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- PDB-2v31: Structure of First Catalytic Cysteine Half-domain of mouse ubiqui... -

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Basic information

Entry
Database: PDB / ID: 2v31
TitleStructure of First Catalytic Cysteine Half-domain of mouse ubiquitin- activating enzyme
ComponentsUBIQUITIN-ACTIVATING ENZYME E1 X
KeywordsLIGASE / PHOSPHORYLATION / CATALYTIC DOMAIN / HETERONUCLEAR NMR / FIRST CATALYTIC CYSTEINE HALF-DOMAIN / E1 PROTEIN / ATP-BINDING / UBIQUITINATION / NUCLEOTIDE-BINDING / UBL CONJUGATION PATHWAY
Function / homology
Function and homology information


Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / rough endoplasmic reticulum membrane / desmosome / Antigen processing: Ubiquitination & Proteasome degradation / heterochromatin / ubiquitin-dependent protein catabolic process / endosome membrane / protein ubiquitination ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / rough endoplasmic reticulum membrane / desmosome / Antigen processing: Ubiquitination & Proteasome degradation / heterochromatin / ubiquitin-dependent protein catabolic process / endosome membrane / protein ubiquitination / lysosomal membrane / DNA damage response / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily ...Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR / CYANA
AuthorsJaremko, L. / Jaremko, M. / Wojciechowski, W. / Filipek, R. / Szczepanowski, R.H. / Bochtler, M. / Zhukov, I.
Citation
Journal: To be Published
Title: Structure of First Catalytic Cysteine Half-Domain of Mouse Ubiquitin-Activating Enzyme
Authors: Jaremko, L. / Jaremko, M. / Wojciechowski, W. / Filipek, R. / Szczepanowski, R.H. / Bohtler, M. / Zhukov, I.
#1: Journal: J.Biomol.NMR / Year: 2006
Title: NMR Assignment of Structurally Uncharacterised Fragment of Recombinant Mouse Ubiquitin-Activating Enzyme
Authors: Jaremko, L. / Jaremko, M. / Filipek, R. / Wojciechowski, W. / Szczepanowski, R.H. / Bochtler, M. / Zhukov, I.
History
DepositionJun 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Version format compliance
Revision 1.2Oct 24, 2018Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / struct_sheet
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 / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN-ACTIVATING ENZYME E1 X


Theoretical massNumber of molelcules
Total (without water)12,1961
Polymers12,1961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200LOWEST ENERGY
RepresentativeModel #2

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Components

#1: Protein UBIQUITIN-ACTIVATING ENZYME E1 X / UBIQUITIN-ACTIVATING ENZYME E1 / E1


Mass: 12195.825 Da / Num. of mol.: 1
Fragment: FIRST CATALYTIC CYSTEINE HALF-DOMAIN, RESIDUES 203-312
Source method: isolated from a natural source / Details: TWO ADDITIONAL RESIDUES EF ON N-TERMINI / Source: (natural) MUS MUSCULUS (house mouse) / References: UniProt: Q02053
Sequence detailsEXTRA EF ON N-TERMINI

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM / pH: 6.5 / Temperature: 287.0 K

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
Sparkystructure solution
RefinementMethod: CYANA / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 20

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