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- PDB-1e2g: Human thymidylate kinase complexed with ADP, TDP and a magnesium-ion -

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Basic information

Entry
Database: PDB / ID: 1e2g
TitleHuman thymidylate kinase complexed with ADP, TDP and a magnesium-ion
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / P-LOOP
Function / homology
Function and homology information


thymidine biosynthetic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / myoblast differentiation / nucleoside diphosphate kinase activity / dTTP biosynthetic process / response to cadmium ion ...thymidine biosynthetic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / myoblast differentiation / nucleoside diphosphate kinase activity / dTTP biosynthetic process / response to cadmium ion / cellular response to growth factor stimulus / response to estrogen / mitochondrial matrix / phosphorylation / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / THYMIDINE-5'-PHOSPHATE / THYMIDINE-5'-DIPHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOstermann, N. / Schlichting, I. / Brundiers, R. / Konrad, M. / Reinstein, J. / Veit, T. / Goody, R.S. / Lavie, A.
CitationJournal: Structure / Year: 2000
Title: Insights Into the Phosphoryltransfer Mechanism of Human Thymidylate Kinase Gained from Crystal Structures of Enzyme Complexes Along the Reaction Coordinate
Authors: Ostermann, N. / Schlichting, I. / Brundiers, R. / Konrad, M. / Reinstein, J. / Veit, T. / Goody, R.S. / Lavie, A.
History
DepositionMay 22, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2536
Polymers24,0531
Non-polymers1,2005
Water4,846269
1
A: THYMIDYLATE KINASE
hetero molecules

A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,50512
Polymers48,1052
Non-polymers2,40010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6240 Å2
ΔGint-89.6 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.100, 101.100, 49.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-402-

MG

21A-2183-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein THYMIDYLATE KINASE / / TMPK


Mass: 24052.533 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23919, dTMP kinase

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Non-polymers , 5 types, 274 molecules

#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 200 TO ALA GLY, SER, HIS INSERTED AT THE N-TERMINUS THE ACTIVE ...ENGINEERED RESIDUE IN CHAIN A, ARG 200 TO ALA GLY, SER, HIS INSERTED AT THE N-TERMINUS THE ACTIVE SITE CONTAINS A MIXTURE OF NUCLEOTIDES, ADP TMP AND ADP + TDP. CORRESPONDINGLY, THE P-LOOP HAS TWO CONFORMATIONS.
Sequence detailsSAMPLE COMTAINS SER183, ILE184, ASP190, AND A ILE191 (CONFIRMED BY THE DNA SEQUENCE AND ELECTRON ...SAMPLE COMTAINS SER183, ILE184, ASP190, AND A ILE191 (CONFIRMED BY THE DNA SEQUENCE AND ELECTRON DENSITY OF SIDE-CHAINS). POSSIBLE ERROR IN SWISSPROT ENTRY.

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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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: VAPOR DIFFUSION AT 293 K MIXING 2 MICROLITERS OF A SOLUTION CONTAINING THE ENZYME, NUCLEOTIDES, AND 50 MM MGCL2 WITH 2 MICROLITERS OF A SOLUTION CONTAINING 21% PEG 3350, 100 MM TRIS HCL PH 8. ...Details: VAPOR DIFFUSION AT 293 K MIXING 2 MICROLITERS OF A SOLUTION CONTAINING THE ENZYME, NUCLEOTIDES, AND 50 MM MGCL2 WITH 2 MICROLITERS OF A SOLUTION CONTAINING 21% PEG 3350, 100 MM TRIS HCL PH 8.0 AND 50 MICROLITERS OF DEAD SEA WATER.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: MIRROR
RadiationMonochromator: NO / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→50.5 Å / Num. obs: 28445 / % possible obs: 99.4 % / Redundancy: 4.9 % / Rsym value: 0.052 / Net I/σ(I): 19
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.296 / % possible all: 99.6

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2859 0.1 %RANDOM
Rwork0.191 ---
obs-28445 99.4 %-
Refinement stepCycle: LAST / Resolution: 1.7→50.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 0 75 269 1952
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d1.3
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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