- PDB-4skn: A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACI... -
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基本情報
登録情報
データベース: PDB / ID: 4skn
タイトル
A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA
要素
DNA (5'-D(*AP*AP*AP*GP*CP*CP*GP*CP*CP*C)-3')
DNA (5'-D(*TP*GP*GP*GP*(D1P)P*GP*GP*CP*TP*T)-3')
PROTEIN (URACIL-DNA GLYCOSYLASE)
キーワード
HYDROLASE/DNA / DNA GLYCOSYLASE / DNA BASE EXCISION REPAIR / URACIL / DNA / HYDROLASE-DNA COMPLEX
機能・相同性
機能・相同性情報
base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Chromatin modifications during the maternal to zygotic transition (MZT) / base-excision repair / damaged DNA binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus 類似検索 - 分子機能
Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta 類似検索 - ドメイン・相同性
解像度: 2.9→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / 交差検証法: THROUGHOUT / σ(F): 2.9 詳細: THE ELECTRON DENSITY FOR THE DNA 5' OF THE URACIL-CONTAINING NUCLEOTIDE IS POOR. THE COBALAMIN HAS BEEN MODELLED AS THE 5-COORDINATES REDUCED COB(II)ALAMIN (B12R), SINCE THERE IS NO ELECTRON ...詳細: THE ELECTRON DENSITY FOR THE DNA 5' OF THE URACIL-CONTAINING NUCLEOTIDE IS POOR. THE COBALAMIN HAS BEEN MODELLED AS THE 5-COORDINATES REDUCED COB(II)ALAMIN (B12R), SINCE THERE IS NO ELECTRON DENSITY FOR AN ADENOSYL GROUP LINKED TO THE COBALT ATOM. HOWEVER, A HALF-OCCUPIED 5'-DEOXYADENOSINE HAS BEEN BUILT INTO ELECTRON DENSITY IN THE ACTIVE SITE (RESIDUES A803 AND AND C803). RESIDUES A801 AND A802 (AND C801, C802) REPRESENT AN EQUIMOLAR MIXTURE OF SUBSTRATE AND PRODUCT, SUCCINYL- AND METHYLMALONYL-COENZYME A.