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- PDB-1kqo: Crystal structure of NMN/NaMN adenylyltransferase complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1kqo
TitleCrystal structure of NMN/NaMN adenylyltransferase complexed with deamido-NAD
ComponentsNICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
KeywordsTRANSFERASE / nucleotidyltransferase superfamily
Function / homology
Function and homology information


negative regulation of apoptotic DNA fragmentation / protein ADP-ribosyltransferase-substrate adaptor activity / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / ATP generation from poly-ADP-D-ribose / NAD+ biosynthetic process ...negative regulation of apoptotic DNA fragmentation / protein ADP-ribosyltransferase-substrate adaptor activity / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / ATP generation from poly-ADP-D-ribose / NAD+ biosynthetic process / neuron projection maintenance / response to wounding / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / nuclear body / negative regulation of DNA-templated transcription / chromatin / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
Nicotinamide/nicotinate mononucleotide adenylyltransferase, eukaryotic / : / Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINIC ACID ADENINE DINUCLEOTIDE / Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhou, T. / Kurnasov, O. / Tomchick, D.R. / Binns, D.D. / Grishin, N.V. / Marquez, V.E. / Osterman, A.L. / Zhang, H.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure of Hhuman of Nicotinamide/Nicotinic Acid Mononucleotide Adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin.
Authors: Zhou, T. / Kurnasov, O. / Tomchick, D.R. / Binns, D.D. / Grishin, N.V. / Marquez, V.E. / Osterman, A.L. / Zhang, H.
History
DepositionJan 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 22, 2014Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
B: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
C: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
D: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
E: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
F: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,88812
Polymers191,8956
Non-polymers3,9936
Water7,332407
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.245, 90.391, 137.673
Angle α, β, γ (deg.)90.00, 117.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE / NMNAT


Mass: 31982.502 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HAN9, nicotinamide-nucleotide adenylyltransferase
#2: Chemical
ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N6O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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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: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Na Formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
2100 mMHEPES1droppH7.2
30.5 M1dropNaCl
42 mMdithiothreitol1drop
51 mMEDTA1drop
60.03 %Brij-351drop
710 mMNAD1drop
80.1 Msodium acetate1reservoirpH4.2-4.6
91.6-1.8 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 7, 2001 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 99394 / Num. obs: 95507 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellHighest resolution: 2.5 Å
Reflection
*PLUS
Num. measured all: 275083 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 96.4 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.246 4453 Random
Rwork0.21 --
all-88627 -
obs-88627 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11250 0 264 407 11921
Refinement
*PLUS
Highest resolution: 2.5 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.53

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