000250230828386), (0.004760138026, -0.000259143166144, 0.999988636901)468.776978965, 470.620182629, -0.917289052013
2given(-0.999999592686, 8.23324330158E-5, -0.000898804015591), (-8.14226118716E-5, -0.999999484363, -0.00101224720772), (-0.00089888689291, -0.00101217361245, 0.999999083753)470.307671002, 470.392024982, 0.419795524684
3given(-0.999998652913, 0.00129238367424, -0.00101188722307), (-0.00129095290042, -0.999998167947, -0.00141334440001), (-0.00101371195246, -0.00141203619737, 0.99999848927)470.123603442, 470.882622925, 0.581915753548
4given(-0.99999887932, 0.000856700124793, 0.00122777174427), (-0.000857808552007, -0.99999922478, -0.000902553769624), (0.00122699757455, -0.000903605951252, 0.999998838986)469.591574891, 470.613759759, -0.0348336281392
5given(0.980480731264, 0.196603792712, -0.00211761914031), (0.196600420309, -0.980482220922, -0.00169976200336), (-0.00241046757433, 0.00125025907899, -0.999996313242)-41.0180567761, 419.842797116, 471.629412777
6given(0.197059664096, -0.980387833569, -0.00268040613811), (-0.980385415883, -0.197067335294, 0.00298356903973), (-0.00345327528231, 0.00203988997367, -0.999991956837)419.956232494, 511.021820792, 471.673787733
7given(-0.980461978772, -0.196685561858, 0.00301627903211), (-0.196677712248, 0.980464441783, 0.00271217702664), (-0.00349080039983, 0.00206595159478, -0.999991773044)510.93637534, 50.0753785933, 471.660692964
8given(-0.000457171477143, -0.999998167909, -0.00185880955066), (0.999997038722, -0.000452726265273, -0.00239114733027), (0.00239030141756, -0.00185989721057, 0.99999541361)470.774579332, 0.79827286454, -0.0814158214123
9given(-0.99999887932, 0.000856700124793, 0.00122777174427), (-0.000857808552007, -0.99999922478, -0.000902553769624), (0.00122699757455, -0.000903605951252, 0.999998838986)469.591574891, 470.613759759, -0.0348336281392
10given(-0.000836201293371, 0.999999290673, 0.00084818660208), (-0.999999172708, -0.000837029628444, 0.000976710933221), (0.00097742019773, -0.000847369173436, 0.999999163307)-0.0434458303655, 470.0852668, 0.000401796661663
11given(-0.198908388806, 0.98001589212, -0.00207462151758), (0.980015479514, 0.198902529419, -0.00272831508643), (-0.00226114467598, -0.00257584595936, -0.999994126104)52.0281128821, -41.30524136, 472.617760828

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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
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 apoform at pH 7.8 / Type: COMPLEX / Entity ID: all / 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: 7.8
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 in the storage buffer (50 mM Tris, pH 8.0, 2.5 mM TCEP) was diluted with the cryoEM buffer (50 mM HEPES, pH 7.8, 100 mM KCl, 2 mM MgCl2).
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
7MOLREP11.9.02model fitting
8UCSF ChimeraX1.5model fitting
11RELION4final Euler assignment
14Coot0.9.8.1model refinement
15PHENIX1.21rc1_4985model refinement
16ISOLDE1.5model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191909 / 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: 92.25 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001827752
ELECTRON MICROSCOPYf_angle_d0.445337776
ELECTRON MICROSCOPYf_chiral_restr0.0414496
ELECTRON MICROSCOPYf_plane_restr0.00355000
ELECTRON MICROSCOPYf_dihedral_angle_d3.06934064
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints7.95277560281E-13
ens_2d_2BBELECTRON MICROSCOPYNCS constraints4.8733442593E-11
ens_3d_2GGELECTRON MICROSCOPYNCS constraints8.00357726514E-13
ens_4d_2HHELECTRON MICROSCOPYNCS constraints8.39583496316E-13
ens_5d_2HHELECTRON MICROSCOPYNCS constraints7.83546951776E-13
ens_5d_3HHELECTRON MICROSCOPYNCS constraints1.91331556106E-11
ens_5d_4HHELECTRON MICROSCOPYNCS constraints2.17203560146E-11
ens_5d_5HHELECTRON MICROSCOPYNCS constraints5.88600819661E-13
ens_5d_6HHELECTRON MICROSCOPYNCS constraints8.39583496316E-13
ens_5d_7HHELECTRON MICROSCOPYNCS constraints7.44313142145E-13
ens_5d_8HHELECTRON MICROSCOPYNCS constraints4.20117696293E-10

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