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- PDB-8cav: Discovery of the lanthipeptide Curvocidin and structural insights... -

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Basic information

Entry
Database: PDB / ID: 8cav
TitleDiscovery of the lanthipeptide Curvocidin and structural insights into its trifunctional synthetase CuvL
Components
  • CuvA
  • Serine/threonine protein kinase
KeywordsBIOSYNTHETIC PROTEIN / lanthipeptide
Function / homology
Function and homology information


peptide modification / carbohydrate metabolic process / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / metal ion binding
Similarity search - Function
Lanthionine synthetase C-like protein / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like / Six-hairpin glycosidase-like superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / non-specific serine/threonine protein kinase / Uncharacterized protein
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsSigurdsson, A. / Martins, B.M. / Duettmann, S.A. / Jasyk, M. / Dimos-Roehl, B. / Schoepf, F. / Gemannter, M. / Knittel, C.H. / Schnegotyzki, R. / Schmid, B. ...Sigurdsson, A. / Martins, B.M. / Duettmann, S.A. / Jasyk, M. / Dimos-Roehl, B. / Schoepf, F. / Gemannter, M. / Knittel, C.H. / Schnegotyzki, R. / Schmid, B. / Kosol, S. / Gonzalez-Viegas, M. / Seidel, M. / Huegelland, M. / Leimkuehler, S. / Dobbek, H. / Mainz, A. / Suessmuth, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008 390540038 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Discovery of the Lanthipeptide Curvocidin and Structural Insights into its Trifunctional Synthetase CuvL.
Authors: Sigurdsson, A. / Martins, B.M. / Duttmann, S.A. / Jasyk, M. / Dimos-Rohl, B. / Schopf, F. / Gemander, M. / Knittel, C.H. / Schnegotzki, R. / Schmid, B. / Kosol, S. / Pommerening, L. / ...Authors: Sigurdsson, A. / Martins, B.M. / Duttmann, S.A. / Jasyk, M. / Dimos-Rohl, B. / Schopf, F. / Gemander, M. / Knittel, C.H. / Schnegotzki, R. / Schmid, B. / Kosol, S. / Pommerening, L. / Gonzales-Viegaz, M. / Seidel, M. / Hugelland, M. / Leimkuhler, S. / Dobbek, H. / Mainz, A. / Sussmuth, R.D.
History
DepositionJan 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine protein kinase
B: Serine/threonine protein kinase
D: CuvA
G: CuvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,43412
Polymers196,9004
Non-polymers1,5348
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-78 kcal/mol
Surface area70070 Å2
Unit cell
Length a, b, c (Å)84.370, 116.130, 97.410
Angle α, β, γ (deg.)90.00, 106.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABDG

#1: Protein Serine/threonine protein kinase


Mass: 92965.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Gene: Tcur_0376 / Production host: Escherichia coli (E. coli) / References: UniProt: D1A2F7
#2: Protein CuvA


Mass: 5485.151 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Gene: Tcur_0378 / Production host: Escherichia coli (E. coli) / References: UniProt: D1A2F9

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Non-polymers , 4 types, 24 molecules

#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.34 Å3/Da / Density % sol: 47 % / Description: elongated paralelipiped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1 M CAPS pH 10.5, 40% MPD (condition E5 from JCSG screen, Molecular Dimensions, UK)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918841 Å / Relative weight: 1
ReflectionResolution: 2.87→49.33 Å / Num. obs: 40774 / % possible obs: 98.1 % / Redundancy: 4.88 % / CC1/2: 0.983 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.286 / Net I/av σ(I): 6.15 / Net I/σ(I): 6.15
Reflection shellResolution: 2.87→3.04 Å / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 6499 / CC1/2: 0.436 / Rrim(I) all: 0.166

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Processing

Software
NameVersionClassification
autoXDSV1.0data collection
PHENIX1.17.1phasing
PHENIX1.17.1refinement
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→46.76 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2934 2037 5 %
Rwork0.2371 --
obs0.2399 40742 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.87→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13122 0 96 16 13234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.872
X-RAY DIFFRACTIONf_dihedral_angle_d17.0974949
X-RAY DIFFRACTIONf_chiral_restr0.0432046
X-RAY DIFFRACTIONf_plane_restr0.012481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-2.930.39351310.36392487X-RAY DIFFRACTION96
2.93-3.010.35361360.34122578X-RAY DIFFRACTION99
3.01-3.090.38161350.31712572X-RAY DIFFRACTION98
3.09-3.180.31071360.30592577X-RAY DIFFRACTION99
3.18-3.280.33481360.28912591X-RAY DIFFRACTION99
3.28-3.40.31811370.27112594X-RAY DIFFRACTION99
3.4-3.530.33031370.25672600X-RAY DIFFRACTION99
3.53-3.690.2991320.24752510X-RAY DIFFRACTION96
3.69-3.890.28171370.23262606X-RAY DIFFRACTION99
3.89-4.130.29581360.21932585X-RAY DIFFRACTION99
4.13-4.450.2561380.19922627X-RAY DIFFRACTION99
4.45-4.90.27531360.19162587X-RAY DIFFRACTION99
4.9-5.610.24751350.22412550X-RAY DIFFRACTION97
5.61-7.060.31341380.24662632X-RAY DIFFRACTION99
7.06-46.760.25981370.19222609X-RAY DIFFRACTION97
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)
10.9181-0.24650.80510.2273-0.21160.6196-0.1064-0.7273-0.2896-0.23580.1635-0.01350.0867-0.10020.0150.3606-0.00840.01930.4940.10190.3827-30.19310.454129.8687
20.05270.70980.12430.92180.4750.5591-0.1506-0.08990.2085-0.15190.07020.00440.2380.0047-0.00050.34120.02010.00860.36160.03520.4968-41.356714.4887-0.2059
30.51690.02720.18590.3759-0.24320.5769-0.0337-0.09560.06370.1085-0.02220.05790.01220.08560.00010.2940.02040.03580.22640.01730.3033-14.576826.48912.5668
40.8761-0.33510.35881.2578-0.14290.3633-0.05820.1594-0.0708-0.0494-0.0880.1276-0.03020.0532-0.00070.2482-0.0224-0.00340.32090.06890.2772-3.211824.172-0.581
50.401-0.8164-0.3061.2924-0.51640.77310.2330.02980.1261-0.0051-0.0888-0.09040.1444-0.01360.00170.41370.0829-0.04410.4097-0.04850.38678.1401-13.740427.3164
60.09480.01580.0371.39070.1030.6856-0.04370.1064-0.2040.28160.02970.15490.26480.0789-0.00150.46510.15550.03080.55510.04520.482322.2612-17.898559.4123
70.7217-0.2003-0.18210.5510.2662-0.02760.11430.29490.031-0.21910.0888-0.523-0.33660.09310.00020.40960.0727-0.01250.6226-0.03470.521532.23131.307360.14
80.7007-0.43190.01980.24370.32341.2565-0.2192-0.1302-0.05340.0470.11890.0355-0.02510.0059-0.00890.31870.0692-0.00930.28520.02990.2337-1.220516.451156.4306
90.1191-0.0831-0.0360.06430.02740.01130.1876-0.02460.06420.0644-0.00380.2419-0.0073-0.159600.4374-0.06110.1470.37460.15740.5287-57.28928.44739.5959
100.0708-0.071-0.01890.06840.01290.00060.04950.0196-0.00310.0552-0.0240.0080.1349-0.09190.01110.6889-0.5909-0.13750.62670.22140.2099-50.8554-3.43127.8862
110.8839-0.40.18781.119-0.38780.13750.0963-0.0025-0.1128-0.11840.0790.22070.00290.04690.14251.2230.1972-0.2492-0.0440.02910.1805-37.1561-4.94917.3417
120.1414-0.1836-0.02840.4749-0.02290.01990.0384-0.0441-0.12110.14980.0511-0.02710.14760.0576-0.06450.86540.3236-0.2370.4596-0.1560.4859-28.81144.57141.4683
130.75470.1226-0.68510.1909-0.42561.1318-0.56280.1809-0.40010.326-0.64390.3271-0.05170.0259-0.08240.5934-0.009-0.05670.5986-0.09661.430119.8183-32.265346.774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 200 )
2X-RAY DIFFRACTION2chain 'A' and (resid 201 through 363 )
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 645 )
4X-RAY DIFFRACTION4chain 'A' and (resid 646 through 865 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 200 )
6X-RAY DIFFRACTION6chain 'B' and (resid 201 through 363 )
7X-RAY DIFFRACTION7chain 'B' and (resid 364 through 482 )
8X-RAY DIFFRACTION8chain 'B' and (resid 483 through 863 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 5 )
10X-RAY DIFFRACTION10chain 'D' and (resid 6 through 10 )
11X-RAY DIFFRACTION11chain 'D' and (resid 11 through 15 )
12X-RAY DIFFRACTION12chain 'D' and (resid 16 through 20 )
13X-RAY DIFFRACTION13chain 'G' and (resid 113 through 123 )

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