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- PDB-8wwx: Ube1L acts akin to a mitt, that mediates UbcH8 binding and orches... -

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Basic information

Entry
Database: PDB / ID: 8wwx
TitleUbe1L acts akin to a mitt, that mediates UbcH8 binding and orchestrates "E1-E2" interaction
ComponentsUbiquitin-like modifier-activating enzyme 7
KeywordsLIGASE / Ubiquitin Fold Domain / Ube1L / Uba7 / UFD / beta-grasp domain / UbcH8
Function / homology
Function and homology information


ISG15 activating enzyme activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / ISG15-protein conjugation / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / protein modification process / DDX58/IFIH1-mediated induction of interferon-alpha/beta / modification-dependent protein catabolic process / ISG15 antiviral mechanism / ubiquitin-protein transferase activity ...ISG15 activating enzyme activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / ISG15-protein conjugation / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / protein modification process / DDX58/IFIH1-mediated induction of interferon-alpha/beta / modification-dependent protein catabolic process / ISG15 antiviral mechanism / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein ubiquitination / innate immune response / DNA damage response / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
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 / 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
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing / molecular dynamics / torsion angle dynamics
AuthorsDag, C. / Elgin, E.S. / Lee, W. / Ziarek, J.J.
Funding support Turkey, United States, 5items
OrganizationGrant numberCountry
Other government104T193 Turkey
Other government120Z594 Turkey
Other government122Z747 Turkey
National Science Foundation (NSF, United States)DBI-2051595 United States
National Science Foundation (NSF, United States)DBI-1902076 United States
CitationJournal: To Be Published
Title: Ube1L acts akin to a mitt, that mediates UbcH8 binding and orchestrates "E1-E2" interaction
Authors: Dag, C. / Elgin, E.S. / Ziarek, J.J. / Lee, W.
History
DepositionOct 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-like modifier-activating enzyme 7


Theoretical massNumber of molelcules
Total (without water)10,2621
Polymers10,2621
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin-like modifier-activating enzyme 7 / Uba7 Ubiquitin Fold Domain


Mass: 10261.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Uba7 (Ube1L) Ubiquitin Fold Domain / Source: (gene. exp.) Homo sapiens (human) / Gene: UBA7 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: P41226

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1N-HSQC
121isotropic13D HN(CA)CB
131isotropic13D HN(CO)CA
141isotropic13D 1H-15N NOESY
151isotropic13D 1H-13C NOESY aliphatic
161isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 20 mM TRIS, 0.02 % sodium azide, 20 mM sodium chloride, 90% H2O/10% D2O
Details: 0.4 mM [U-100% 13C; U-100% 15N] Uba7, 20 mM Tris, 20 mM sodium chloride, 0.02 % sodium azide
Label: Uba7 UFD / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTRISnatural abundance1
0.02 %sodium azidenatural abundance1
20 mMsodium chloridenatural abundance1
Sample conditionsDetails: 0.4 mM [U-100% 13C; U-100% 15N] Uba7, 20 mM sodium phosphate, 100 mM sodium chloride, 0.02 % sodium azide
Ionic strength: 40 mM / Label: U-100% 13C; U-100% 15N] Uba7 / pH: 7.6 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.chemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leerefinement
XEASYBartels et al.peak picking
Refinement
MethodSoftware ordinal
simulated annealing1
molecular dynamics2
torsion angle dynamics3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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