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- PDB-2bth: Peripheral-subunit binding domains from mesophilic, thermophilic,... -

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Basic information

Entry
Database: PDB / ID: 2bth
TitlePeripheral-subunit binding domains from mesophilic, thermophilic, and hyperthermophilic bacteria fold by ultrafast, apparently two-state transitions
ComponentsDIHYDROLIPOYLLYSINE-RESIDUE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX
KeywordsTRANSFERASE / ACYLTRANSFERASE / LIPOYL
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 / cytoplasm / cytosol
Similarity search - Function
E3-binding domain / : / Dihydrolipoamide Transferase / 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. ...E3-binding domain / : / Dihydrolipoamide Transferase / 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 / Few Secondary Structures / Irregular
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
AuthorsFerguson, N. / Allen, M.D.
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
DepositionMay 31, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Other
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 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 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIHYDROLIPOYLLYSINE-RESIDUE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX


Theoretical massNumber of molelcules
Total (without water)5,0091
Polymers5,0091
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 / 20ACCEPTED
RepresentativeModel #1

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Components

#1: Protein/peptide DIHYDROLIPOYLLYSINE-RESIDUE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX / E3-BINDING DOMAIN / E2


Mass: 5008.610 Da / Num. of mol.: 1 / Fragment: RESIDUES 108-152 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P07016, UniProt: P0AFG6*PLUS, dihydrolipoyllysine-residue succinyltransferase
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 166 TO TRP
Sequence detailsGLY-SER AT THE N-TERMINUS IS THE REMAINS OF A THROMBIN CLEAVAGE SITE. HIS TO TRP MUTATION IS A ...GLY-SER AT THE N-TERMINUS IS THE REMAINS OF A THROMBIN CLEAVAGE SITE. HIS TO TRP MUTATION IS A DELIBERATE MUTATION TO ALLOW FOR FOLDING STUDIES

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

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Sample preparation

DetailsContents: 50 MM POTASSIUM PHOSPHATE, 10% D2
Sample conditionspH: 6.5 / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
Azarastructure solution
ANSIGstructure solution
CNSstructure solution
RefinementSoftware ordinal: 1 / Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL ABOVE
NMR ensembleConformer selection criteria: ACCEPTED / Conformers calculated total number: 20 / Conformers submitted total number: 20

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