- PDB-5fku: cryo-EM structure of the E. coli replicative DNA polymerase compl... -
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基本情報
登録情報
データベース: PDB / ID: 5fku
タイトル
cryo-EM structure of the E. coli replicative DNA polymerase complex in DNA free state (DNA polymerase III alpha, beta, epsilon, tau complex)
要素
DNA POLYMERASE III SUBUNIT ALPHADNA polymerase III holoenzyme
DNA POLYMERASE III SUBUNIT BETADNA polymerase III holoenzyme
DNA POLYMERASE III SUBUNIT EPSILONDNA polymerase III holoenzyme
DNA POLYMERASE III SUBUNIT TAUDNA polymerase III holoenzyme
キーワード
TRANSFERASE (転移酵素) / DNA REPLICATION (DNA複製) / DNA POLYMERASE III ALPHA / DNA POLYMERASE III BETA / DNA POLYMERASE III EPSILON / DNA POLYMERASE III TAU
機能・相同性
機能・相同性情報
DNA polymerase III, core complex / DNA polymerase III, clamp loader complex / Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA clamp loader activity / DNA polymerase III complex / lagging strand elongation / replisome / DNA replication proofreading ...DNA polymerase III, core complex / DNA polymerase III, clamp loader complex / Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA clamp loader activity / DNA polymerase III complex / lagging strand elongation / replisome / DNA replication proofreading / regulation of DNA-templated DNA replication initiation / exonuclease activity / DNA strand elongation involved in DNA replication / DNA polymerase processivity factor activity / leading strand elongation / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA複製 / DNAポリメラーゼ / DNA-directed DNA polymerase activity / DNA修復 / DNA damage response / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / metal ion binding / 細胞質基質 / 細胞質 類似検索 - 分子機能
: / : / DNA polymerase III subunit alpha, C-terminal domain / DNA polymerase 3, epsilon subunit / DNA polymerase III epsilon subunit, exonuclease domain / Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain ...: / : / DNA polymerase III subunit alpha, C-terminal domain / DNA polymerase 3, epsilon subunit / DNA polymerase III epsilon subunit, exonuclease domain / Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / DNA polymerase III, tau subunit, domain V / DNA polymerase III subunit tau, DnaB-binding domain IV / DNA polymerase III, tau subunit, domain V superfamily / DNA polymerase III, subunit gamma/tau, helical lid domain / DNA polymerase III subunits tau domain IV DnaB-binding / DNA polymerase III tau subunit V interacting with alpha / DNA polymerase III, subunit gamma/ tau, N-terminal / DNA polymerase III, gamma subunit, domain III / DNA polymerase III subunits gamma and tau domain III / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / エキソヌクレアーゼ / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / DNA polymerase III, delta subunit / Exonuclease, RNase T/DNA polymerase III / EXOIII / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / ClpA/B family / : / Ribonuclease H superfamily / Ribonuclease H-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase 類似検索 - ドメイン・相同性
DNA polymerase III subunit epsilon / DNA polymerase III subunit tau / Beta sliding clamp / DNA polymerase III subunit alpha 類似検索 - 構成要素
ジャーナル: Elife / 年: 2015 タイトル: cryo-EM structures of the replicative DNA polymerase reveal its dynamic interactions with the DNA sliding clamp, exonuclease and . 著者: Rafael Fernandez-Leiro / Julian Conrad / Sjors Hw Scheres / Meindert H Lamers / 要旨: The replicative DNA polymerase PolIIIα from is a uniquely fast and processive enzyme. For its activity it relies on the DNA sliding clamp β, the proofreading exonuclease ε and the C-terminal ...The replicative DNA polymerase PolIIIα from is a uniquely fast and processive enzyme. For its activity it relies on the DNA sliding clamp β, the proofreading exonuclease ε and the C-terminal domain of the clamp loader subunit τ. Due to the dynamic nature of the four-protein complex it has long been refractory to structural characterization. Here we present the 8 Å resolution cryo-electron microscopy structures of DNA-bound and DNA-free states of the PolIII-clamp-exonuclease-τ complex. The structures show how the polymerase is tethered to the DNA through multiple contacts with the clamp and exonuclease. A novel contact between the polymerase and clamp is made in the DNA bound state, facilitated by a large movement of the polymerase tail domain and τ. These structures provide crucial insights into the organization of the catalytic core of the replisome and form an important step towards determining the structure of the complete holoenzyme.
A: DNA POLYMERASE III SUBUNIT ALPHA B: DNA POLYMERASE III SUBUNIT BETA C: DNA POLYMERASE III SUBUNIT BETA D: DNA POLYMERASE III SUBUNIT EPSILON E: DNA POLYMERASE III SUBUNIT TAU
ENGINEERED RESIDUE IN CHAIN A, ALA 921 TO LEU ENGINEERED RESIDUE IN CHAIN A, MET 923 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, ALA 921 TO LEU ENGINEERED RESIDUE IN CHAIN A, MET 923 TO LEU ENGINEERED RESIDUE IN CHAIN D, THR 183 TO LEU ENGINEERED RESIDUE IN CHAIN D, MET 185 TO LEU ENGINEERED RESIDUE IN CHAIN D, ALA 186 TO PRO ENGINEERED RESIDUE IN CHAIN D, PHE 187 TO LEU
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実験情報
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実験
実験
手法: 電子顕微鏡法
EM実験
試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法
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試料調製
構成要素
名称: DNA POLYMERASE III CATALYTIC COMPLEX (ALPHA, EPSILON, BETA, TAU) タイプ: COMPLEX
緩衝液
名称: 25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT / pH: 7.5 / 詳細: 25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT
試料
濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持
詳細: HOLEY CARBON
急速凍結
装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 詳細: LIQUID ETHANE
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電子顕微鏡撮影
実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡
モデル: FEI TITAN KRIOS / 日付: 2014年5月12日 詳細: TITAN KRIOS GOOD MICROGRAPHS WERE SELECTED FOR DIGITISATION