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- PDB-8raj: NMR structure of PKS docking domains -

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Basic information

Entry
Database: PDB / ID: 8raj
TitleNMR structure of PKS docking domains
Components
  • Beta-ketoacyl synthase
  • Trimethylamine monooxygenase
KeywordsPROTEIN BINDING / DOCKING DOMAIN / POLYKETIDE SYNTHASE
Function / homology
Function and homology information


metabolic process / N,N-dimethylaniline monooxygenase activity / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / DIM/DIP cell wall layer assembly / secondary metabolite biosynthetic process / fatty acid synthase activity / transaminase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity ...metabolic process / N,N-dimethylaniline monooxygenase activity / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / DIM/DIP cell wall layer assembly / secondary metabolite biosynthetic process / fatty acid synthase activity / transaminase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / pyridoxal phosphate binding / flavin adenine dinucleotide binding / NADP binding / plasma membrane / cytoplasm
Similarity search - Function
Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / PKS_PP_betabranch / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Aminotransferase class-III / Aminotransferase class-III / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / FAD/NAD(P)-binding domain superfamily / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Beta-ketoacyl synthase / Carrier domain-containing protein
Similarity search - Component
Biological speciesMethylorubrum extorquens AM1 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsScat, S. / Weissman, K.J. / Chagot, B.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Rsc Chem Biol / Year: 2024
Title: Insights into docking in megasynthases from the investigation of the toblerol trans -AT polyketide synthase: many alpha-helical means to an end.
Authors: Scat, S. / Weissman, K.J. / Chagot, B.
History
DepositionDec 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-ketoacyl synthase
B: Trimethylamine monooxygenase


Theoretical massNumber of molelcules
Total (without water)11,6772
Polymers11,6772
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Beta-ketoacyl synthase


Mass: 6649.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens AM1 (bacteria)
Gene: MexAM1_META2p0008 / Plasmid: pBG102 / Details (production host): pET27 derivative / Production host: Escherichia coli (E. coli) / References: UniProt: C5B3B7
#2: Protein/peptide Trimethylamine monooxygenase


Mass: 5027.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens AM1 (bacteria)
Gene: MexAM1_META2p0010 / Plasmid: pBG102 / Details (production host): pE27 derivative / Production host: Escherichia coli (E. coli) / References: UniProt: C5B3B9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
162isotropic12D 1H-13C HSQC
121isotropic12D 1H-15N HSQC
172isotropic12D 1H-15N HSQC
131isotropic13D HNCA
182isotropic13D HNCA
141isotropic13D HNCO
192isotropic13D HNCO
1101isotropic13D HN(CA)CB
1112isotropic13D HN(CA)CB
1121isotropic13D HN(CA)CO
1132isotropic13D HN(CA)CO
1141isotropic13D CBCA(CO)NH
1152isotropic13D CBCA(CO)NH
1171isotropic13D (H)CCH-TOCSY
1182isotropic13D (H)CCH-TOCSY
1161isotropic13D CCH-TOCSY
1192isotropic13D CCH-TOCSY
1201isotropic13D C(CO)NH
1232isotropic13D C(CO)NH
1211isotropic13D H(CCO)NH
1222isotropic13D H(CCO)NH
1241isotropic13D 1H-13C NOESY
1252isotropic13D 1H-13C NOESY
1271isotropic13D 1H-15N NOESY
1262isotropic13D 1H-15N NOESY
1281isotropic13D 1H-13C NOESY aromatic
1292isotropic13D 1H-13C NOESY aromatic
1331isotropic13D HNHA
1322isotropic13D HNHA

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 13C; U-100% 15N] TobC, 2 mM TobE, 100 mM sodium phosphate, 90% H2O/10% D2O15N_13C_C_E90% H2O/10% D2O
solution21 mM [U-100% 13C; U-100% 15N] TobE, 2 mM TobC, 100 mM sodium phosphate, 90% H2O/10% D2O15N_13C_E_C90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTobC[U-100% 13C; U-100% 15N]1
2 mMTobEnatural abundance1
100 mMsodium phosphatenatural abundance1
1 mMTobE[U-100% 13C; U-100% 15N]2
2 mMTobCnatural abundance2
100 mMsodium phosphatenatural abundance2
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
CcpNmr Analysis AssignVranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, and Laue ED.chemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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