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- PDB-5ayx: Crystal structure of Human Quinolinate Phosphoribosyltransferase -

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Basic information

Entry
Database: PDB / ID: 5ayx
TitleCrystal structure of Human Quinolinate Phosphoribosyltransferase
ComponentsNicotinate-nucleotide pyrophosphorylase [carboxylating]
KeywordsTRANSFERASE / QUINOLINATE PHOSPHORIBOSYLTRANSFERASE / NAD BIOSYNTHESIS / NADC
Function / homology
Function and homology information


quinolinate catabolic process / nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / Nicotinate metabolism / NAD+ metabolic process / NAD+ biosynthetic process / catalytic complex / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldehyde Oxidoreductase; domain 3 ...Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldehyde Oxidoreductase; domain 3 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKang, G.B. / Kim, M.-K. / Im, Y.J. / Lee, J.H. / Youn, H.-S. / An, J.Y. / Lee, J.-G. / Fukuoka, S.-I. / Eom, S.H.
CitationJournal: Sci Rep / Year: 2016
Title: Structural Insights into the Quaternary Catalytic Mechanism of Hexameric Human Quinolinate Phosphoribosyltransferase, a Key Enzyme in de novo NAD Biosynthesis
Authors: Youn, H.-S. / Kim, T.G. / Kim, M.-K. / Kang, G.B. / Kang, J.Y. / Lee, J.-G. / An, J.Y. / Park, K.R. / Lee, Y. / Im, Y.J. / Lee, J.H. / Eom, S.H.
History
DepositionSep 14, 2015Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 3, 2016ID: 3LAR
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinate-nucleotide pyrophosphorylase [carboxylating]
B: Nicotinate-nucleotide pyrophosphorylase [carboxylating]
C: Nicotinate-nucleotide pyrophosphorylase [carboxylating]
D: Nicotinate-nucleotide pyrophosphorylase [carboxylating]
E: Nicotinate-nucleotide pyrophosphorylase [carboxylating]
F: Nicotinate-nucleotide pyrophosphorylase [carboxylating]


Theoretical massNumber of molelcules
Total (without water)191,6806
Polymers191,6806
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24400 Å2
ΔGint-146 kcal/mol
Surface area61630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.178, 137.122, 92.650
Angle α, β, γ (deg.)90.00, 103.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nicotinate-nucleotide pyrophosphorylase [carboxylating] / Quinolinate phosphoribosyltransferase [decarboxylating] / QPRTase


Mass: 31946.672 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QPRT / Plasmid: PET21A / Production host: Escherichia coli (E. coli)
References: UniProt: Q15274, nicotinate-nucleotide diphosphorylase (carboxylating)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5
Details: 100MM MES-NAOH (PH 5.0), 7-15% (W/V) PEG-MME 2000, 10MM KSCN, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2004
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 42775 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Net I/σ(I): 18.3
Reflection shellResolution: 2.8→2.9 Å / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC6.5.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JBM

2jbm


Resolution: 2.8→48 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflectionSelection details
Rfree0.259 2227 RANDOM
Rwork0.201 --
obs-42761 -
Displacement parametersBiso mean: 64 Å2
Baniso -1Baniso -2Baniso -3
1-15.935 Å20 Å21.044 Å2
2---28.724 Å20 Å2
3---12.79 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12480 0 0 33 12513
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree: 0.356 / Rfactor Rwork: 0.259

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