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- PDB-9rpm: Structure of Arabidopsis thaliana nicotinate mononucleotide adeny... -

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Basic information

Entry
Database: PDB / ID: 9rpm
TitleStructure of Arabidopsis thaliana nicotinate mononucleotide adenylyltransferase in complex with nicotinate mononucleotide (NaMN)
ComponentsNicotinamide/nicotinic acid mononucleotide adenylyltransferase
KeywordsTRANSFERASE / NAD metabolism / NaMN / Arabidopsis thaliana / NaMNAT
Function / homology
Function and homology information


pollen tube growth / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / pollen development / nicotinate-nucleotide adenylyltransferase activity / NAD+ biosynthetic process / ATP binding / metal ion binding / nucleus
Similarity search - Function
Nicotinamide/nicotinate mononucleotide adenylyltransferase, eukaryotic / : / Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
NICOTINATE MONONUCLEOTIDE / Nicotinamide/nicotinic acid mononucleotide adenylyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.66 Å
AuthorsSorci, L. / Cianci, M. / Fortunato, C. / Gasparrini, M. / Raffaelli, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Arabidopsis thaliana nicotinate mononucleotide adenylyltransferase: unveiling the molecular determinants and evolutionary origin of nicotinic acid mononucleotide recognition.
Authors: Sorci, L. / Cianci, M. / Fortunato, C. / Gasparrini, M. / Raffaelli, N.
History
DepositionJun 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotinamide/nicotinic acid mononucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1283
Polymers29,7681
Non-polymers3602
Water23413
1
A: Nicotinamide/nicotinic acid mononucleotide adenylyltransferase
hetero molecules

A: Nicotinamide/nicotinic acid mononucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2556
Polymers59,5362
Non-polymers7194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3770 Å2
ΔGint-25 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.347, 43.347, 433.508
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Nicotinamide/nicotinic acid mononucleotide adenylyltransferase / NMN/NaMN adenylyltransferase / Nicotinamide mononucleotide adenylyltransferase / NMN ...NMN/NaMN adenylyltransferase / Nicotinamide mononucleotide adenylyltransferase / NMN adenylyltransferase / Nicotinate-nucleotide adenylyltransferase / NaMN adenylyltransferase


Mass: 29768.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NMNAT, At5g55810, MDF20.25 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: F4K687, nicotinamide-nucleotide adenylyltransferase, nicotinate-nucleotide adenylyltransferase
#2: Chemical ChemComp-NCN / NICOTINATE MONONUCLEOTIDE / NAMN


Mass: 335.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14NO9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM TRIS pH 8-9, 100-200 mM MgCl2, and 20-40% (w/v) poly ethylene glycol.

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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: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.66→37.54 Å / Num. obs: 7846 / % possible obs: 98.45 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Biso Wilson estimate: 66.77 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.041 / Net I/σ(I): 11.7
Reflection shellResolution: 2.66→2.76 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 678 / CC1/2: 0.95 / CC star: 0.987 / Rpim(I) all: 0.535 / % possible all: 87.93

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSBUILT=20210323data reduction
Aimless0.7.4data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.66→37.54 Å / SU ML: 0.1611 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.5855
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3048 383 4.9 %
Rwork0.2614 7433 -
obs0.2636 7816 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.74 Å2
Refinement stepCycle: LAST / Resolution: 2.66→37.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 23 13 1809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00151826
X-RAY DIFFRACTIONf_angle_d0.40772472
X-RAY DIFFRACTIONf_chiral_restr0.039288
X-RAY DIFFRACTIONf_plane_restr0.0039311
X-RAY DIFFRACTIONf_dihedral_angle_d19.9741707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-3.040.31031190.31632289X-RAY DIFFRACTION95.94
3.05-3.840.3271180.29922458X-RAY DIFFRACTION99.5
3.84-37.540.29691460.2372686X-RAY DIFFRACTION99.75

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