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- PDB-9hs1: Crystal structure of the Escherichia coli nucleosidase PpnN (part... -

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Basic information

Entry
Database: PDB / ID: 9hs1
TitleCrystal structure of the Escherichia coli nucleosidase PpnN (partial alarmone form)
ComponentsPyrimidine/purine nucleotide 5'-monophosphate nucleosidase
KeywordsHYDROLASE / nucleosidase / pppgpp / gmp
Function / homology
Function and homology information


inosinate nucleosidase activity / pyrimidine-5'-nucleotide nucleosidase activity / pyrimidine-5'-nucleotide nucleosidase / AMP nucleosidase / AMP nucleosidase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / guanosine tetraphosphate binding / protein homotetramerization / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
: / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, C-terminal domain / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, N-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase PpnN-like superfamily / Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases / : / LOG family / Possible lysine decarboxylase
Similarity search - Domain/homology
Chem-0O2 / GUANINE / 5-O-phosphono-alpha-D-ribofuranose / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsBaerentsen, R.L. / Brodersen, D.E.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0028072 Denmark
Novo Nordisk FoundationNNF18OC0030646 Denmark
CitationJournal: Structure / Year: 2025
Title: Catalytic mechanism and differential alarmone regulation of a conserved stringent nucleosidase
Authors: Baerentsen, R.L. / Kronborg, K. / Brodersen, D.E. / Zhang, Y.E.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
B: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
C: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
D: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,89811
Polymers206,1664
Non-polymers2,7337
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9890 Å2
ΔGint-13 kcal/mol
Surface area72170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.655, 152.655, 224.541
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase / AMP nucleosidase / CMP nucleosidase / GMP nucleosidase / IMP nucleosidase / UMP nucleosidase / dTMP ...AMP nucleosidase / CMP nucleosidase / GMP nucleosidase / IMP nucleosidase / UMP nucleosidase / dTMP nucleosidase


Mass: 51541.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal Histag / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ppnN, ygdH, b2795, JW2766 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0ADR8, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, pyrimidine-5'-nucleotide nucleosidase, AMP nucleosidase
#2: Chemical ChemComp-0O2 / guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)


Mass: 683.140 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H18N5O20P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-HSX / 5-O-phosphono-alpha-D-ribofuranose / 5-O-phosphono-alpha-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
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: 3.21 Å3/Da / Density % sol: 61.62 % / Description: Octahedral
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 7 mg/ml 0.1M NaCl 0.1M BICINE pH 9.0 30% v/v PEG 500 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.36→49.63 Å / Num. obs: 108735 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 56.27 Å2 / CC1/2: 0.99 / CC star: 1 / Rrim(I) all: 0.06 / Net I/σ(I): 13.71
Reflection shellResolution: 2.36→2.45 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.66 / Num. unique obs: 10721 / CC1/2: 0.36 / CC star: 0.73 / Rrim(I) all: 1.45 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→49.63 Å / SU ML: 0.3751 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2414 5438 5 %
Rwork0.1941 103218 -
obs0.1964 108656 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.76 Å2
Refinement stepCycle: LAST / Resolution: 2.36→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14175 0 167 298 14640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814624
X-RAY DIFFRACTIONf_angle_d0.951519820
X-RAY DIFFRACTIONf_chiral_restr0.05242190
X-RAY DIFFRACTIONf_plane_restr0.00842587
X-RAY DIFFRACTIONf_dihedral_angle_d8.41872004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.390.38511860.37283356X-RAY DIFFRACTION98.72
2.39-2.420.41041770.34623396X-RAY DIFFRACTION99.8
2.42-2.450.40321850.32953375X-RAY DIFFRACTION99.97
2.45-2.480.38191730.33163399X-RAY DIFFRACTION99.97
2.48-2.510.34691790.30743417X-RAY DIFFRACTION100
2.51-2.550.34611890.30613366X-RAY DIFFRACTION100
2.55-2.580.30781780.26653411X-RAY DIFFRACTION100
2.58-2.620.311730.25883406X-RAY DIFFRACTION100
2.62-2.660.32221750.2433405X-RAY DIFFRACTION100
2.66-2.70.29931670.24653408X-RAY DIFFRACTION100
2.7-2.750.30871680.2383423X-RAY DIFFRACTION100
2.75-2.80.27371610.23363436X-RAY DIFFRACTION100
2.8-2.860.29741900.24353394X-RAY DIFFRACTION99.97
2.86-2.910.29841610.25133452X-RAY DIFFRACTION100
2.91-2.980.32411770.25253381X-RAY DIFFRACTION100
2.98-3.050.3041810.25773450X-RAY DIFFRACTION100
3.05-3.120.27141960.23263406X-RAY DIFFRACTION99.94
3.12-3.210.27531660.21443429X-RAY DIFFRACTION100
3.21-3.30.26782040.21153410X-RAY DIFFRACTION100
3.3-3.410.26281760.19783447X-RAY DIFFRACTION100
3.41-3.530.24851920.1953429X-RAY DIFFRACTION100
3.53-3.670.21611920.18093444X-RAY DIFFRACTION99.97
3.67-3.840.23371800.17443454X-RAY DIFFRACTION99.97
3.84-4.040.2121780.16813455X-RAY DIFFRACTION100
4.04-4.290.20211820.15513457X-RAY DIFFRACTION100
4.29-4.620.18111980.14463480X-RAY DIFFRACTION100
4.62-5.090.19631820.15163511X-RAY DIFFRACTION100
5.09-5.820.21741840.18483524X-RAY DIFFRACTION100
5.82-7.330.24171910.19023565X-RAY DIFFRACTION100
7.34-49.630.18651970.14953732X-RAY DIFFRACTION99.42

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