- PDB-2d07: Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2d07
Title
Crystal Structure of SUMO-3-modified Thymine-DNA Glycosylase
Components
G/T mismatch-specific thymine DNA glycosylase
Ubiquitin-like protein SMT3B
Keywords
HYDROLASE
Function / homology
Function and homology information
G/T mismatch-specific thymine-DNA glycosylase activity / thymine-DNA glycosylase / G/U mismatch-specific uracil-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / base-excision repair, AP site formation / depyrimidination ...G/T mismatch-specific thymine-DNA glycosylase activity / thymine-DNA glycosylase / G/U mismatch-specific uracil-DNA glycosylase activity / TET1,2,3 and TDG demethylate DNA / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / base-excision repair, AP site formation / depyrimidination / Vitamin D (calciferol) metabolism / : / sodium ion binding / DNA N-glycosylase activity / mismatched DNA binding / SUMO binding / Displacement of DNA glycosylase by APEX1 / SUMOylation of SUMOylation proteins / uracil DNA N-glycosylase activity / SUMOylation of RNA binding proteins / chloride ion binding / ubiquitin-like protein ligase binding / regulation of embryonic development / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA damage response and repair proteins / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / epigenetic regulation of gene expression / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / protein kinase C binding / transcription coregulator activity / SUMOylation of intracellular receptors / base-excision repair / PML body / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / double-stranded DNA binding / DNA-binding transcription factor binding / nucleic acid binding / damaged DNA binding / protein domain specific binding / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane Similarity search - Function
G/T mismatch-specific thymine DNA glycosylasee TDG-like, eukaryotes / Uracil DNA glycosylase family 2 / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...G/T mismatch-specific thymine DNA glycosylasee TDG-like, eukaryotes / Uracil DNA glycosylase family 2 / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi