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- PDB-2lzj: Refined solution structure and dynamics of First Catalytic Cystei... -

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Basic information

Entry
Database: PDB / ID: 2lzj
TitleRefined solution structure and dynamics of First Catalytic Cysteine Half-domain from mouse E1 enzyme
ComponentsUbiquitin-like modifier-activating enzyme 1
KeywordsLIGASE / Catalytic half-domain / Mouse E1 enzyme / Beta-barrel architecture / Flexible thermini / Ubiquitinylation / Protein degradation
Function / homology
Function and homology information


E1 ubiquitin-activating enzyme / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin activating enzyme activity / desmosome / rough endoplasmic reticulum membrane / Antigen processing: Ubiquitination & Proteasome degradation / heterochromatin / ubiquitin-dependent protein catabolic process / protein ubiquitination / endosome membrane ...E1 ubiquitin-activating enzyme / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin activating enzyme activity / desmosome / rough endoplasmic reticulum membrane / Antigen processing: Ubiquitination & Proteasome degradation / heterochromatin / ubiquitin-dependent protein catabolic process / protein ubiquitination / endosome membrane / 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 / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / 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 / simulated annealing
AuthorsJaremko, M. / Jaremko, L. / Nowakowski, M. / Szczepanowski, R.H. / Filipek, R. / Wojciechowski, M. / Bochtler, M. / Ejchart, A.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: NMR structural studies of the first catalytic half-domain of ubiquitin activating enzyme.
Authors: Jaremko, M. / Jaremko, L. / Nowakowski, M. / Wojciechowski, M. / Szczepanowski, R.H. / Panecka, R. / Zhukov, I. / Bochtler, M. / Ejchart, A.
History
DepositionOct 3, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-like modifier-activating enzyme 1


Theoretical massNumber of molelcules
Total (without water)12,1961
Polymers12,1961
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Ubiquitin-like modifier-activating enzyme 1 / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1 X / Ubiquitin-like modifier- ...Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1 X / Ubiquitin-like modifier-activating enzyme 1 X


Mass: 12195.825 Da / Num. of mol.: 1 / Fragment: First Catalytic Cysteine Half-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Uba1, Sbx, Ube1, Ube1ax, Ube1x / Plasmid: pRS416 and pRS413 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02053

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HNHA
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D HN(CO)CA
11113D CBCA(CO)NH
11213D 1H-15N NOESY
11313D 1H-13C NOESY aliphatic
11413D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] First Cysteine Catalytic Half-domain, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] First Cysteine Catalytic Half-domain, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMFirst Cysteine Catalytic Half-domain-1[U-100% 13C; U-100% 15N]1
1 mMFirst Cysteine Catalytic Half-domain-2[U-100% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 6.5 ambient 298 K
250 6.5 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA4001
Bruker AvanceBrukerAVANCE7002
Varian UnityPlusVarianUNITYPLUS5003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorerefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichpeak picking
SparkyGoddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1558 / NOE intraresidue total count: 330 / NOE long range total count: 621 / NOE medium range total count: 150 / NOE sequential total count: 457
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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