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- PDB-4kww: The crystal structure of human quinolinic acid phosphoribosyltran... -

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Basic information

Entry
Database: PDB / ID: 4kww
TitleThe crystal structure of human quinolinic acid phosphoribosyltransferase in complex with its inhibitor phthalic acid
ComponentsNicotinate-nucleotide pyrophosphorylase [carboxylating]
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / NAD / metabolism / type II phosphoribosyltransferase / quinolinic acid / PRPP / brain / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
PHTHALIC ACID / Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMalik, S.S. / Dimeka, P.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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,04012
Polymers187,0436
Non-polymers9976
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26270 Å2
ΔGint-171 kcal/mol
Surface area54260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.837, 179.837, 121.371
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 286
2112B1 - 286
3112C1 - 286
4112D1 - 286
5112E1 - 286
6112F1 - 286

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.919403, 0.389433, -0.055132), (0.389887, 0.883919, -0.258215), (-0.051825, -0.258899, -0.964513)-121.00372, 21.67869, -24.25299
3given(0.801116, 0.588674, -0.108054), (0.58824, -0.807733, -0.039269), (-0.110395, -0.032103, -0.993369)-11.26966, 30.18148, -27.34076
4given(-0.491751, -0.859587, 0.138895), (0.866666, -0.467779, 0.173415), (-0.084093, 0.205653, 0.975005)-96.70951, 51.3946, -4.83146
5given(0.11992, -0.986723, 0.109531), (-0.986529, -0.130801, -0.098241), (0.111263, -0.096275, -0.989117)-58.53702, -68.17285, -13.2885
6given(-0.512571, 0.85464, -0.082839), (-0.846658, -0.486993, 0.214492), (0.142972, 0.180079, 0.973206)-93.60927, -57.56944, 9.37693

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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: Chemical
ChemComp-PHT / PHTHALIC ACID


Mass: 166.131 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H6O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.03 Å3/Da / Density % sol: 59.39 %
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, 4 mM phthalic acid, 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: 2.55→155.8 Å / Num. all: 73606 / Num. obs: 73606 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.5 % / Rsym value: 0.168 / Net I/σ(I): 16.6
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 18.1 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 3.7 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JBM

2jbm


Resolution: 2.55→155.74 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.398 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23086 3708 5 %RANDOM
Rwork0.19483 ---
all0.19664 73606 --
obs0.19664 69874 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.864 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å2-0 Å2
2--0.34 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.55→155.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12171 0 72 205 12448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01912499
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.97517096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39251702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11323.952415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.939151742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4731554
X-RAY DIFFRACTIONr_chiral_restr0.0970.22037
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219485
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A833MEDIUM POSITIONAL0.120.5
B833MEDIUM POSITIONAL0.130.5
C833MEDIUM POSITIONAL0.120.5
D833MEDIUM POSITIONAL0.130.5
E833MEDIUM POSITIONAL0.170.5
F833MEDIUM POSITIONAL0.10.5
A1136TIGHT THERMAL5.990.5
B1136TIGHT THERMAL8.580.5
C1136TIGHT THERMAL3.840.5
D1136TIGHT THERMAL5.870.5
E1136TIGHT THERMAL3.660.5
F1136TIGHT THERMAL3.80.5
A833MEDIUM THERMAL7.352
B833MEDIUM THERMAL9.012
C833MEDIUM THERMAL4.652
D833MEDIUM THERMAL6.772
E833MEDIUM THERMAL4.872
F833MEDIUM THERMAL4.532
LS refinement shellResolution: 2.55→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 279 -
Rwork0.273 5037 -
obs--98.55 %

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