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- PDB-6o0g: M.tb MenD bound to Intermediate I and Inhibitor -

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Basic information

Entry
Database: PDB / ID: 6o0g
TitleM.tb MenD bound to Intermediate I and Inhibitor
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Keywordstransferase/transferase inhibitor / menaquinone biosynthesis / ThDP dependent / decarboxylation / C-C bond ligation / Inhibitor complex / SEPHCHC synthase / MenD / TRANSFERASE / transferase-transferase inhibitor 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 / 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 (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2-OXOGLUTARIC ACID / 1,4-dihydroxy-2-naphthoic acid / FORMIC ACID / TRIETHYLENE GLYCOL / Chem-TOG / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJohnston, J.M. / Bashiri, G. / Bulloch, E.M.M. / Jirgis, E.M.N. / Chuang, H. / Nigon, L.V. / Baker, E.N.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Allosteric regulation of menaquinone (vitamin K2) biosynthesis in the human pathogenMycobacterium tuberculosis.
Authors: Bashiri, G. / Nigon, L.V. / Jirgis, E.N.M. / Ho, N.A.T. / Stanborough, T. / Dawes, S.S. / Baker, E.N. / Bulloch, E.M.M. / Johnston, J.M.
History
DepositionFeb 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: 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
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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

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)243,22228
Polymers240,2764
Non-polymers2,94624
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24970 Å2
ΔGint-77 kcal/mol
Surface area67490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.674, 143.452, 172.741
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 60068.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: menD, Rv0555
Production host: Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: P9WK11, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

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Non-polymers , 10 types, 448 molecules

#2: Chemical
ChemComp-DNA / 1,4-dihydroxy-2-naphthoic acid / 1,4-dihydroxynaphthalene-2-carboxylic acid


Mass: 204.179 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#6: Chemical ChemComp-TOG / 4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3 -ium-2-yl]-4-oxidanyl-butanoic acid / ThDP and decarboxylated 2-oxoglutarate adduct, covalent intermediate I, carboanion form


Mass: 526.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24N4O10P2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsThe ligand TOG is a covalent cofactor intermediate. The form is more tetrahedral around the C21 ...The ligand TOG is a covalent cofactor intermediate. The form is more tetrahedral around the C21 carbon that the restraints dictionary accounts for. Please release these planar restraints for proper refinement.

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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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: HEPES/MOPS, PEG 4K, CA mix, glycerol

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→48.39 Å / Num. obs: 98344 / % possible obs: 100 % / Redundancy: 14.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.284 / Rpim(I) all: 0.076 / Rrim(I) all: 0.294 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.44143.1547850.3480.8663.26999.9
13.15-48.3911.80.03468910.010.03698.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.15data scaling
PHENIX1.14_3260refinement
REFMACrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ESU

5esu


Resolution: 2.4→48.327 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.25
RfactorNum. reflection% reflection
Rfree0.2409 4848 4.94 %
Rwork0.1925 --
obs0.1949 98221 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.1 Å2 / Biso mean: 52.4888 Å2 / Biso min: 20.15 Å2
Refinement stepCycle: final / Resolution: 2.4→48.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15492 0 195 424 16111
Biso mean--50.52 47.03 -
Num. residues----2130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.42730.36071690.316630303199
2.4273-2.45580.34341670.310430663233
2.4558-2.48580.36131480.31230653213
2.4858-2.51720.34421560.296631323288
2.5172-2.55040.35611530.289430443197
2.5504-2.58530.33391580.282330983256
2.5853-2.62220.36561630.284430823245
2.6222-2.66140.30131450.263530873232
2.6614-2.70290.31181920.259530663258
2.7029-2.74730.27821410.252731183259
2.7473-2.79460.31411640.249230743238
2.7946-2.84540.35361710.238230553226
2.8454-2.90020.321580.234530903248
2.9002-2.95930.28341630.2231193282
2.9593-3.02370.27641780.22230573235
3.0237-3.0940.23461510.216330953246
3.094-3.17140.31630.213931073270
3.1714-3.25710.24551660.199631093275
3.2571-3.35290.23671480.187231163264
3.3529-3.46110.25161660.175931083274
3.4611-3.58480.21311500.17631313281
3.5848-3.72830.1851750.178231043279
3.7283-3.89790.2181480.16931153263
3.8979-4.10330.20621640.164931313295
4.1033-4.36020.21781640.150231333297
4.3602-4.69660.17161700.145131203290
4.6966-5.16870.21921550.151931753330
5.1687-5.91550.20121520.172332103362
5.9155-7.44860.23111630.175832053368
7.4486-48.33670.18991870.158233313518
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)
11.0185-0.0008-0.09581.0535-0.15511.2088-0.0353-0.0709-0.3387-0.0169-0.0125-0.03940.2564-0.00290.05150.3263-0.00660.04520.25360.03350.34-5.6096-13.786-3.3812
21.4834-0.3805-0.6420.865-0.31860.7506-0.0613-0.22020.13560.3367-0.0124-0.17320.13920.06310.07190.4313-0.00780.02120.48670.00420.2788-4.981412.086424.8035
31.35510.17760.00230.4610.21930.5321-0.0015-0.09260.02950.11950.0048-0.01140.0458-0.020.00120.4050.03360.05490.42440.02050.3284-15.99479.760317.8429
41.6623-0.1176-0.85430.50030.78011.56250.09120.1430.1104-0.0105-0.33870.2032-0.1472-0.14140.28780.37090.0061-0.00910.49060.00170.3908-28.60964.68781.1897
50.44090.23650.42031.09831.10641.6995-0.0742-0.2182-0.07930.0175-0.14710.3043-0.0653-0.39710.18650.36990.06020.04610.587-0.06860.5003-34.35977.868410.6997
61.03090.3123-0.02560.6040.00531.0087-0.04840.0754-0.3154-0.06410.0146-0.11820.17580.05280.02970.33630.04170.06860.2801-0.01430.415216.6822-8.6144-25.621
72.05990.78190.20581.9810.01030.7718-0.00910.01420.156-0.1815-0.067-0.0592-0.08130.02060.03320.45850.00440.04870.36320.07120.316212.055227.7718-41.0977
81.48870.33050.00871.9945-0.6020.3989-0.07340.1795-0.067-0.31130.0184-0.13590.02520.09730.06210.43140.00420.10210.40060.02480.380233.142814.2087-34.9846
90.4774-0.1139-0.53010.03560.12120.54750.44830.52330.71710.2531-0.384-0.6674-0.5908-0.2235-0.0930.6454-0.0205-0.03430.67040.14790.833838.977220.5286-15.453
100.2873-0.30010.51712.3625-0.31821.0094-0.15590.150.0159-0.19520.1273-0.5246-0.10590.22750.02450.4453-0.03740.11730.49190.1020.568641.979221.2164-31.5035
111.3205-0.4703-0.70070.40570.43191.64190.0422-0.14560.2243-0.1-0.0519-0.0723-0.28020.2282-0.03020.3018-0.0155-0.01490.35140.01230.378322.152716.7683-1.7504
120.623-0.86970.06931.1951-0.08360.0130.0717-0.02430.3579-0.2588-0.2042-0.2994-0.1951-0.10620.02330.5533-0.01180.12770.38020.01650.60128.838716.0671-15.0012
131.49210.35420.25171.48640.52531.7774-0.0806-0.08070.38680.1353-0.10950.1005-0.11720.08540.13360.3129-0.01420.02280.3215-0.00430.383810.685218.77736.2753
141.36820.1934-0.65840.7974-0.15170.7893-0.0904-0.3596-0.360.1639-0.0444-0.18050.1960.31240.12730.36370.103-0.01470.47760.14930.467530.776-10.60685.515
151.16870.2732-0.00020.1524-0.18881.1078-0.0369-0.0928-0.2907-0.0079-0.015-0.21480.25530.34190.0510.38310.1350.0750.53670.08020.660342.9785-9.1216-11.4405
161.76490.4235-0.48050.7014-0.72990.73570.0159-0.03480.24930.175-0.04610.0695-0.2927-0.17870.00840.41150.06060.02730.3183-0.03430.3636-14.981417.1867-17.3974
170.2082-0.5608-0.24582.44780.23660.46390.22740.3694-0.3178-0.3265-0.44350.24290.5059-0.89630.18440.7778-0.020.01370.7724-0.04150.5986-1.168218.1152-2.5581
181.4233-0.2196-0.27111.3068-0.07011.26290.0255-0.02920.382-0.0317-0.0627-0.0541-0.1437-0.00680.04740.37920.02580.00990.3112-0.01050.3982-3.71822.2397-22.776
191.41190.1849-0.06080.76690.3680.4627-0.00620.3515-0.2265-0.2027-0.04620.0910.024-0.19110.03840.4006-0.0056-0.02790.4026-0.09260.3145-17.6357-9.3051-36.702
201.4830.3581-0.09810.6826-0.18321.3401-0.0350.0995-0.0378-0.0658-0.02170.19770.0885-0.30830.02890.3073-0.03060.02560.4361-0.0850.3648-31.4304-6.1509-18.8585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:208)A1 - 208
2X-RAY DIFFRACTION2(chain A and resid 209:273)A209 - 273
3X-RAY DIFFRACTION3(chain A and resid 274:447)A274 - 447
4X-RAY DIFFRACTION4(chain A and resid 448:498)A448 - 498
5X-RAY DIFFRACTION5(chain A and resid 499:554)A499 - 554
6X-RAY DIFFRACTION6(chain B and resid 1:210)B1 - 210
7X-RAY DIFFRACTION7(chain B and resid 211:344)B211 - 344
8X-RAY DIFFRACTION8(chain B and resid 345:468)B345 - 468
9X-RAY DIFFRACTION9(chain B and resid 469:504)B469 - 504
10X-RAY DIFFRACTION10(chain B and resid 505:554)B505 - 554
11X-RAY DIFFRACTION11(chain C and resid 2:108)C2 - 108
12X-RAY DIFFRACTION12(chain C and resid 109:126)C109 - 126
13X-RAY DIFFRACTION13(chain C and resid 127:209)C127 - 209
14X-RAY DIFFRACTION14(chain C and resid 210:476)C210 - 476
15X-RAY DIFFRACTION15(chain C and resid 477:554)C477 - 554
16X-RAY DIFFRACTION16(chain D and resid 2:106)D2 - 106
17X-RAY DIFFRACTION17(chain D and resid 107:122)D107 - 122
18X-RAY DIFFRACTION18(chain D and resid 123:208)D123 - 208
19X-RAY DIFFRACTION19(chain D and resid 209:421)D209 - 421
20X-RAY DIFFRACTION20(chain D and resid 422:554)D422 - 554

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