Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural characterization of NrnC identifies unifying features of dinucleotidases.
Journal, issue, pages	Elife, Vol. 10, Year 2021
Publish date	Sep 17, 2021
Authors	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 Abstract	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.
External links	Elife / PubMed:34533457 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.42 - 3.69 Å
Structure data	23941 7mqb EMDB-23941, PDB-7mqb: Bartonella henselae NrnC bound to pGG. D4 Symmetry Method: EM (single particle) / Resolution: 3.25 Å 23942 7mqc EMDB-23942, PDB-7mqc: Bartonella henselae NrnC bound to pGG. C1 reconstruction. Method: EM (single particle) / Resolution: 3.64 Å 23943 7mqd EMDB-23943, PDB-7mqd: Bartonella henselae NrnC complexed with pAGG. D4 symmetry. Method: EM (single particle) / Resolution: 3.25 Å 23944 7mqe EMDB-23944, PDB-7mqe: Bartonella henselae NrnC complexed with pAGG. C1 reconstruction. Method: EM (single particle) / Resolution: 3.69 Å 23945 7mqf EMDB-23945, PDB-7mqf: Bartonella henselae NrnC complexed with pAAAGG. D4 symmetry. Method: EM (single particle) / Resolution: 2.88 Å 23946 7mqg EMDB-23946, PDB-7mqg: Bartonella henselae NrnC complexed with pAAAGG. C1 reconstruction. Method: EM (single particle) / Resolution: 3.25 Å 23947 7mqh EMDB-23947, PDB-7mqh: Bartonella henselae NrnC complexed with pAAAGG in the presence of Ca2+. D4 Symmetry. Method: EM (single particle) / Resolution: 3.1 Å 23948 7mqi EMDB-23948, PDB-7mqi: Bartonella henselae NrnC complexed with pAAAGG in the presence of Ca2+. C1 reconstruction. Method: EM (single particle) / Resolution: 3.21 Å PDB-7mpl: Bartonella henselae NrnC bound to pGG Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-7mpm: Bartonella henselae NrnC bound to pAA Method: X-RAY DIFFRACTION / Resolution: 1.95 Å PDB-7mpn: Bartonella henselae NrnC bound to pGC Method: X-RAY DIFFRACTION / Resolution: 1.94 Å PDB-7mpo: Bartonella henselae NrnC bound to pAp Method: X-RAY DIFFRACTION / Resolution: 1.95 Å PDB-7mpp: Bartonella henselae NrnC cleaving pGG in the presence of Mg2+ Method: X-RAY DIFFRACTION / Resolution: 2.0 Å PDB-7mpq: Bartonella henselae NrnC cleaving pGG in the presence of Mn2+ Method: X-RAY DIFFRACTION / Resolution: 2.35 Å PDB-7mpr: Brucella melitensis NrnC Method: X-RAY DIFFRACTION / Resolution: 1.42 Å PDB-7mps: Brucella melitensis NrnC with engaged loop Method: X-RAY DIFFRACTION / Resolution: 1.45 Å PDB-7mpt: Brucella melitensis NrnC with bound Mg2+ Method: X-RAY DIFFRACTION / Resolution: 1.75 Å PDB-7mpu: Brucella melitensis NrnC bound to pGG Method: X-RAY DIFFRACTION / Resolution: 1.72 Å
Chemicals	ChemComp-HOH: WATER / Water ChemComp-A3P: ADENOSINE-3'-5'-DIPHOSPHATE / Adenosine 3',5'-bisphosphate ChemComp-5GP: GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate ChemComp-MG: Unknown entry ChemComp-MN: Unknown entry ChemComp-SO4: SULFATE ION / Sulfate ChemComp-EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH bufferYM / HEPES ChemComp-PO4*: PHOSPHATE ION / Phosphate
Source	bartonella henselae (bacteria) synthetic construct (others) brucella melitensis (bacteria)
Keywords	RNA BINDING PROTEIN/RNA / RNase / bacteria / enzyme / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex