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- PDB-1fyc: INNER LIPOYL DOMAIN FROM HUMAN PYRUVATE DEHYDROGENASE (PDH) COMPL... -

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Basic information

Entry
Database: PDB / ID: 1fyc
TitleINNER LIPOYL DOMAIN FROM HUMAN PYRUVATE DEHYDROGENASE (PDH) COMPLEX, NMR, 1 STRUCTURE
ComponentsDIHYDROLIPOAMIDE ACETYLTRANSFERASE (E2P)
KeywordsTRANSFERASE / ACYLTRANSFERASE DIHYDROLIPOAMIDE / SUBUNIT / UNLIPOYLATED
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / : / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / tricarboxylic acid cycle ...dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / : / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / tricarboxylic acid cycle / glucose metabolic process / mitochondrial matrix / intracellular membrane-bounded organelle / mitochondrion / identical protein binding
Similarity search - Function
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / 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) ...Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / 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, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHoward, M.J. / Fuller, C. / Broadhurst, R.W. / Quinn, J. / Yeaman, S.J. / Perham, R.N.
CitationJournal: Gastroenterology / Year: 1998
Title: Three-dimensional structure of the major autoantigen in primary biliary cirrhosis.
Authors: Howard, M.J. / Fuller, C. / Broadhurst, R.W. / Perham, R.N. / Tang, J.G. / Quinn, J. / Diamond, A.G. / Yeaman, S.J.
History
DepositionFeb 21, 1997Processing site: BNL
Revision 1.0Sep 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIHYDROLIPOAMIDE ACETYLTRANSFERASE (E2P)


Theoretical massNumber of molelcules
Total (without water)11,6611
Polymers11,6611
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 80MEAN STRUCTURE FROM 26 CHOSEN HAVING LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein DIHYDROLIPOAMIDE ACETYLTRANSFERASE (E2P)


Mass: 11661.315 Da / Num. of mol.: 1 / Fragment: LIPOYL DOMAIN
Source method: isolated from a genetically manipulated source
Details: DIHYDROLIPOAMIDE ACETYLTRANSFERASE SUBUNIT OF THE PYRUVATE DEHYDROGENASE (PDH) MULTIENZYME COMPLEX (UNLIPOYLATED DOMAIN)
Source: (gene. exp.) Homo sapiens (human) / Description: EXPRESSED AS A GST FUSION PROTEIN / Organ: LIVER / Plasmid: HLIP / Production host: Escherichia coli (E. coli)
References: UniProt: P10515, dihydrolipoyllysine-residue acetyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TCOSY
141HSQC-NOESY
151HSQC-TOCSY

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AM500 / Manufacturer: Bruker / Model: AM500 / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
ANSIG3.3structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAM BE FOUND IN P.M. RICAUD ET AL., JOURNAL OF MOLECULAR BIOLOGY, 264, 179-190, 1996
NMR ensembleConformer selection criteria: MEAN STRUCTURE FROM 26 CHOSEN HAVING LEAST RESTRAINT VIOLATION
Conformers calculated total number: 80 / Conformers submitted total number: 1

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