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- PDB-8dse: Human NAMPT in complex with substrate NAM and activator quercitrin -

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Basic information

Entry
Database: PDB / ID: 8dse
TitleHuman NAMPT in complex with substrate NAM and activator quercitrin
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / NAD biosynthesis enzyme:activator complex
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase activity / nicotinamide phosphoribosyltransferase / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / : / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression ...nicotinamide phosphoribosyltransferase activity / nicotinamide phosphoribosyltransferase / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / : / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression / cell junction / cell-cell signaling / nuclear speck / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
Nicotinamide phosphoribosyl transferase / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldolase-type TIM barrel
Similarity search - Domain/homology
NICOTINAMIDE / PHOSPHATE ION / Chem-QCT / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.428 Å
AuthorsRatia, K. / Xiong, R. / Shen, Z. / Thatcher, G.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG067771 United States
CitationJournal: Biochemistry / Year: 2023
Title: Mechanism of Allosteric Modulation of Nicotinamide Phosphoribosyltransferase to Elevate Cellular NAD.
Authors: Ratia, K.M. / Shen, Z. / Gordon-Blake, J. / Lee, H. / Laham, M.S. / Krider, I.S. / Christie, N. / Ackerman-Berrier, M. / Penton, C. / Knowles, N.G. / Musku, S.R. / Fu, J. / Velma, G.R. / ...Authors: Ratia, K.M. / Shen, Z. / Gordon-Blake, J. / Lee, H. / Laham, M.S. / Krider, I.S. / Christie, N. / Ackerman-Berrier, M. / Penton, C. / Knowles, N.G. / Musku, S.R. / Fu, J. / Velma, G.R. / Xiong, R. / Thatcher, G.R.J.
History
DepositionJul 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotinamide phosphoribosyltransferase
B: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,76911
Polymers113,3322
Non-polymers1,4379
Water17,511972
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-78 kcal/mol
Surface area32170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.865, 106.786, 82.689
Angle α, β, γ (deg.)90.000, 96.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nicotinamide phosphoribosyltransferase / NAmPRTase / Nampt / Pre-B-cell colony-enhancing factor 1 / Pre-B cell-enhancing factor / Visfatin


Mass: 56666.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT, PBEF, PBEF1 / Production host: Escherichia coli (E. coli)
References: UniProt: P43490, nicotinamide phosphoribosyltransferase

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Non-polymers , 5 types, 981 molecules

#2: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-QCT / 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside / quercitrin


Mass: 448.377 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20O11 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 972 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.2 M NaCl, 20% glycerol and 13-18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.428→19.86 Å / Num. obs: 190913 / % possible obs: 98.5 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.049 / Rrim(I) all: 0.095 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.43-1.451.70.4541189068090.6720.4380.6321.170.8
7.82-19.863.60.042413211530.9950.0260.04916.493.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.16_3549refinement
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E5D

2e5d


Resolution: 1.428→19.858 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1835 9587 5.02 %
Rwork0.1649 181272 -
obs0.1658 190859 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.58 Å2 / Biso mean: 18.4133 Å2 / Biso min: 7.84 Å2
Refinement stepCycle: final / Resolution: 1.428→19.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7471 0 95 972 8538
Biso mean--19.24 28.35 -
Num. residues----937
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4284-1.44460.31321870.2795365759
1.4446-1.46160.25513010.2552601098
1.4616-1.47940.24983150.22356131100
1.4794-1.49810.23113240.21996083100
1.4981-1.51780.21923400.20836128100
1.5178-1.53860.21653620.20296013100
1.5386-1.56060.23163510.19526139100
1.5606-1.58390.21073300.18696068100
1.5839-1.60860.20233220.18036120100
1.6086-1.6350.21652920.18056145100
1.635-1.66320.21333520.17876117100
1.6632-1.69340.19863060.17716140100
1.6934-1.72590.2043210.1756139100
1.7259-1.76110.20213340.17726120100
1.7611-1.79940.19533270.16976110100
1.7994-1.84120.19473290.16976116100
1.8412-1.88730.20923410.17136080100
1.8873-1.93820.19163180.1686119100
1.9382-1.99520.19132940.17016144100
1.9952-2.05960.19533110.16276157100
2.0596-2.13310.19423060.1636125100
2.1331-2.21840.18333270.1626135100
2.2184-2.31920.18763220.16546156100
2.3192-2.44130.19623300.16656130100
2.4413-2.59390.18363250.16556096100
2.5939-2.79370.17283460.16556154100
2.7937-3.07390.18493090.16456179100
3.0739-3.51660.17153380.15386131100
3.5166-4.42240.14093260.13556160100
4.4224-19.8580.14893010.14566270100

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