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- PDB-1w4k: Peripheral-subunit binding domains from mesophilic, thermophilic,... -

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Basic information

Entry
Database: PDB / ID: 1w4k
TitlePeripheral-subunit binding domains from mesophilic, thermophilic, and hyperthermophilic bacteria fold by ultrafast, apparently two-state transitions
ComponentsPYRUVATE DEHYDROGENASE E2
KeywordsTRANSFERASE / ULTRAFAST FOLDING
Function / homology
Function and homology information


lipoic acid binding / acetyltransferase activity / cytoplasm
Similarity search - Function
E3-binding domain / Dihydrolipoamide Transferase / : / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain ...E3-binding domain / Dihydrolipoamide Transferase / : / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Pyruvate dehydrogenase E2 (Dihydrolipoamide acetyltransferase)
Similarity search - Component
Biological speciesPYROBACULUM AEROPHILUM (archaea)
MethodSOLUTION NMR
AuthorsFerguson, N. / Sharpe, T.D. / Schartau, P.J. / Allen, M.D. / Johnson, C.M. / Sato, S. / Fersht, A.R.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Ultra-Fast Barrier-Limited Folding in the Peripheral Subunit-Binding Domain Family.
Authors: Ferguson, N. / Sharpe, T.D. / Schartau, P.J. / Sato, S. / Allen, M.D. / Johnson, C.M. / Rutherford, T.J. / Fersht, A.R.
History
DepositionJul 23, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PYRUVATE DEHYDROGENASE E2


Theoretical massNumber of molelcules
Total (without water)5,2601
Polymers5,2601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20NO VIOLATIONS >0.25
RepresentativeModel #1

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Components

#1: Protein PYRUVATE DEHYDROGENASE E2 / DIHYDROLIPOAMIDE ACETYLTRANSFERASE


Mass: 5260.013 Da / Num. of mol.: 1 / Fragment: RESIDUES 93-141 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROBACULUM AEROPHILUM (archaea) / Plasmid: PRSETA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8ZUR6, dihydrolipoyllysine-residue acetyltransferase
Compound detailsENGINEERED MUTATION LEU 112 ALA AND TYR 132 TRP
Sequence detailsL146A DESTABILISATION FOR BIOPHYSICAL STUDIES Y166W ENGINEERED FLUOROPHORE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N LABELED PROTEIN

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Sample preparation

DetailsContents: 95% H2O/ 5% D2O, 3MM SAMPLE
Sample conditionsIonic strength: 100 / pH: 6.2 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
ANSIGstructure solution
CNSstructure solution
RefinementSoftware ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: NO VIOLATIONS >0.25 / Conformers calculated total number: 20 / Conformers submitted total number: 20

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