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- PDB-1bbl: THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE E3-BINDING DOMAIN OF ... -

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Entry
Database: PDB / ID: 1bbl
TitleTHREE-DIMENSIONAL SOLUTION STRUCTURE OF THE E3-BINDING DOMAIN OF THE DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE CORE FROM THE 2-OXOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX OF ESCHERICHIA COLI
ComponentsDIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
KeywordsGLYCOLYSIS
Function / homology
Function and homology information


L-lysine catabolic process to acetyl-CoA via saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / lipoic acid binding / oxoglutarate dehydrogenase complex / tricarboxylic acid cycle / cytosol / cytoplasm
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) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex / Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsClore, G.M. / Robien, M.A. / Gronenborn, A.M.
CitationJournal: Biochemistry / Year: 1992
Title: Three-dimensional solution structure of the E3-binding domain of the dihydrolipoamide succinyltransferase core from the 2-oxoglutarate dehydrogenase multienzyme complex of Escherichia coli.
Authors: Robien, M.A. / Clore, G.M. / Omichinski, J.G. / Perham, R.N. / Appella, E. / Sakaguchi, K. / Gronenborn, A.M.
History
DepositionFeb 20, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)5,5091
Polymers5,5091
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)1 / -
Representative

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Components

#1: Protein DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE


Mass: 5509.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P07016, UniProt: P0AFG6*PLUS, 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

RefinementSoftware ordinal: 1
Details: DETAILS OF THE STRUCTURE DETERMINATION AND ALL STRUCTURAL STATISTICS ARE GIVEN IN THE PAPER CITED ON *JRNL* RECORDS ABOVE. THE STRUCTURES ARE BASED ON 630 INTERPROTON DISTANCE RESTRAINTS ...Details: DETAILS OF THE STRUCTURE DETERMINATION AND ALL STRUCTURAL STATISTICS ARE GIVEN IN THE PAPER CITED ON *JRNL* RECORDS ABOVE. THE STRUCTURES ARE BASED ON 630 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NOE MEASUREMENTS; AND 46 PHI AND 35 PSI BACKBONE TORSION ANGLE RESTRAINTS AND 20 CHI1 SIDE CHAIN TORSION ANGLE RESTRAINTS DERIVED FROM COUPLING CONSTANTS AND NOE DATA. THE LATTER ARE OBTAINED USING THE CONFORMATIONAL GRID SEARCH PROGRAM STEREOSEARCH (M.NILGES,G.M.CLORE,A.M.GRONENBORN (1990) BIOPOLYMERS 29, 813-822). THE METHOD USED TO DETERMINE THE STRUCTURES IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (M.NILGES,G.M.CLORE, A.M.GRONENBORN, FEBS LETT. 229, 317-324 (1988)). THIS ENTRY CONTAINS THE SIMULATED ANNEALING RESONANCE MINIMIZED AVERAGE STRUCTURE. THE COORDINATES OF 56 INDIVIDUAL STRUCTURES ARE PRESENTED IN PROTEIN DATA BANK ENTRY 1BAL. (SA)R RESTRAINED MINIMIZED MEAN STRUCTURE WAS DERIVED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL SA STRUCTURES BEST FITTED TO RESIDUES 14 - 30 AND 39 - 47, AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. RESIDUES 1 - 11 AND 48 - 51 ARE COMPLETELY DISORDERED AND ARE NOT INCLUDED IN THE COORDINATE SET. THE QUANTITY PRESENTED IN COLUMNS 61 - 66 OF THIS ENTRY HAS NO MEANING. THE QUANTITY PRESENTED IN COLUMNS 61 - 66 OF ENTRY 1BAL REPRESENTS THE ATOMIC RMS DEVIATIONS OF THE 56 INDIVIDUAL STRUCTURES ABOUT THE MEAN STRUCTURE. ALL THE INTERPROTON DISTANCE AND TORSION ANGLE RESTRAINTS ARE PRESENTED IN PROTEIN DATA BANK ENTRY R1BBLMR.
NMR ensembleConformers submitted total number: 1

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