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- PDB-4kwv: Crystal Structure of human apo-QPRT -

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Basic information

Entry
Database: PDB / ID: 4kwv
TitleCrystal Structure of human apo-QPRT
ComponentsNicotinate-nucleotide pyrophosphorylase [carboxylating]
KeywordsTRANSFERASE / NAD / metabolism / type II phosphoribosyltransferase / quinolinic acid / PRPP / brain
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 / cytoplasm / cytosol
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: 2.797 Å
AuthorsMalik, S.S. / Patterson, D.N. / Ncube, Z. / Toth, E.A.
CitationJournal: Proteins / Year: 2014
Title: The crystal structure of human quinolinic acid phosphoribosyltransferase in complex with its inhibitor phthalic acid.
Authors: Malik, S.S. / Patterson, D.N. / Ncube, Z. / Toth, E.A.
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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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)187,0436
Polymers187,0436
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24800 Å2
ΔGint-178 kcal/mol
Surface area55590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.562, 178.562, 121.597
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 1 / Auth seq-ID: 2 - 286 / Label seq-ID: 6 - 290

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.790948, -0.600402, 0.117978), (-0.600847, -0.798563, -0.035775), (0.115692, -0.042591, -0.992372)-9.70541, -31.36872, -13.01025
3given(0.127701, 0.986358, -0.103875), (0.9862, -0.137407, -0.092354), (-0.105367, -0.090648, -0.990293)-60.06545, 65.85323, -26.52612
4given(-0.51366, 0.844822, -0.149763), (-0.854261, -0.48731, 0.181017), (0.079946, 0.220918, 0.97201)-100.47288, -46.21812, 3.52331
5given(-0.924284, -0.377878, 0.053925), (-0.378838, 0.890852, -0.250729), (0.046705, -0.252174, -0.966554)-119.95996, -25.91493, -16.14164
6given(-0.489763, -0.868312, 0.07853), (0.859476, -0.465721, 0.210726), (-0.146403, 0.1707, 0.974386)-90.28703, 62.47688, -10.41579

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Components

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


Mass: 31173.826 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QPRT / 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.: 15 / 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: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM MES, pH 6.5, 0.1 M sodium phosphate monobasic, 0.1 M potassium phosphate monobasic, 1.6-2.1 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2012
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.797→154.7 Å / Num. all: 55406 / Num. obs: 55406 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.145 / Net I/σ(I): 10.8
Reflection shellResolution: 2.797→2.85 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.947 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JBM

2jbm


Resolution: 2.797→42.93 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / ESU R: 0.979 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23744 2812 5.1 %RANDOM
Rwork0.212 ---
all0.2133 55406 --
obs0.2133 52565 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.107 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.4 Å20 Å2
2--0.4 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.797→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11986 0 0 15 12001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01912237
X-RAY DIFFRACTIONr_bond_other_d00.0211625
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.96616784
X-RAY DIFFRACTIONr_angle_other_deg3.83326553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.56151714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54424.534386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.177151601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3021537
X-RAY DIFFRACTIONr_chiral_restr0.0640.22036
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02114309
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022594
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3636 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A8.66
B7.82
C13.36
D11.37
E7.31
F13.06
LS refinement shellResolution: 2.797→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 204 -
Rwork0.318 3806 -
obs--98.5 %

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