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- PDB-9mnn: Crystal structure of L. monocytogenes MenD with Mg2+ and intermed... -

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Basic information

Entry
Database: PDB / ID: 9mnn
TitleCrystal structure of L. monocytogenes MenD with Mg2+ and intermediate I bound
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsTRANSFERASE / SEPHCHC synthase Decarboxylase 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
Similarity search - Function
Menaquinone biosynthesis protein MenD, middle domain / Middle domain of thiamine pyrophosphate / 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 / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
Chem-TD6 / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesListeria monocytogenes 10403S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.79 Å
AuthorsKlein, M. / Given, F.M. / Ho, N.A.T. / Allison, T.M. / Johnston, J.M.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Marsden FundM1208 New Zealand
Other governmentGerman Academic Exchange Service/Deutscher Akademischer Austauschdienst (DAAD)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structures of Listeria monocytogenes MenD in ThDP-bound and in-crystallo captured intermediate I-bound forms.
Authors: Bailey, M. / Given, F.M. / Ho, N.A.T. / Pearce, F.G. / Allison, T.M. / Johnston, J.M.
History
DepositionDec 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,5064
Polymers64,9301
Non-polymers5763
Water48627
1
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules

A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules

A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules

A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,02216
Polymers259,7184
Non-polymers2,30412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area24710 Å2
ΔGint-164 kcal/mol
Surface area69350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.226, 175.226, 100.228
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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Components

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


Mass: 64929.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes 10403S (bacteria)
Gene: menD, LMRG_01292 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H3GD77, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase
#2: Chemical ChemComp-TD6 / (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid


Mass: 527.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N4O10P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, MOPS/HEPES-Na pH 7.5, CaCl2, MgCl2, glycerol, ThDP, TCEP

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.76→47.59 Å / Num. obs: 23604 / % possible obs: 99.1 % / Redundancy: 31.2 % / CC1/2: 0.996 / Net I/σ(I): 10.3
Reflection shellResolution: 2.76→2.91 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3200 / CC1/2: 0.384

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.79→45.16 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2637
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2502 1166 5.07 %
Rwork0.1868 21854 -
obs0.1901 23020 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.88 Å2
Refinement stepCycle: LAST / Resolution: 2.79→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 0 35 27 4594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814684
X-RAY DIFFRACTIONf_angle_d1.02086363
X-RAY DIFFRACTIONf_chiral_restr0.0565711
X-RAY DIFFRACTIONf_plane_restr0.0075819
X-RAY DIFFRACTIONf_dihedral_angle_d18.06661739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.910.39461390.29152616X-RAY DIFFRACTION97.97
2.91-3.070.30811400.24732695X-RAY DIFFRACTION100
3.07-3.260.30491420.2372704X-RAY DIFFRACTION100
3.26-3.510.3151360.22082706X-RAY DIFFRACTION100
3.51-3.870.27211460.19752715X-RAY DIFFRACTION99.51
3.87-4.420.23871400.17542721X-RAY DIFFRACTION99.34
4.42-5.570.23961490.14982781X-RAY DIFFRACTION99.9
5.57-45.160.18421740.15332916X-RAY DIFFRACTION99.68

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