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- PDB-3v8e: Crystal structure of the yeast nicotinamidase Pnc1p bound to the ... -

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Basic information

Entry
Database: PDB / ID: 3v8e
TitleCrystal structure of the yeast nicotinamidase Pnc1p bound to the inhibitor nicotinaldehyde
ComponentsNicotinamidase
KeywordsHYDROLASE
Function / homology
Function and homology information


nicotinate nucleotide salvage / negative regulation of DNA amplification / nicotinamidase activity / nicotinamidase / rDNA heterochromatin formation / subtelomeric heterochromatin formation / peroxisome / chromosome, telomeric region / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.71 Å
AuthorsHoadley, K.A. / Smith, B.C. / Denu, J.M. / Keck, J.L.
CitationJournal: Biochemistry / Year: 2012
Title: Structural and Kinetic Isotope Effect Studies of Nicotinamidase (Pnc1) from Saccharomyces cerevisiae.
Authors: Smith, B.C. / Anderson, M.A. / Hoadley, K.A. / Keck, J.L. / Cleland, W.W. / Denu, J.M.
History
DepositionDec 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Nicotinamidase
B: Nicotinamidase
C: Nicotinamidase
D: Nicotinamidase
E: Nicotinamidase
F: Nicotinamidase
G: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,57621
Polymers175,9487
Non-polymers62814
Water5,260292
1
A: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2253
Polymers25,1351
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2253
Polymers25,1351
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2253
Polymers25,1351
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2253
Polymers25,1351
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2253
Polymers25,1351
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2253
Polymers25,1351
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2253
Polymers25,1351
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)298.717, 298.717, 112.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Nicotinamidase / Nicotine deamidase / NAMase


Mass: 25135.426 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PNC1, YGL037C / Production host: Escherichia coli (E. coli) / References: UniProt: P53184, nicotinamidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein was dialyzed against buffer containing 15 mM Tris pH 7.5, 50 mM NaCl, 4 mM MgCl2, 10 mM Na Citrate and 5 % glycerol and the inhibitor nicotinaldehyde was added at a 4:1 ratio. The ...Details: Protein was dialyzed against buffer containing 15 mM Tris pH 7.5, 50 mM NaCl, 4 mM MgCl2, 10 mM Na Citrate and 5 % glycerol and the inhibitor nicotinaldehyde was added at a 4:1 ratio. The protein (5 mg/ml) was mixed with mother liquor (1.6 M NaOAc, 10 % ethylene glycol, 0.1 M HEPES pH 7.4) at a 1:1 (vol) ratio. Crystals were formed by hanging drop vapor diffusion. Crystals were transferred to a cryoprotectant solution (1.5 M NaOAc, 20% ethylene glycol, 0.1M HEPES pH 7.4) and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2009
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 101157 / Num. obs: 101147 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 %
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.348 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementResolution: 2.71→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 14.478 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 5058 5 %RANDOM
Rwork0.18108 ---
obs0.18221 96087 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.356 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å20 Å2
2--0.68 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.71→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12397 0 14 292 12703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212775
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.94317388
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20751519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03524.773616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.253152212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9031549
X-RAY DIFFRACTIONr_chiral_restr0.0880.21918
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219709
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.713→2.783 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 331 -
Rwork0.311 6911 -
obs--97.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2366-0.0923-0.14651.6253-0.75372.2446-0.05250.00760.02110.17860.00490.0949-0.1198-0.16780.04760.0487-0.06050.02120.1714-0.03920.0894-43.140180.627333.0865
21.4269-0.17640.36861.9255-0.72492.39450.03150.1589-0.1801-0.1339-0.0869-0.12020.12040.25080.05540.0199-0.0201-0.00280.2309-0.0440.1559-9.895380.15823.326
31.31470.33750.10511.74660.11662.8352-0.13520.2372-0.2873-0.17810.0712-0.12160.36160.24590.0640.1574-0.08860.05520.1907-0.09130.1314-51.469449.695620.5429
42.36780.09650.21321.5214-0.16472.9218-0.0667-0.0430.3371-0.1886-0.01350.3849-0.3079-0.44930.08020.1688-0.1107-0.06080.355-0.09730.2622-84.203657.723412.7688
52.2958-0.2151-0.14142.1174-0.10681.9566-0.0386-0.3884-0.0990.2258-0.0566-0.03840.24630.070.09530.4144-0.05190.00550.1020.08190.1686-66.666135.3137-24.5335
62.41080.44110.27133.1302-0.00341.73740.13780.3439-0.2922-0.5373-0.1005-0.10030.2510.1574-0.03740.80260.06740.02410.08960.0550.4079-64.90885.5067-41.8976
72.07060.4979-0.19872.66270.06042.3292-0.0223-0.4441-0.52130.1560.0807-0.05830.3571-0.1295-0.05840.2692-0.293-0.05730.590.02190.5154-97.945527.048820.731
80.0085-0.0370.02530.208-0.01650.42520.0068-0.00660.0036-0.012-0.01430.02360.15820.02040.00740.1041-0.06860.01510.2282-0.04030.2834-47.987260.731115.8357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 216
2X-RAY DIFFRACTION2B1 - 216
3X-RAY DIFFRACTION3C1 - 216
4X-RAY DIFFRACTION4D1 - 216
5X-RAY DIFFRACTION5E1 - 216
6X-RAY DIFFRACTION6F1 - 216
7X-RAY DIFFRACTION7G1 - 216
8X-RAY DIFFRACTION8B401 - 480

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