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- PDB-5z2p: ThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketogl... -

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Basic information

Entry
Database: PDB / ID: 5z2p
TitleThDP-Mn2+ complex of R413K variant of EcMenD soaked with 2-ketoglutarate for 5 min
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsTRANSFERASE / complex
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
FORMIC ACID / : / Chem-TD6 / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsQin, M.M. / Guo, Z.H.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Hong Kong
CitationJournal: Biochem. J. / Year: 2018
Title: Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis.
Authors: Qin, M.M. / Song, H.G. / Dai, X. / Chen, Y.Z. / Guo, Z.H.
History
DepositionJan 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)497,14849
Polymers491,2468
Non-polymers5,90141
Water45,3262516
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
F: 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)248,68928
Polymers245,6234
Non-polymers3,06624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24480 Å2
ΔGint-118 kcal/mol
Surface area67690 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
E: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
G: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,45921
Polymers245,6234
Non-polymers2,83617
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23310 Å2
ΔGint-118 kcal/mol
Surface area67370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.260, 90.270, 167.070
Angle α, β, γ (deg.)83.430, 76.140, 63.490
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...
21(CHAIN B AND ((RESID 1 AND (NAME N OR NAME...
31(CHAIN C AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...
41(CHAIN D AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...
51(CHAIN E AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...
61(CHAIN F AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...
71(CHAIN G AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...
81(CHAIN H AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(CHAIN A AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...A0
211(CHAIN B AND ((RESID 1 AND (NAME N OR NAME...B0
311(CHAIN C AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...C0
411(CHAIN D AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...D0
511(CHAIN E AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...E0
611(CHAIN F AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...F0
711(CHAIN G AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...G0
811(CHAIN H AND (RESSEQ 1:5 OR (RESID 6 AND (NAME...H0

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 61405.766 Da / Num. of mol.: 8 / Mutation: R413K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: menD, b2264, JW5374 / Variant: 1 / Production host: Escherichia coli (E. coli)
References: UniProt: P17109, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

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Non-polymers , 5 types, 2557 molecules

#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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2516 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.14M Magnesium formate, 12% PEG 3350, 0.1M HEPES PH 7.5
PH range: 7.2-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→20.64 Å / Num. obs: 159070 / % possible obs: 78.1 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2 % / Rmerge(I) obs: 0.127 / % possible all: 77.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.24data extraction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EJ8

5ej8


Resolution: 2.3→20.64 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 18.68
RfactorNum. reflection% reflection
Rfree0.207 2015 1.27 %
Rwork0.165 157043 -
obs0.166 159058 78.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.02 Å2 / Biso mean: 16.72 Å2 / Biso min: 4.13 Å2
Refinement stepCycle: final / Resolution: 2.3→20.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34123 0 352 2516 36991
Biso mean--18.15 21.77 -
Num. residues----4448
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A18798X-RAY DIFFRACTIONPOSITIONAL0
12B18798X-RAY DIFFRACTIONPOSITIONAL0
13C18798X-RAY DIFFRACTIONPOSITIONAL0
14D18798X-RAY DIFFRACTIONPOSITIONAL0
15E18798X-RAY DIFFRACTIONPOSITIONAL0
16F18798X-RAY DIFFRACTIONPOSITIONAL0
17G18798X-RAY DIFFRACTIONPOSITIONAL0
18H18798X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35740.23341480.1793111371128578
2.3574-2.42110.20991390.1844112071134678
2.4211-2.49220.27661350.1836114671160280
2.4922-2.57250.23851570.1814114991165680
2.5725-2.66430.25961490.1845116141176382
2.6643-2.77070.21451210.183299451006669
2.7707-2.89650.25461500.185103891053972
2.8965-3.04870.23551510.1767120491220084
3.0487-3.23910.18551570.172118981205583
3.2391-3.48810.20761520.161115721172481
3.4881-3.83710.18421390.1502113821152179
3.8371-4.38760.17391110.14049697980867
4.3876-5.51050.16571540.14119411209583
5.5105-20.63770.16751520.1543112461139878

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