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- PDB-3nwy: Structure and allosteric regulation of the uridine monophosphate ... -

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Basic information

Entry
Database: PDB / ID: 3nwy
TitleStructure and allosteric regulation of the uridine monophosphate kinase from Mycobacterium tuberculosis
ComponentsUridylate kinase
KeywordsTRANSFERASE / allosterically activated form / AAK fold / UMP kinase
Function / homology
Function and homology information


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Uridylate kinase, bacteria / Uridylate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / URIDINE-5'-DIPHOSPHATE / Uridylate kinase / Uridylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsLabesse, G. / Munier-Lehmann, H.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural and functional characterization of the Mycobacterium tuberculosis uridine monophosphate kinase: insights into the allosteric regulation.
Authors: Labesse, G. / Benkali, K. / Salard-Arnaud, I. / Gilles, A.M. / Munier-Lehmann, H.
History
DepositionJul 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uridylate kinase
B: Uridylate kinase
C: Uridylate kinase
D: Uridylate kinase
E: Uridylate kinase
F: Uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,29913
Polymers177,7556
Non-polymers3,5437
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20240 Å2
ΔGint-106 kcal/mol
Surface area48330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.710, 175.480, 65.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Uridylate kinase / UK / Uridine monophosphate kinase / UMP kinase / UMPK


Mass: 29625.893 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT2951, MTCY274.14c, pyrH, Rv2883c / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P65929, UniProt: P9WHK5*PLUS, UMP kinase
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: Na/K Tartrate 1.1 M HEPES pH 7.7 0.1 M MPD 2%, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9185 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2009
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9185 Å / Relative weight: 1
ReflectionResolution: 2.47→87.7 Å / Num. all: 57384 / Num. obs: 51899 / % possible obs: 90.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.121 / Rsym value: 0.044 / Net I/σ(I): 12.2
Reflection shellResolution: 2.49→2.6 Å / % possible all: 61.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 2.54→87.7 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.888 / SU B: 17.771 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 1.341 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26859 2372 5.2 %RANDOM
Rwork0.20474 ---
obs0.20813 43188 86.11 %-
all-53194 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2---1.13 Å20 Å2
3---0.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3338 Å0.3338 Å
Luzzati d res low-0.3338 Å
Luzzati sigma a0.3338 Å0.3338 Å
Refinement stepCycle: LAST / Resolution: 2.54→87.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9987 0 217 142 10346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210332
X-RAY DIFFRACTIONr_bond_other_d0.0020.026704
X-RAY DIFFRACTIONr_angle_refined_deg1.402214020
X-RAY DIFFRACTIONr_angle_other_deg0.915316346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14851350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6323.575400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.686151671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8431585
X-RAY DIFFRACTIONr_chiral_restr0.0760.21663
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022030
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_it0.5061.56667
X-RAY DIFFRACTIONr_mcbond_other0.0651.52858
X-RAY DIFFRACTIONr_mcangle_it0.932210584
X-RAY DIFFRACTIONr_scbond_it1.13633665
X-RAY DIFFRACTIONr_scangle_it1.9164.53436
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.604 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 14 -
Rwork0.338 311 -
obs--8.37 %
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)
10.79750.05530.40930.8961-0.60180.8559-0.03160.03570.01010.0446-0.0054-0.0368-0.011-0.01830.0370.0739-0.0352-0.00020.12530.01170.074169.683117.980524.3794
20.34660.10820.11731.0231-0.28181.76540.0033-0.07250.00930.0071-0.05870.0411-0.0963-0.05170.05530.0712-0.01860.02760.146-0.01070.069363.870832.765550.4923
30.4815-0.19570.46711.0134-0.18591.75340.0366-0.0030.0215-0.05350.0016-0.0083-0.03490.1775-0.03820.071-0.07420.02080.1662-0.02430.049996.368245.734846.4041
41.18740.39620.66960.5874-0.27761.92370.03360.0122-0.085-0.0180.0045-0.0406-0.20840.0451-0.03810.1028-0.05860.02590.1472-0.03080.040397.678137.570322.5679
51.08240.41020.87170.85660.24081.81290.0784-0.0744-0.10360.02480.0654-0.15340.091-0.0239-0.14380.05-0.0089-0.03350.09630.0290.12689.105612.420438.612
61.2750.07360.03810.8526-0.11371.5309-0.00420.00360.1446-0.13680.0030.0849-0.0692-0.05660.00120.14780.0003-0.02920.08350.01590.094368.052251.130834.4693
71.90750.01010.7751.23210.88432.91050.0757-0.0338-0.02710.0304-0.00420.22270.2918-0.3977-0.07150.0519-0.0958-0.00780.1790.01070.092850.414313.17622.4329
82.94780.7358-0.12021.34151.4641.97410.0187-0.1437-0.1868-0.0092-0.13710.16990.017-0.26780.11850.0799-0.03460.0260.16030.08960.162449.248420.482854.3779
92.55410.03030.31662.1575-0.25861.95940.3236-0.22530.3464-0.0428-0.10090.0299-0.42050.2989-0.22270.1633-0.09870.09470.1351-0.12490.11495.747163.183656.1222
102.6221-0.7599-0.17221.3395-0.18291.3298-0.02350.2398-0.24120.00240.0513-0.0915-0.06180.0905-0.02780.0245-0.05240.04480.2085-0.10350.0962111.854226.392112.7129
111.4077-1.92590.38662.86450.59713.62120.50410.0598-0.20780.03620.2096-0.3180.69040.8558-0.71370.21920.1806-0.34810.1944-0.18450.4553106.31955.572837.9342
121.69711.0424-0.07464.11020.12190.6111-0.0119-0.06240.4935-0.1302-0.01860.0307-0.2092-0.02260.03060.19950.013-0.01530.0088-0.0050.171371.432369.923135.6224
130.21190.1469-0.10180.0959-0.01590.23840.00950.0244-0.01390.0171-0.0387-0.0128-0.045-0.03060.02920.0522-0.00420.00770.21440.03980.075975.561432.445538.9326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 176
2X-RAY DIFFRACTION1A262
3X-RAY DIFFRACTION2B29 - 176
4X-RAY DIFFRACTION2B262 - 263
5X-RAY DIFFRACTION3C29 - 176
6X-RAY DIFFRACTION3C262
7X-RAY DIFFRACTION4D29 - 176
8X-RAY DIFFRACTION4D262
9X-RAY DIFFRACTION5E29 - 176
10X-RAY DIFFRACTION5E262
11X-RAY DIFFRACTION6F29 - 176
12X-RAY DIFFRACTION6F262
13X-RAY DIFFRACTION7A177 - 261
14X-RAY DIFFRACTION8B177 - 261
15X-RAY DIFFRACTION9C177 - 261
16X-RAY DIFFRACTION10D177 - 261
17X-RAY DIFFRACTION11E177 - 261
18X-RAY DIFFRACTION12F177 - 261
19X-RAY DIFFRACTION13W9 - 516

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