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- PDB-9hg3: Crystal structure of M. smegmatis GMP reductase in complex with G... -

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Basic information

Entry
Database: PDB / ID: 9hg3
TitleCrystal structure of M. smegmatis GMP reductase in complex with GMP and GTP.
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDolezal, M. / 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
DepositionNov 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
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
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43770 Å2
ΔGint-235 kcal/mol
Surface area130290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.080, 145.930, 146.320
Angle α, β, γ (deg.)90.000, 95.929, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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
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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 0.03 M Magnesium chloride 0.03 M Calcium chloride 20% (v/v) Ethylene glycol 8.5% (v/v) PEG 8000 0.1 M Tris/BICINE, pH 8.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 15, 2024
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→112.5 Å / Num. obs: 410206 / % possible obs: 98.42 % / Redundancy: 3.5 % / Biso Wilson estimate: 57.68 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1591 / Rpim(I) all: 0.09933 / Rrim(I) all: 0.1881 / Net I/σ(I): 5.03
Reflection shellResolution: 2.3→2.33 Å / Redundancy: 3.5 % / Rmerge(I) obs: 4.465 / Mean I/σ(I) obs: 0.22 / Num. unique obs: 13569 / CC1/2: 0.087 / CC star: 0.4 / Rpim(I) all: 2.785 / Rrim(I) all: 5.277 / % possible all: 87.28

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Processing

Software
NameVersionClassification
XDS20230630data reduction
XSCALE20230630data scaling
PHASER2.8.3phasing
Coot0.9.8.1 ELmodel building
PHENIX1.21_5204refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→112.48 Å / SU ML: 0.489 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.6976
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2739 10300 5 %
Rwork0.2496 195541 -
obs0.2508 205841 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.41 Å2
Refinement stepCycle: LAST / Resolution: 2.3→112.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26752 0 448 0 27200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00227928
X-RAY DIFFRACTIONf_angle_d0.433638184
X-RAY DIFFRACTIONf_chiral_restr0.04124528
X-RAY DIFFRACTIONf_plane_restr0.00415048
X-RAY DIFFRACTIONf_dihedral_angle_d10.394810168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.41342980.41845719X-RAY DIFFRACTION87.28
2.33-2.350.41113310.40346164X-RAY DIFFRACTION92.52
2.35-2.380.44133350.39736300X-RAY DIFFRACTION96.15
2.38-2.410.43633340.38766333X-RAY DIFFRACTION96.61
2.41-2.440.39383430.38696493X-RAY DIFFRACTION97.88
2.44-2.480.39173390.37526454X-RAY DIFFRACTION97.54
2.48-2.510.37583400.35966474X-RAY DIFFRACTION97.69
2.51-2.550.39763460.35796555X-RAY DIFFRACTION99.75
2.55-2.590.36753470.34256585X-RAY DIFFRACTION99.81
2.59-2.630.36473470.32956621X-RAY DIFFRACTION99.74
2.63-2.680.32433460.32646574X-RAY DIFFRACTION99.75
2.68-2.730.35683470.31796573X-RAY DIFFRACTION99.77
2.73-2.780.36543460.32226589X-RAY DIFFRACTION99.74
2.78-2.840.34223480.32446600X-RAY DIFFRACTION99.54
2.84-2.90.34133470.32676591X-RAY DIFFRACTION99.57
2.9-2.970.36643460.33056581X-RAY DIFFRACTION99.55
2.97-3.040.34613470.3146577X-RAY DIFFRACTION99.47
3.04-3.120.32213470.29726589X-RAY DIFFRACTION99.57
3.12-3.210.31093450.28386560X-RAY DIFFRACTION99.38
3.21-3.320.32523450.2676556X-RAY DIFFRACTION98.94
3.32-3.440.30053480.26516612X-RAY DIFFRACTION99.91
3.44-3.570.30613490.26196623X-RAY DIFFRACTION99.86
3.57-3.740.29313480.24156636X-RAY DIFFRACTION99.83
3.74-3.930.23923480.22536610X-RAY DIFFRACTION99.78
3.93-4.180.20983470.2036595X-RAY DIFFRACTION99.27
4.18-4.50.21693460.19176558X-RAY DIFFRACTION98.91
4.5-4.950.2293440.19876525X-RAY DIFFRACTION98.13
4.96-5.670.22543500.216652X-RAY DIFFRACTION99.87
5.67-7.150.24783520.21766674X-RAY DIFFRACTION99.83
7.15-112.480.17413440.17966568X-RAY DIFFRACTION96.78

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