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- PDB-7mqd: Bartonella henselae NrnC complexed with pAGG. D4 symmetry. -

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Basic information

Entry
Database: PDB / ID: 7mqd
TitleBartonella henselae NrnC complexed with pAGG. D4 symmetry.
Components
  • NanoRNase C
  • RNA (5'-R(P*AP*GP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / RNase / bacteria / enzyme / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / nucleic acid binding / metal ion binding
Similarity search - Function
: / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
RNA / 3'-5' exonuclease
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsLormand, J.D. / Brownfield, B. / Fromme, J.C. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI142400 United States
CitationJournal: Elife / Year: 2021
Title: Structural characterization of NrnC identifies unifying features of dinucleotidases.
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 /
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.
History
DepositionMay 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: NanoRNase C
B: RNA (5'-R(P*AP*GP*G)-3')
C: NanoRNase C
D: RNA (5'-R(P*AP*GP*G)-3')
E: NanoRNase C
F: RNA (5'-R(P*AP*GP*G)-3')
G: NanoRNase C
H: RNA (5'-R(P*AP*GP*G)-3')
I: NanoRNase C
J: RNA (5'-R(P*AP*GP*G)-3')
K: NanoRNase C
L: RNA (5'-R(P*AP*GP*G)-3')
M: NanoRNase C
N: RNA (5'-R(P*AP*GP*G)-3')
O: NanoRNase C
P: RNA (5'-R(P*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)195,37116
Polymers195,37116
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
NanoRNase C


Mass: 23446.725 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: BM1374165_00260 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X5MEI1
#2: RNA chain
RNA (5'-R(P*AP*GP*G)-3')


Mass: 974.660 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1NrnC octamer incubated with pAGG.COMPLEXall0MULTIPLE SOURCES
2NrnC octamerCOMPLEX#11RECOMBINANT
3pAGGCOMPLEX#21SYNTHETIC
Molecular weightValue: 186.621 kDa/nm / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Bartonella henselae (bacteria)38323
33Bartonella henselae (bacteria)38323
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSolium chlorideNaCl1
225 mMTrisC4H11NO31
30.01 %NP-40H(C2H4O)nO(C6H4)C9H191
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4RELION3.1CTF correction
11RELION3.1final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94063 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312224
ELECTRON MICROSCOPYf_angle_d0.60516736
ELECTRON MICROSCOPYf_dihedral_angle_d7.5861872
ELECTRON MICROSCOPYf_chiral_restr0.0462048
ELECTRON MICROSCOPYf_plane_restr0.0042048

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