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- PDB-7oy1: DnrK mutant RTCR -

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Basic information

Entry
Database: PDB / ID: 7oy1
TitleDnrK mutant RTCR
ComponentsCarminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
KeywordsBIOSYNTHETIC PROTEIN / Carminomycin-4-O-methyltransferase variant / Chimeragenesis / aclacinomycin 10-hydroxylase / komodoquinone 10-decarboxylase
Function / homology
Function and homology information


carminomycin 4-O-methyltransferase / daunorubicin biosynthetic process / Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / O-methyltransferase activity / antibiotic biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-3VL / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain-containing protein / Methyltransferase domain-containing protein / Carminomycin 4-O-methyltransferase DnrK / Aclacinomycin 10-hydroxylase RdmB
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
Streptomyces sp. ZEA17I (bacteria)
Streptomyces purpurascens (bacteria)
Streptomyces tsukubensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsDinis, P. / MetsaKetela, M.
CitationJournal: Pnas Nexus / Year: 2023
Title: Evolution-inspired engineering of anthracycline methyltransferases.
Authors: Dinis, P. / Tirkkonen, H. / Wandi, B.N. / Siitonen, V. / Niemi, J. / Grocholski, T. / Metsa-Ketela, M.
History
DepositionJun 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary / Category: chem_comp / pdbx_entry_details
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
B: Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8066
Polymers79,8982
Non-polymers1,9084
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-55 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.400, 105.690, 64.450
Angle α, β, γ (deg.)90.000, 111.183, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB / COMT / Anthracycline 4-O-methyltransferase / 15-demethoxy-epsilon-rhodomycin 10-hydroxylase / 15- ...COMT / Anthracycline 4-O-methyltransferase / 15-demethoxy-epsilon-rhodomycin 10-hydroxylase / 15-demethoxyaclacinomycin T


Mass: 39949.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces peucetius (bacteria), (gene. exp.) Streptomyces sp. ZEA17I (bacteria), (gene. exp.) Streptomyces purpurascens (bacteria), (gene. exp.) Streptomyces tsukubensis ...Source: (gene. exp.) Streptomyces peucetius (bacteria), (gene. exp.) Streptomyces sp. ZEA17I (bacteria), (gene. exp.) Streptomyces purpurascens (bacteria), (gene. exp.) Streptomyces tsukubensis (strain DSM 42081 / NBRC 108919 / NRRL 18488 / 9993) (bacteria)
Gene: dnrK, DKT74_09280, rdmB, STSU_011780, STSU_11775 / Strain: DSM 42081 / NBRC 108919 / NRRL 18488 / 9993 / Production host: Escherichia coli (E. coli)
References: UniProt: Q06528, UniProt: A0A2V2Q0Q4, UniProt: Q54527, UniProt: I2N5E8, carminomycin 4-O-methyltransferase, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3VL / methyl (1R,2R,4S)-2-ethyl-2,5,7-trihydroxy-6,11-dioxo-4-{[2,3,6-trideoxy-3-(dimethylamino)-alpha-L-lyxo-hexopyranosyl]oxy}-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate / aclacinomycin T


Mass: 569.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H35NO10 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate; 0.1 M HEPES 7.0; 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryocooling / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.39→49.71 Å / Num. obs: 29636 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.21 Å2 / Rrim(I) all: 0.138 / Net I/σ(I): 4.1
Reflection shellResolution: 2.39→2.48 Å / Rmerge(I) obs: 0.242 / Num. unique obs: 2854 / Rpim(I) all: 0.169

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TW2

1tw2


Resolution: 2.39→49.7 Å / SU ML: 0.3253 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.9372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2668 1503 5.07 %
Rwork0.2272 28116 -
obs0.2293 29619 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.26 Å2
Refinement stepCycle: LAST / Resolution: 2.39→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 134 264 5438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00955312
X-RAY DIFFRACTIONf_angle_d1.17857282
X-RAY DIFFRACTIONf_chiral_restr0.0734864
X-RAY DIFFRACTIONf_plane_restr0.0319933
X-RAY DIFFRACTIONf_dihedral_angle_d16.0831902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.470.28741170.23182436X-RAY DIFFRACTION95.51
2.47-2.560.28681320.23222589X-RAY DIFFRACTION99.52
2.56-2.660.36261270.23722556X-RAY DIFFRACTION99.89
2.66-2.780.27651300.24942578X-RAY DIFFRACTION99.41
2.78-2.930.31491380.25082569X-RAY DIFFRACTION99.63
2.93-3.110.30551530.24132546X-RAY DIFFRACTION99.63
3.11-3.350.30171470.23322565X-RAY DIFFRACTION99.38
3.35-3.690.27311380.23072531X-RAY DIFFRACTION98.82
3.69-4.220.21761310.20662579X-RAY DIFFRACTION98.94
4.22-5.310.20531430.19612550X-RAY DIFFRACTION99.08
5.31-49.70.23471470.2292617X-RAY DIFFRACTION99.39

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