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Basic information

Entry
Database: PDB / ID: 7mpr
TitleBrucella melitensis NrnC
ComponentsNanoRNase C
KeywordsRNA BINDING PROTEIN / RNase / bacteria / enzyme
Function / homologyribonuclease D activity / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / 3'-5' exonuclease activity / nucleic acid binding / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Ribonuclease D
Function and homology information
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsLormand, J.D. / 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 4, 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NanoRNase C
B: NanoRNase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7495
Polymers46,4612
Non-polymers2883
Water12,484693
1
A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules

A: NanoRNase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,38124
Polymers185,8448
Non-polymers1,53716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
2
B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules

B: NanoRNase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,61216
Polymers185,8448
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)93.320, 93.320, 123.973
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11A-659-

HOH

21B-675-

HOH

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Components

#1: Protein NanoRNase C


Mass: 23230.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: rnd_2, CUC12_07925, NCTC8223_00749 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X1C2S7, ribonuclease D
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 2.0 M Ammonium Sulfate, 19 % xylitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.42→74.56 Å / Num. obs: 103308 / % possible obs: 99.84 % / Redundancy: 15.3 % / CC1/2: 1 / CC star: 1 / Net I/σ(I): 30.58
Reflection shellResolution: 1.42→1.471 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.91 / Num. unique obs: 10058 / CC1/2: 0.782 / CC star: 0.937 / % possible all: 98.78

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PDB_EXTRACT3.27data extraction
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yt3

1yt3


Resolution: 1.42→74.56 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / Phase error: 17.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.181 2000 -Random selection
Rwork0.1653 101295 --
obs-103294 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.99 Å2 / Biso mean: 25.26 Å2 / Biso min: 12.11 Å2
Refinement stepCycle: final / Resolution: 1.42→74.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 15 701 3950
Biso mean--69.9 37.08 -
Num. residues----410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043387
X-RAY DIFFRACTIONf_angle_d0.7184603
X-RAY DIFFRACTIONf_dihedral_angle_d12.7041275
X-RAY DIFFRACTIONf_chiral_restr0.073522
X-RAY DIFFRACTIONf_plane_restr0.008600
LS refinement shellResolution: 1.42→1.471 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2416 195 -
Rwork0.2432 10057 -
obs--98.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35050.3810.62193.55050.64751.78230.04520.0597-0.0256-0.1726-0.08990.3405-0.0406-0.15630.05050.11250.0138-0.02660.132-0.01640.132912.373736.648740.7898
21.2596-1.00250.13831.8298-0.14550.6622-0.01290.09590.0677-0.0661-0.0412-0.047-0.0268-0.00960.05510.1351-0.0207-0.01440.146-0.01420.123123.840931.811445.5409
30.5140.02140.16960.9759-0.3321.7406-0.01010.01530.00090.0017-0.0204-0.0248-0.0662-0.02360.02810.089-0.0118-0.00610.1032-0.00980.115325.231129.415549.4776
43.3099-1.03810.31392.54020.58011.55660.0637-0.01090.07160.17560.0515-0.3785-0.080.1072-0.09240.1516-0.0075-0.0330.094-0.01020.152232.534216.965118.6279
50.36210.15990.0472.98960.45990.4680.014-0.0681-0.03880.34-0.00210.01610.088-0.0952-0.01210.16330.0053-0.0280.13460.00760.116725.72823.380918.1104
65.5695-4.29794.16063.3187-3.21063.12720.09690.00640.03970.14-0.2066-0.6997-0.15750.25960.20070.164-0.0175-0.00930.1701-0.0240.18833.5731-1.31695.9205
71.2531-0.6221-0.6127.82791.73644.64980.05970.0090.0542-0.2172-0.14470.303-0.232-0.37410.08950.13190.0287-0.00010.1581-0.00070.090223.64376.4576-1.656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 0:61)A0 - 61
2X-RAY DIFFRACTION2(chain A and resid 62:140)A62 - 140
3X-RAY DIFFRACTION3(chain A and resid 141:205)A141 - 205
4X-RAY DIFFRACTION4(chain B and resid 1:73)B1 - 73
5X-RAY DIFFRACTION5(chain B and resid 74:178)B74 - 178
6X-RAY DIFFRACTION6(chain B and resid 179:183)B179 - 183
7X-RAY DIFFRACTION7(chain B and resid 184:205)B184 - 205

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