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- PDB-9dqi: D306N Mutant of M.tuberculosis MenD (SEPHCHC Synthase) -

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Basic information

Entry
Database: PDB / ID: 9dqi
TitleD306N Mutant of M.tuberculosis MenD (SEPHCHC Synthase)
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsBIOSYNTHETIC PROTEIN / menaquinone biosynthesis / SEPHCHC Synthase / Mycobacterium tuberculosis / MenD mutant enzyme / allosteric regulator complex (DHNA) / mutant D306N / ThDP-dependent enzyme.
Function / homology
Function and homology information


2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity / menaquinone biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / magnesium ion binding / plasma membrane
Similarity search - Function
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
1,4-dihydroxy-2-naphthoic acid / THIAMINE DIPHOSPHATE / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsJohnston, J.M. / Ho, N.A.T. / Given, F.M. / Bulloch, E.M.M. / Allison, T.M. / Jiao, W.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New ZealandM1208 New Zealand
CitationJournal: Chembiochem / Year: 2025
Title: Apparent Reversal of Allosteric Response in Mycobacterium tuberculosis MenD Reveals Links to Half-of-Sites Reactivity.
Authors: Ho, N.A.T. / Given, F.M. / Stanborough, T. / Klein, M. / Allison, T.M. / Bulloch, E.M.M. / Jiao, W. / Johnston, J.M.
History
DepositionSep 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
D: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
C: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,00519
Polymers240,2724
Non-polymers1,73315
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, In addition to gel filtration, mass photometry, SEC-MALS, analytical ultracentrifugation and SAXS analysis have variously been carried out on this protein. This supports ...Evidence: gel filtration, In addition to gel filtration, mass photometry, SEC-MALS, analytical ultracentrifugation and SAXS analysis have variously been carried out on this protein. This supports predominantly tetramer in solution (with some evidence by mass photometry done at nM concentrations of dimer as well).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22640 Å2
ΔGint-152 kcal/mol
Surface area71460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.565, 139.978, 183.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ADBC

#1: Protein
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / SEPHCHC synthase / Menaquinone biosynthesis protein MenD


Mass: 60067.961 Da / Num. of mol.: 4
Mutation: D306N (also contains an N-terminal hexhistidine expression tag).
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: menD, Rv0555 / Production host: Mycolicibacterium smegmatis (bacteria)
References: UniProt: P9WK11, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

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Non-polymers , 6 types, 202 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DNA / 1,4-dihydroxy-2-naphthoic acid / 1,4-dihydroxynaphthalene-2-carboxylic acid


Mass: 204.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MOPS/HEPES pH 7.5, 6% w/v PEG 8K, 12% v/v ethylene glycol, 0.03M halide mix (NaI, NaBr, NaF).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537319 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537319 Å / Relative weight: 1
ReflectionResolution: 2.39→49.13 Å / Num. obs: 104327 / % possible obs: 100 % / Redundancy: 26.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.033 / Rrim(I) all: 0.17 / Χ2: 0.99 / Net I/σ(I): 16.7 / Num. measured all: 2806983
Reflection shellResolution: 2.39→2.43 Å / % possible obs: 100 % / Redundancy: 26.7 % / Rmerge(I) obs: 3.14 / Num. measured all: 136691 / Num. unique obs: 5126 / CC1/2: 0.579 / Rpim(I) all: 0.618 / Rrim(I) all: 3.201 / Χ2: 0.67 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→49.13 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 5244 5.03 %
Rwork0.1951 --
obs0.1969 104204 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15548 0 105 187 15840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416114
X-RAY DIFFRACTIONf_angle_d0.62122106
X-RAY DIFFRACTIONf_dihedral_angle_d5.4512360
X-RAY DIFFRACTIONf_chiral_restr0.0442613
X-RAY DIFFRACTIONf_plane_restr0.0072949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.420.38172080.32813254X-RAY DIFFRACTION100
2.42-2.450.34411700.30883265X-RAY DIFFRACTION100
2.45-2.480.3711650.30053266X-RAY DIFFRACTION100
2.48-2.510.33171560.28843262X-RAY DIFFRACTION100
2.51-2.540.3151550.26953313X-RAY DIFFRACTION100
2.54-2.570.30681920.25673192X-RAY DIFFRACTION100
2.57-2.610.27891750.25033274X-RAY DIFFRACTION100
2.61-2.650.26751630.23613275X-RAY DIFFRACTION100
2.65-2.690.31311840.2393263X-RAY DIFFRACTION100
2.69-2.740.3041770.23483276X-RAY DIFFRACTION100
2.74-2.780.26211840.22753243X-RAY DIFFRACTION100
2.78-2.830.28871760.23233289X-RAY DIFFRACTION100
2.83-2.890.29321640.24753265X-RAY DIFFRACTION100
2.89-2.950.30821790.25753248X-RAY DIFFRACTION100
2.95-3.010.32071790.26063304X-RAY DIFFRACTION100
3.01-3.080.28461630.25423315X-RAY DIFFRACTION100
3.08-3.160.30081750.23953247X-RAY DIFFRACTION100
3.16-3.240.26861580.2283301X-RAY DIFFRACTION100
3.24-3.340.25711630.21113302X-RAY DIFFRACTION100
3.34-3.450.24551530.20473303X-RAY DIFFRACTION100
3.45-3.570.23111810.19813285X-RAY DIFFRACTION100
3.57-3.710.22021640.19353325X-RAY DIFFRACTION100
3.71-3.880.20631810.18313303X-RAY DIFFRACTION100
3.88-4.090.23361790.17473312X-RAY DIFFRACTION100
4.09-4.340.20721840.17113321X-RAY DIFFRACTION100
4.34-4.680.18781910.15593324X-RAY DIFFRACTION100
4.68-5.150.21151980.15913324X-RAY DIFFRACTION100
5.15-5.890.21831560.17543381X-RAY DIFFRACTION100
5.89-7.420.20511830.17833400X-RAY DIFFRACTION100
7.42-49.130.16931880.16323528X-RAY DIFFRACTION99

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