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- PDB-1kr2: CRYSTAL STRUCTURE OF HUMAN NMN/NAMN ADENYLYL TRANSFERASE COMPLEXE... -

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Basic information

Entry
Database: PDB / ID: 1kr2
TitleCRYSTAL STRUCTURE OF HUMAN NMN/NAMN ADENYLYL TRANSFERASE COMPLEXED WITH TIAZOFURIN ADENINE DINUCLEOTIDE (TAD)
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
Chem-TAD / Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)195,90012
Polymers191,8956
Non-polymers4,0056
Water12,737707
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.477, 89.391, 137.753
Angle α, β, γ (deg.)90.00, 117.42, 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-TAD / BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE DINUCLEOTIDE


Mass: 667.480 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H27N7O13P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 707 / 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: 3.74 Å3/Da / Density % sol: 67.14 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
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 2, 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: 2.3→20 Å / Num. obs: 132752 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 30.7
Reflection
*PLUS
Highest resolution: 2.25 Å / Num. measured all: 453541
Reflection shell
*PLUS
% possible obs: 85.5 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KR2

Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.231 6128 RANDOM
Rwork0.203 --
all-126076 -
obs-121210 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11227 0 258 707 12192
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0014
X-RAY DIFFRACTIONc_angle_deg1.7
Refinement
*PLUS
Highest resolution: 2.25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.014

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