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- PDB-1ghk: SOLUTION STRUCTURE OF THE LIPOYL DOMAIN OF THE 2-OXOGLUTARATE DEH... -

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Entry
Database: PDB / ID: 1ghk
TitleSOLUTION STRUCTURE OF THE LIPOYL DOMAIN OF THE 2-OXOGLUTARATE DEHYDROGENASE COMPLEX FROM AZOTOBACTER VINELAND II, NMR, 25 STRUCTURES
ComponentsE2, THE DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX
KeywordsACYLTRANSFERASE / GLYCOLYSIS / TRANSFERASE / LIPOYL
Function / homology
Function and homology information


L-lysine catabolic process to acetyl-CoA via saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / tricarboxylic acid cycle / cytosol
Similarity search - Function
: / Dihydrolipoamide succinyltransferase / 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 succinyltransferase / 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 succinyltransferase component of 2-oxoglutarate dehydrogenase complex
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodSOLUTION NMR
AuthorsBerg, A. / Vervoort, J. / De Kok, A.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Solution structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii.
Authors: Berg, A. / Vervoort, J. / de Kok, A.
#1: Journal: Eur.J.Biochem. / Year: 1995
Title: Sequential 1H and 15N Nuclear Magnetic Resonance Assignments and Secondary Structure of the Lipoyl Domain of the 2-Oxoglutarate Dehydrogenase Complex from Azotobacter Vinelandii. Evidence for ...Title: Sequential 1H and 15N Nuclear Magnetic Resonance Assignments and Secondary Structure of the Lipoyl Domain of the 2-Oxoglutarate Dehydrogenase Complex from Azotobacter Vinelandii. Evidence for High Structural Similarity with the Lipoyl Domain of the Pyruvate Dehydrogenase Complex
Authors: Berg, A. / Smits, O. / De Kok, A. / Vervoort, J.
History
DepositionJan 16, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Item: _pdbx_database_status.process_site
Revision 1.4May 1, 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

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: E2, THE DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX


Theoretical massNumber of molelcules
Total (without water)8,3531
Polymers8,3531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / -
Representative

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Components

#1: Protein E2, THE DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX / E2


Mass: 8353.437 Da / Num. of mol.: 1 / Fragment: LIPOYL DOMAIN, RESIDUES 1-79
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P20708, dihydrolipoyllysine-residue succinyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 25

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