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- PDB-7mps: Brucella melitensis NrnC with engaged loop -

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Basic information

Entry
Database: PDB / ID: 7mps
TitleBrucella melitensis NrnC with engaged loop
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 / Resolution: 1.45 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
C: NanoRNase C
D: NanoRNase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,12421
Polymers92,9224
Non-polymers2,20217
Water24,5181361
1
A: NanoRNase C
B: NanoRNase C
hetero molecules

A: NanoRNase C
B: NanoRNase C
hetero molecules

A: NanoRNase C
B: NanoRNase C
hetero molecules

A: NanoRNase C
B: NanoRNase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,05640
Polymers185,8448
Non-polymers4,21232
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
2
C: NanoRNase C
D: NanoRNase C
hetero molecules

C: NanoRNase C
D: NanoRNase C
hetero molecules

C: NanoRNase C
D: NanoRNase C
hetero molecules

C: NanoRNase C
D: NanoRNase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,44044
Polymers185,8448
Non-polymers4,59636
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
Unit cell
Length a, b, c (Å)110.671, 110.671, 110.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
NanoRNase C


Mass: 23230.486 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: rnd_2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X1C2S7, ribonuclease D
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1361 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M HEPES, 2.0 M Ammonium sulfate, 20 % 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: 1.45→110.671 Å / Num. obs: 233668 / % possible obs: 99.9 % / Redundancy: 10.1 % / CC1/2: 1 / Rpim(I) all: 0.021 / Rrim(I) all: 0.067 / Rsym value: 0.063 / Net I/av σ(I): 8.5 / Net I/σ(I): 21.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.45-1.5390.8830.9339740.7020.3070.9370.88399.6
1.53-1.6210.30.561.4322060.1830.590.56100
1.62-1.7310.10.3482.1303010.1150.3670.348100
1.73-1.8710.60.2043.6282280.0660.2140.204100
1.87-2.05100.1196.2259430.040.1260.119100
2.05-2.2910.70.0749.9235650.0240.0780.074100
2.29-2.65100.05712.5207250.0190.0610.05799.9
2.65-3.2410.50.04614.5175550.0150.0480.046100
3.24-4.599.80.03518.6136220.0120.0370.03599.9
4.59-110.67110.20.02920.875490.0090.0310.029100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yt3

1yt3


Resolution: 1.45→110.671 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1664 2016 -
Rwork0.1527 231634 -
obs0.1528 233650 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.12 Å2 / Biso mean: 23.896 Å2 / Biso min: 11.68 Å2
Refinement stepCycle: final / Resolution: 1.45→110.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6446 0 125 1363 7934
Biso mean--41.66 36.82 -
Num. residues----815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066805
X-RAY DIFFRACTIONf_angle_d0.8499241
X-RAY DIFFRACTIONf_dihedral_angle_d20.4552581
X-RAY DIFFRACTIONf_chiral_restr0.0791036
X-RAY DIFFRACTIONf_plane_restr0.0051182
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4504-1.48670.23441320.23731636299
1.4867-1.52690.22431420.199516512100
1.5269-1.57180.21571470.188416496100
1.5718-1.62260.20471410.173916556100
1.6226-1.68060.18671370.167916511100
1.6806-1.74790.17651480.157816510100
1.7479-1.82740.18681440.152816489100
1.8274-1.92380.16171480.152716550100
1.9238-2.04430.17741450.153416550100
2.0443-2.20220.16511390.147816596100
2.2022-2.42380.15291450.149616514100
2.4238-2.77460.18591490.155316589100
2.7746-3.49570.15021470.150116604100
3.4957-110.6710.14851520.137116795100
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)
11.57060.6619-0.24922.46170.09311.2464-0.0130.0784-0.0301-0.1857-0.014-0.39080.10340.17550.03250.13090.0190.0530.16150.02670.17935.9183-7.309542.9168
20.2114-0.57-0.13671.9255-0.00120.55370.01030.0805-0.0471-0.0874-0.04670.07280.0411-0.0390.03950.1433-0.01150.01970.17690.02430.150924.74762.300445.5816
30.49110.04820.02691.06260.05731.27-0.01130.05380.0171-0.0223-0.0162-0.04810.0532-0.02520.03330.1221-0.0120.01730.15630.02550.134827.25055.010849.6629
41.0715-0.333-0.08872.08960.89231.36640.0164-0.03760.07090.05830.0514-0.2548-0.06490.0503-0.04680.1131-0.0203-0.03580.12320.0010.150226.434123.547980.0375
54.05463.9309-0.34467.5459-0.09711.09890.0027-0.05730.1213-0.0547-0.00220.22980.0682-0.0254-0.04750.13930.0065-0.02950.14140.00750.129124.79342.938575.6839
60.5474-0.276-0.22931.15230.30.8236-0.0235-0.0393-0.01390.1475-0.0229-0.02040.0515-0.03430.04990.1444-0.0203-0.0360.14090.00620.138322.998910.195678.0903
71.28890.70760.21322.55050.26821.17690.00080.07780.0875-0.0754-0.01960.3094-0.1111-0.13920.01790.14590.0064-0.02920.1430.00460.178118.976850.097197.4426
81.225-0.8039-0.16981.52870.03940.7480.01710.09660.1609-0.1254-0.0037-0.0841-0.0990.0732-0.00740.1506-0.0302-0.01580.13610.0030.137931.896245.823296.9814
91.6145-0.7213-0.462.27071.35442.52480.0443-0.0226-0.10710.0747-0.0099-0.0508-0.04980.0256-0.02180.1404-0.0087-0.01140.13580.03390.134632.636438.3485111.1836
102.75540.2637-0.62281.0591-0.51841.5148-0.0243-0.0138-0.09770.06860.0280.01910.12010.055-0.00990.1427-0.00230.00810.13280.02260.110440.459823.2133136.0684
110.7625-0.8613-0.07831.2922-0.09250.72740.0406-0.0134-0.0254-0.0082-0.0280.0230.0316-0.0127-0.01570.1537-0.01390.00890.15480.01730.127734.236831.5312128.4809
120.7121-0.24530.10390.8441-0.27871.1029-0.0006-0.07230.04710.1324-0.0012-0.0213-0.10370.09480.00480.1701-0.02070.01440.15390.01530.145737.496137.9459132.2747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:71)A2 - 71
2X-RAY DIFFRACTION2(chain A and resid 72:140)A72 - 140
3X-RAY DIFFRACTION3(chain A and resid 141:204)A141 - 204
4X-RAY DIFFRACTION4(chain B and resid 0:95)B0 - 95
5X-RAY DIFFRACTION5(chain B and resid 96:114)B96 - 114
6X-RAY DIFFRACTION6(chain B and resid 115:204)B115 - 204
7X-RAY DIFFRACTION7(chain C and resid 2:73)C2 - 73
8X-RAY DIFFRACTION8(chain C and resid 74:164)C74 - 164
9X-RAY DIFFRACTION9(chain C and resid 165:204)C165 - 204
10X-RAY DIFFRACTION10(chain D and resid 2:60)D2 - 60
11X-RAY DIFFRACTION11(chain D and resid 61:113)D61 - 113
12X-RAY DIFFRACTION12(chain D and resid 114:204)D114 - 204

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