EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Structural characterization of NrnC identifies unifying features of dinucleotidases.
ジャーナル・号・ページ	Elife, Vol. 10, Year 2021
掲載日	2021年9月17日
著者	Justin D Lormand / Soo-Kyoung Kim / George A Walters-Marrah / Bryce A Brownfield / J Christopher Fromme / Wade C Winkler / Jonathan R Goodson / Vincent T Lee / Holger Sondermann /
PubMed 要旨	RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. ...RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses, we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC and Orn employ similar structural features that distinguish these two classes of dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures, together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases, indicate convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.
リンク	Elife / PubMed:34533457 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	1.42 - 3.69 Å
構造データ	23941 7mqb EMDB-23941, PDB-7mqb: Bartonella henselae NrnC bound to pGG. D4 Symmetry 手法: EM (単粒子) / 解像度: 3.25 Å 23942 7mqc EMDB-23942, PDB-7mqc: Bartonella henselae NrnC bound to pGG. C1 reconstruction. 手法: EM (単粒子) / 解像度: 3.64 Å 23943 7mqd EMDB-23943, PDB-7mqd: Bartonella henselae NrnC complexed with pAGG. D4 symmetry. 手法: EM (単粒子) / 解像度: 3.25 Å 23944 7mqe EMDB-23944, PDB-7mqe: Bartonella henselae NrnC complexed with pAGG. C1 reconstruction. 手法: EM (単粒子) / 解像度: 3.69 Å 23945 7mqf EMDB-23945, PDB-7mqf: Bartonella henselae NrnC complexed with pAAAGG. D4 symmetry. 手法: EM (単粒子) / 解像度: 2.88 Å 23946 7mqg EMDB-23946, PDB-7mqg: Bartonella henselae NrnC complexed with pAAAGG. C1 reconstruction. 手法: EM (単粒子) / 解像度: 3.25 Å 23947 7mqh EMDB-23947, PDB-7mqh: Bartonella henselae NrnC complexed with pAAAGG in the presence of Ca2+. D4 Symmetry. 手法: EM (単粒子) / 解像度: 3.1 Å 23948 7mqi EMDB-23948, PDB-7mqi: Bartonella henselae NrnC complexed with pAAAGG in the presence of Ca2+. C1 reconstruction. 手法: EM (単粒子) / 解像度: 3.21 Å PDB-7mpl: Bartonella henselae NrnC bound to pGG 手法: X-RAY DIFFRACTION / 解像度: 1.8 Å PDB-7mpm: Bartonella henselae NrnC bound to pAA 手法: X-RAY DIFFRACTION / 解像度: 1.95 Å PDB-7mpn: Bartonella henselae NrnC bound to pGC 手法: X-RAY DIFFRACTION / 解像度: 1.94 Å PDB-7mpo: Bartonella henselae NrnC bound to pAp 手法: X-RAY DIFFRACTION / 解像度: 1.95 Å PDB-7mpp: Bartonella henselae NrnC cleaving pGG in the presence of Mg2+ 手法: X-RAY DIFFRACTION / 解像度: 2.0 Å PDB-7mpq: Bartonella henselae NrnC cleaving pGG in the presence of Mn2+ 手法: X-RAY DIFFRACTION / 解像度: 2.35 Å PDB-7mpr: Brucella melitensis NrnC 手法: X-RAY DIFFRACTION / 解像度: 1.42 Å PDB-7mps: Brucella melitensis NrnC with engaged loop 手法: X-RAY DIFFRACTION / 解像度: 1.45 Å PDB-7mpt: Brucella melitensis NrnC with bound Mg2+ 手法: X-RAY DIFFRACTION / 解像度: 1.75 Å PDB-7mpu: Brucella melitensis NrnC bound to pGG 手法: X-RAY DIFFRACTION / 解像度: 1.72 Å
化合物	ChemComp-HOH: WATER ChemComp-A3P: ADENOSINE-3'-5'-DIPHOSPHATE / アデノシン3′,5′-ビスりん酸 ChemComp-5GP: GUANOSINE-5'-MONOPHOSPHATE / GMP ChemComp-MG: Unknown entry / マグネシウムジカチオン ChemComp-MN: Unknown entry ChemComp-SO4: SULFATE ION / 硫酸ジアニオン ChemComp-EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / pH緩衝剤YM ChemComp-PO4*: PHOSPHATE ION / ホスファ-ト
由来	bartonella henselae (バクテリア) synthetic construct (人工物) brucella melitensis (マルタ熱菌)
キーワード	RNA BINDING PROTEIN/RNA / RNase / bacteria / enzyme / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex