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- PDB-36wj: Mevalonate kinase from Saccharomyces cerevisiae with isopentenyl ... -

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Basic information

Entry
Database: PDB / ID: 36wj
TitleMevalonate kinase from Saccharomyces cerevisiae with isopentenyl pyrophosphate (IPP) bound
ComponentsMevalonate kinase
KeywordsTRANSFERASE / metabolic enzyme / mevalonate pathway
Function / homology
Function and homology information


mevalonate kinase / mevalonate kinase activity / Lanosterol biosynthesis / ergosterol biosynthetic process / isopentenyl diphosphate biosynthetic process, mevalonate pathway / farnesyl diphosphate biosynthetic process, mevalonate pathway / magnesium ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mevalonate kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Mevalonate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.07 Å
AuthorsD'Emilia, R.L.S. / Ragwan, E.R. / Chang, V. / Kung, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116029 United States
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Structural basis of mevalonate pathway regulation by feedback inhibition of mevalonate kinase.
Authors: D'Emilia, R.L.S. / McCaskey, K.A. / Ragwan, E.R. / Kim, J.H. / Chang, V. / Tang, M.M. / Kung, Y.
History
DepositionJul 3, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8905
Polymers51,4951
Non-polymers3954
Water2,234124
1
A: Mevalonate kinase
hetero molecules

A: Mevalonate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,78010
Polymers102,9912
Non-polymers7898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4660 Å2
ΔGint-38 kcal/mol
Surface area36420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.450, 83.450, 262.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Mevalonate kinase / MK / MvK / Ergosterol biosynthesis protein 12 / Regulation of autonomous replication protein 1


Mass: 51495.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ERG12, RAR1, YMR208W, YM8261.02 / Production host: Escherichia coli (E. coli) / References: UniProt: P07277, mevalonate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.44 Å3/Da / Density % sol: 72.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES pH 6.0, 900-1100 mM sodium potassium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.07→83.97 Å / Num. obs: 56693 / % possible obs: 98.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 36.6 Å2 / CC1/2: 0.958 / Net I/σ(I): 5.6
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 4.7 % / Num. unique obs: 4331 / CC1/2: 0.431 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.07→79.54 Å / SU ML: 0.2576 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4154
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 2829 5 %
Rwork0.1963 53762 -
obs0.1977 56591 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.42 Å2
Refinement stepCycle: LAST / Resolution: 2.07→79.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 23 124 3589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673577
X-RAY DIFFRACTIONf_angle_d0.88964857
X-RAY DIFFRACTIONf_chiral_restr0.0482564
X-RAY DIFFRACTIONf_plane_restr0.0057625
X-RAY DIFFRACTIONf_dihedral_angle_d14.19241297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.10.41681180.37362187X-RAY DIFFRACTION80.71
2.1-2.140.32781410.34192670X-RAY DIFFRACTION98.7
2.14-2.180.34991400.32412657X-RAY DIFFRACTION98.59
2.18-2.230.35581390.28882660X-RAY DIFFRACTION98.83
2.23-2.280.3141420.28362685X-RAY DIFFRACTION98.88
2.28-2.330.28711410.26392678X-RAY DIFFRACTION99.02
2.33-2.390.28641410.25522695X-RAY DIFFRACTION99.13
2.39-2.450.24171420.2472680X-RAY DIFFRACTION98.88
2.45-2.520.22751330.23512572X-RAY DIFFRACTION94.38
2.52-2.60.26841420.21512700X-RAY DIFFRACTION99.34
2.6-2.70.29281440.23022718X-RAY DIFFRACTION99.44
2.7-2.810.22591420.21992710X-RAY DIFFRACTION99.48
2.81-2.930.22381430.20272711X-RAY DIFFRACTION99.41
2.93-3.090.24521430.19922735X-RAY DIFFRACTION99.28
3.09-3.280.20931420.1972736X-RAY DIFFRACTION98.9
3.28-3.530.21491410.18482714X-RAY DIFFRACTION98.28
3.54-3.890.18581390.15622642X-RAY DIFFRACTION94.62
3.89-4.450.15941470.14352806X-RAY DIFFRACTION99.9
4.45-5.610.18611510.15172855X-RAY DIFFRACTION99.44
5.61-79.540.21331580.17832951X-RAY DIFFRACTION97.25
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)
10.8659196763080.07888370653340.9538110129290.1489297259840.1103188902970.930098457259-0.00880115397910.0962015264355-0.0642028750483-0.0136314373540.0570229852189-0.04091950789290.04471884029820.1124371341186.40374027842E-100.258010676343-0.00786846138816-0.004623957340670.389590354849-0.05056986064420.313399686609-3.89021437043-24.076885435231.3531576873
20.4846737792150.2557660096210.7643493857250.3648503994240.2675365024350.794427830490.0199902718013-0.0731642907204-0.03309038661390.0670294229067-0.01243896866190.02000131736010.0218667144186-0.210014140547-8.2372096212E-100.2539843422670.01849042376860.01103098340050.356787445757-0.02069872111260.293144843842-3.31997284298-18.610587308155.0411714366
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -7 through 208 )-7 - 2081 - 216
22chain 'A' and (resid 209 through 443 )209 - 443217 - 451

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