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- PDB-2roq: Solution Structure of the thiolation-thioesterase di-domain of en... -

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Basic information

Entry
Database: PDB / ID: 2roq
TitleSolution Structure of the thiolation-thioesterase di-domain of enterobactin synthetase component F
ComponentsEnterobactin synthetase component F
KeywordsTRANSFERASE / EntF / T-TE / PCP / thioesterase / peptidyl carrier protein / thiolation domain / enterobactin / non-ribosomal peptide synthetase / NRPS / alpha/beta-hydrolase / didomain / Enterobactin biosynthesis / Ion transport / Iron / Iron transport / Ligase / Multifunctional enzyme / Phosphopantetheine / Transport
Function / homology
Function and homology information


L-serine-[L-seryl-carrier protein] ligase / enterobactin synthase / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin synthetase complex / enterobactin biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / nucleotidyltransferase activity / ATP binding / plasma membrane ...L-serine-[L-seryl-carrier protein] ligase / enterobactin synthase / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin synthetase complex / enterobactin biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / nucleotidyltransferase activity / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / Condensation domain / Condensation domain / Amino acid adenylation domain / Thioesterase / Thioesterase domain / ACP-like / AMP-binding, conserved site / Putative AMP-binding domain signature. ...Polyketide synthase, thioesterase domain / Thioesterase / Condensation domain / Condensation domain / Amino acid adenylation domain / Thioesterase / Thioesterase domain / ACP-like / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / 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
Enterobactin synthase component F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsFrueh, D.P. / Arthanari, H. / Koglin, A. / Vosburg, D.A. / Bennett, A.E. / Walsh, C.T. / Wagner, G.
CitationJournal: Nature / Year: 2008
Title: Dynamic thiolation-thioesterase structure of a non-ribosomal peptide synthetase
Authors: Frueh, D.P. / Arthanari, H. / Koglin, A. / Vosburg, D.A. / Bennett, A.E. / Walsh, C.T. / Wagner, G.
History
DepositionApr 5, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterobactin synthetase component F


Theoretical massNumber of molelcules
Total (without water)37,5191
Polymers37,5191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Enterobactin synthetase component F / Enterochelin synthase F / Serine-activating enzyme / Seryl-AMP ligase


Mass: 37519.285 Da / Num. of mol.: 1 / Fragment: TTE, UNP residues 960-1293 / Mutation: S48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Ent / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11454, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1283D HNCO
1383D HNCA
1483D HN(CA)CB
1583D HN(CO)CA
1683D HN(CA)CO
1753D HNCO-NUS
1853D HNCA-NUS
1953D 13Cdet-MQ-HACACO
11083D C(CO)NH
11183D H(CCO)NH
11262D 1H-15N HSQC
11373D HNCO-NUS
11493D (H)CCH-COSY
11513D 1H-15N NOESY
11633D C(CO)NH
11733D H(CCO)NH
11833D (H)CCH-TOCSY
11943D-TS-NOESY-HSQC
12044D-TS-HSQC-NOESY-HSQC
12143D-HSQC-NOESY
12223D-HN(CA)NH-NUS
12323D HN(COCA)CB
NMR detailsText: NUS: non-uniformly sampled. TS: time-shared. All experiments are TROSY except for the TS-HSQC-NOESY.HN(CA)NH is double TROSY.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 15N] TTE, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
20.3 mM [U-13C; U-15N; U-2H] TTE, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
30.3 mM 1H-Me-ILV-U-2H-U13C-U15N TTE, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
40.3 mM 1H-13C-Me-ILV-U-2H-U12C-U15N TTE, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
50.3 mM [U-98% 13C; U-98% 15N] TTE, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
60.1 mM 15N-selective-K or ILVYFG TTE, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
70.3 mM 13C'-Pro-U-15N TTE, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
80.3 mM 70%2H-U15-U13C TTE, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
90.3 mM [U-13C; U-15N] TTE, 20 mM sodium phosphate, 150 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMTTE[U-100% 15N]1
20 mMsodium phosphate1
150 mMsodium chloride1
1 mMEDTA1
1 mMDTT1
0.3 mMTTE[U-13C; U-15N; U-2H]2
20 mMsodium phosphate2
150 mMsodium chloride2
1 mMEDTA2
1 mMDTT2
0.3 mMTTE1H-Me-ILV-U-2H-U13C-U15N3
20 mMsodium phosphate3
150 mMsodium chloride3
1 mMEDTA3
1 mMDTT3
0.3 mMTTE1H-13C-Me-ILV-U-2H-U12C-U15N4
20 mMsodium phosphate4
150 mMsodium chloride4
1 mMEDTA4
1 mMDTT4
0.3 mMTTE[U-98% 13C; U-98% 15N]5
20 mMsodium phosphate5
150 mMsodium chloride5
1 mMEDTA5
1 mMDTT5
0.1 mMTTE15N-selective-K or ILVYFG6
20 mMsodium phosphate6
150 mMsodium chloride6
1 mMEDTA6
1 mMDTT6
0.3 mMTTE13C'-Pro-U-15N7
20 mMsodium phosphate7
150 mMsodium chloride7
1 mMEDTA7
1 mMDTT7
0.3 mMTTE70%2H-U15-U13C8
20 mMsodium phosphate8
150 mMsodium chloride8
1 mMEDTA8
1 mMDTT8
0.3 mMTTE[U-13C; U-15N]9
20 mMsodium phosphate9
150 mMsodium chloride9
1 mMEDTA9
1 mMDTT9
Sample conditionsIonic strength: 150 mM NaCl, 20 mM NaPI / pH: 6.72 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIBrukerAVANCE II9001
Bruker AvanceBrukerAVANCE7502
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CARA1.8.2Rochus Kellerchemical shift assignment
TALOSCornilescu, Delaglio and Baxtorsion angles prediction
NMRPipe5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOL2kKoradi, Billeter and Wuthrichdata analysis
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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