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- PDB-1qjo: INNERMOST LIPOYL DOMAIN OF THE PYRUVATE DEHYDROGENASE FROM ESCHER... -

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Basic information

Entry
Database: PDB / ID: 1qjo
TitleINNERMOST LIPOYL DOMAIN OF THE PYRUVATE DEHYDROGENASE FROM ESCHERICHIA COLI
ComponentsDIHYDROLIPOAMIDE ACETYLTRANSFERASE
KeywordsDIHYDROLIPOAMIDE ACETYLTRANSFERASE / LIPOYL DOMAIN / PYRUVATE DEHYDROGENASE
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / lipoic acid binding / pyruvate catabolic process / pyruvate decarboxylation to acetyl-CoA / pyruvate dehydrogenase complex / pyruvate metabolic process / acetyltransferase activity / cytoplasm
Similarity search - Function
Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / : / 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) ...Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / : / 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) / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
MethodSOLUTION NMR / XPLOR
AuthorsJones, D.D. / Howard, M.J. / Perham, R.N.
Citation
Journal: Biochemistry / Year: 2000
Title: Restricted motion of the lipoyl-lysine swinging arm in the pyruvate dehydrogenase complex of Escherichia coli.
Authors: Jones, D.D. / Stott, K.M. / Howard, M.J. / Perham, R.N.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Protein-Protein Interaction Revealed by NMR T(2) Relaxation Experiments: The Lipoyl Domain and E1 Component of the Pyruvate Dehydrogenase Multienzyme Complex of Bacillus Stearothermophilus
Authors: Howard, M.J. / Chauhan, H.J. / Domingo, G.J. / Fuller, C. / Perham, R.N.
History
DepositionJun 29, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_nmr_spectrometer
Item: _citation.page_last / _citation.title ..._citation.page_last / _citation.title / _citation_author.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIHYDROLIPOAMIDE ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)8,3811
Polymers8,3811
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)30 / 60
RepresentativeModel #1

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Components

#1: Protein DIHYDROLIPOAMIDE ACETYLTRANSFERASE


Mass: 8380.669 Da / Num. of mol.: 1 / Fragment: LIPOAMIDE BINDING DOMAIN OF E2P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Cellular location: CYTOPLASM / Gene: E2P_ECOLI / Plasmid: PET11C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06959

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQFCOSY
141HMQC-NOESY
151HMQC-TOCSY

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Sample preparation

DetailsContents: 90% H2O/ 10%D2O
Sample conditionsIonic strength: 20MM NAPI / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AM / Manufacturer: Bruker / Model: AM / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8BRUNGERrefinement
ANSIGstructure solution
RefinementMethod: XPLOR / Software ordinal: 1
Details: THE N-TERMINAL MET IS AN ARTIFACT OF THE EXPRESSION SYSTEM USED AND NO RESTRAINTS WERE USED TO CALCULATE ITS PART IN THE STRUCTURE.
NMR ensembleConformers calculated total number: 60 / Conformers submitted total number: 30

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