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- PDB-2k2q: complex structure of the external thioesterase of the Surfactin-s... -

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Basic information

Entry
Database: PDB / ID: 2k2q
Titlecomplex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain
Components
  • Surfactin synthetase thioesterase subunit
  • Tyrocidine synthetase 3 (Tyrocidine synthetase III)
KeywordsLigase/Hydrolase / thioesterase / a/b-hydrolase / NRPS / non-ribosomal peptide synthetase / type II thioesterase / Antibiotic biosynthesis / Ligase / Multifunctional enzyme / Phosphopantetheine / Sporulation / Stress response / Ligase-Hydrolase COMPLEX
Function / homology
Function and homology information


amide biosynthetic process / secondary metabolite biosynthetic process / organonitrogen compound biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic acid metabolic process / lipid biosynthetic process / sporulation resulting in formation of a cellular spore / phosphopantetheine binding / ligase activity / antibiotic biosynthetic process ...amide biosynthetic process / secondary metabolite biosynthetic process / organonitrogen compound biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic acid metabolic process / lipid biosynthetic process / sporulation resulting in formation of a cellular spore / phosphopantetheine binding / ligase activity / antibiotic biosynthetic process / hydrolase activity / cytoplasm
Similarity search - Function
Thioesterase type II, NRPS/PKS/S-FAS / ACP-like / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding enzyme, C-terminal domain ...Thioesterase type II, NRPS/PKS/S-FAS / ACP-like / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tyrocidine synthase 3 / Surfactin synthase thioesterase subunit
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
Bacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsheterodimeric NMR solution structure of SrfTEII and TycC3-PCP
AuthorsKoglin, A. / Lohr, F. / Bernhard, F. / Rogov, V.V. / Frueh, D.P. / Strieter, E.R. / Mofid, M.R. / Guntert, P. / Wagner, G. / Walsh, C.T. ...Koglin, A. / Lohr, F. / Bernhard, F. / Rogov, V.V. / Frueh, D.P. / Strieter, E.R. / Mofid, M.R. / Guntert, P. / Wagner, G. / Walsh, C.T. / Marahiel, M.A. / Dotsch, V.
CitationJournal: Nature / Year: 2008
Title: Structural basis for the selectivity of the external thioesterase of the surfactin synthetase.
Authors: Koglin, A. / Lohr, F. / Bernhard, F. / Rogov, V.V. / Frueh, D.P. / Strieter, E.R. / Mofid, M.R. / Guntert, P. / Wagner, G. / Walsh, C.T. / Marahiel, M.A. / Dotsch, V.
History
DepositionApr 10, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 19, 2016Group: Structure summary
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrocidine synthetase 3 (Tyrocidine synthetase III)
B: Surfactin synthetase thioesterase subunit


Theoretical massNumber of molelcules
Total (without water)36,5582
Polymers36,5582
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 200
RepresentativeModel #1closest to the average

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Components

#1: Protein Tyrocidine synthetase 3 (Tyrocidine synthetase III)


Mass: 8905.300 Da / Num. of mol.: 1 / Fragment: Acyl carrier 3 domain, UNP residues 3033-3112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Genus: B. brevis / Gene: tycC / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: O30409
#2: Protein Surfactin synthetase thioesterase subunit / Cold shock protein CSI16


Mass: 27652.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Species: subtilis / Gene: srfAD, srfA4 / Species (production host): coli / Production host: Escherichia coli (E. coli)
References: UniProt: Q08788, Hydrolases; Acting on ester bonds; Thioester hydrolases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.75 mM 100% 15N; 90% 2H PCP, 0.70 mM 100% 2H; [1H]-FILV TEII, 25 mM potassium phosphate, 80 mM potassium chloride, 1 mM TCEP, 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMPCP100% 15N; 90% 2H1
0.70 mMTEII100% 2H; [1H]-FILV1
25 mMpotassium phosphate1
80 mMpotassium chloride1
1 mMTCEP1
Sample conditionsIonic strength: 100 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.111Goddardpeak picking
Sparky3.111Goddarddata analysis
Sparky3.111Goddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformers calculated total number: 200 / Conformers submitted total number: 18

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