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- PDB-2ejm: Solution structure of RUH-072, an apo-biotnyl domain form human a... -

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Basic information

Entry
Database: PDB / ID: 2ejm
TitleSolution structure of RUH-072, an apo-biotnyl domain form human acetyl coenzyme A carboxylase
ComponentsMethylcrotonoyl-CoA carboxylase subunit alphaMethylcrotonyl-CoA carboxylase
KeywordsLIGASE / Biotin-requiring enzyme / Biotin / actyl CoA carboxylase / Fatty acid synthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


3-methylcrotonyl-CoA carboxylase complex, mitochondrial / methylcrotonoyl-CoA carboxylase / biotin metabolic process / methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / L-leucine catabolic process / biotin carboxylase activity / branched-chain amino acid catabolic process ...3-methylcrotonyl-CoA carboxylase complex, mitochondrial / methylcrotonoyl-CoA carboxylase / biotin metabolic process / methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / L-leucine catabolic process / biotin carboxylase activity / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / biotin binding / mitochondrial matrix / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain ...Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Carbamoyl-phosphate synthase subdomain signature 2. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRuhul Momen, A.Z.M. / Hirota, H. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of RUH-072, an apo-biotnyl domain form human acetyl coenzyme A carboxylase
Authors: Ruhul Momen, A.Z.M. / Hirota, H. / Hayashi, F. / Yokoyama, S.
History
DepositionMar 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylcrotonoyl-CoA carboxylase subunit alpha


Theoretical massNumber of molelcules
Total (without water)10,5051
Polymers10,5051
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Methylcrotonoyl-CoA carboxylase subunit alpha / Methylcrotonyl-CoA carboxylase / 3-methylcrotonyl-CoA carboxylase 1 / MCCase subunit alpha / 3-methylcrotonyl-CoA:carbon dioxide ...3-methylcrotonyl-CoA carboxylase 1 / MCCase subunit alpha / 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha / 3- methylcrotonyl-CoA carboxylase biotin-containing subunit


Mass: 10504.741 Da / Num. of mol.: 1 / Fragment: C-terminal domain of acetyl CoA carboxylase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: MCCC1, MCCA / Plasmid: PO50719-21 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96RQ3, methylcrotonoyl-CoA carboxylase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.29mM Domain U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90%H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.04Johnson, B.A.data analysis
KUJIRA0.955Kobayashi, N.data analysis
CYANA1.07Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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