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- PDB-3zm9: The mechanism of allosteric coupling in choline kinase a1 reveale... -

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Basic information

Entry
Database: PDB / ID: 3zm9
TitleThe mechanism of allosteric coupling in choline kinase a1 revealed by a rationally designed inhibitor
ComponentsCHOLINE KINASE ALPHA
KeywordsTRANSFERASE / NEGATIVE COOPERATIVITY / ALLOSTERIC MECHANISM / ELASTIC NETWORK ANALYSIS
Function / homology
Function and homology information


ethanolamine kinase / choline kinase / Synthesis of PE / ethanolamine kinase activity / choline kinase activity / CDP-choline pathway / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity ...ethanolamine kinase / choline kinase / Synthesis of PE / ethanolamine kinase activity / choline kinase activity / CDP-choline pathway / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity / lipid transport / Synthesis of PC / cellular response to glucose starvation / lipid droplet / lipid metabolic process / protein tyrosine kinase activity / protein homodimerization activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Choline/ethanolamine kinase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-QMQ / Choline kinase alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSahun-Roncero, M. / Rubio-Ruiz, B. / Saladino, G. / Conejo-Garcia, A. / Espinosa, A. / Velazquez-Campoy, A. / Gervasio, F.L. / Entrena, A. / Hurtado-Guerrero, R.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: The Mechanism of Allosteric Coupling in Choline Kinase A1 Revealed by a Rationally Designed Inhibitor
Authors: Sahun-Roncero, M. / Rubio-Ruiz, B. / Saladino, G. / Conejo-Garcia, A. / Espinosa, A. / Velazquez-Campoy, A. / Gervasio, F.L. / Entrena, A. / Hurtado-Guerrero, R.
History
DepositionFeb 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Apr 17, 2013Group: Refinement description
Revision 1.3May 1, 2013Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: CHOLINE KINASE ALPHA
B: CHOLINE KINASE ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8944
Polymers89,9092
Non-polymers9852
Water6,846380
1
A: CHOLINE KINASE ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4472
Polymers44,9541
Non-polymers4931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHOLINE KINASE ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4472
Polymers44,9541
Non-polymers4931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.746, 121.214, 131.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2499, 0.8541, -0.4562), (0.8557, -0.4153, -0.3088), (-0.4532, -0.3133, -0.8346)
Vector: -3.81403, -12.6665, -33.7814)

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Components

#1: Protein CHOLINE KINASE ALPHA / CK / CHETK-ALPHA / ETHANOLAMINE KINASE / EK / CK / CHETK-ALPHA / ETHANOLAMINE KINASE / EK / CHOLINE KINASE A1


Mass: 44954.457 Da / Num. of mol.: 2 / Fragment: RESIDUES 75-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMALC2X / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P35790, choline kinase, ethanolamine kinase
#2: Chemical ChemComp-QMQ / 1-(4-(4-(4-((6-amino-9H-purin-9-yl)methyl)phenyl)butyl)benzyl)-4- (dimethylamino)pyridinium


Mass: 492.638 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H34N7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.39 % / Description: NONE

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Data collection

DiffractionMean temperature: 73 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 69213 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / % possible all: 83.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G15

3g15


Resolution: 1.9→131.86 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.576 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22873 1722 2.5 %RANDOM
Rwork0.2013 ---
obs0.20199 67403 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.097 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2--1.91 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.9→131.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5813 0 74 380 6267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.026106
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9818237
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3515715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4623.267303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.785151106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1851547
X-RAY DIFFRACTIONr_chiral_restr0.0910.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214673
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 108 -
Rwork0.263 3805 -
obs--78.24 %
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)
10.03190.0830.15290.32870.29451.39980.0124-0.02330.0087-0.0275-0.04680.0248-0.0168-0.00820.03440.06620.0099-0.01670.1091-0.04160.0189-12.37097.023-5.1876
20.4933-0.5308-0.07350.63370.23570.5059-0.0552-0.0365-0.00070.02810.026-0.0262-0.0615-0.02490.02920.0380.00050.02080.05030.00290.10261.4271-24.497-26.4321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A80 - 457
2X-RAY DIFFRACTION2B87 - 457

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