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- PDB-5ej5: EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 1.5 h -

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Basic information

Entry
Database: PDB / ID: 5ej5
TitleEcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 1.5 h
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsTRANSFERASE / Post-decarboxylation intermediate
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 / protein homodimerization activity
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 (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold ...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 (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-TD6 / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsSong, H.G. / Dong, C. / Chen, Y.Z. / Sun, Y.R. / Guo, Z.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
Authors: Song, H.G. / Dong, C. / Qin, M.M. / Chen, Y.Z. / Sun, Y.R. / Liu, J.J. / Chan, W. / Guo, Z.H.
History
DepositionNov 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
C: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
D: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
E: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
F: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
G: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
H: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)496,86632
Polymers491,4708
Non-polymers5,39524
Water29,4001632
1
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2168
Polymers122,8682
Non-polymers1,3496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-47 kcal/mol
Surface area37970 Å2
MethodPISA
2
C: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
D: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2168
Polymers122,8682
Non-polymers1,3496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-46 kcal/mol
Surface area38040 Å2
MethodPISA
3
E: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
F: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2168
Polymers122,8682
Non-polymers1,3496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-47 kcal/mol
Surface area38020 Å2
MethodPISA
4
G: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
H: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2168
Polymers122,8682
Non-polymers1,3496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-47 kcal/mol
Surface area38130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.760, 90.800, 170.100
Angle α, β, γ (deg.)75.79, 83.29, 64.34
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 61433.781 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 substr. MG1655 / Gene: menD, b2264, JW5374 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P17109, 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.: 8 / Source method: obtained synthetically / Formula: C16H25N4O10P2S
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1632 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.16 M magnesium formate, 1% tascimate pH 7.0, 0.02 M HEPES pH 7.0, 14% PEG 3350 and 2% PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→36.28 Å / Num. obs: 194725 / % possible obs: 92.4 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 5.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.8 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.3→33.759 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 9871 5.07 %
Rwork0.183 --
obs0.1857 194703 92.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→33.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34466 0 320 1632 36418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00835910
X-RAY DIFFRACTIONf_angle_d1.14149085
X-RAY DIFFRACTIONf_dihedral_angle_d13.77412931
X-RAY DIFFRACTIONf_chiral_restr0.0495423
X-RAY DIFFRACTIONf_plane_restr0.0066405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.32843380.25366457X-RAY DIFFRACTION95
2.3261-2.35350.30273350.22686267X-RAY DIFFRACTION96
2.3535-2.38220.29413620.21426349X-RAY DIFFRACTION95
2.3822-2.41230.27593360.21536404X-RAY DIFFRACTION96
2.4123-2.44410.29623700.21766392X-RAY DIFFRACTION96
2.4441-2.47750.28033410.21186398X-RAY DIFFRACTION96
2.4775-2.51290.27413190.20316388X-RAY DIFFRACTION96
2.5129-2.55040.28923190.2096390X-RAY DIFFRACTION96
2.5504-2.59030.28343220.21566448X-RAY DIFFRACTION96
2.5903-2.63270.26473300.20346391X-RAY DIFFRACTION96
2.6327-2.67810.30652750.20675234X-RAY DIFFRACTION96
2.6781-2.72680.26022370.21344675X-RAY DIFFRACTION96
2.7268-2.77920.29443510.2146432X-RAY DIFFRACTION96
2.7792-2.83590.29363740.21866457X-RAY DIFFRACTION96
2.8359-2.89750.24684170.20346239X-RAY DIFFRACTION96
2.8975-2.96490.2683540.26400X-RAY DIFFRACTION96
2.9649-3.0390.26453560.20086479X-RAY DIFFRACTION96
3.039-3.12110.22933270.19496431X-RAY DIFFRACTION96
3.1211-3.21290.23553140.196446X-RAY DIFFRACTION96
3.2129-3.31650.23893640.18626355X-RAY DIFFRACTION96
3.3165-3.43490.24143500.19176373X-RAY DIFFRACTION96
3.4349-3.57230.22942620.18234647X-RAY DIFFRACTION69
3.5723-3.73470.24612310.20084896X-RAY DIFFRACTION73
3.7347-3.93130.20232490.17445214X-RAY DIFFRACTION95
3.9313-4.17720.2213430.16476293X-RAY DIFFRACTION95
4.1772-4.4990.173070.14446368X-RAY DIFFRACTION95
4.499-4.95050.16363220.13776447X-RAY DIFFRACTION97
4.9505-5.66390.19053640.14156552X-RAY DIFFRACTION98
5.6639-7.12490.19653230.15976529X-RAY DIFFRACTION98
7.1249-33.76240.17573790.14576481X-RAY DIFFRACTION98

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