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- PDB-8vhu: Crystal structure of dATP bound E. coli class Ia ribonucleotide r... -

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Basic information

Entry
Database: PDB / ID: 8vhu
TitleCrystal structure of dATP bound E. coli class Ia ribonucleotide reductase alpha construct fused with the C-terminal tail of E. coli class Ia beta subunit
ComponentsFusion protein of Ribonucleoside-diphosphate reductase 1 subunits alpha and beta
KeywordsOXIDOREDUCTASE / Ribonucleotide reductase / allosteric regulation / nucleotide binding / subunit interaction
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / iron ion binding / ATP binding ...ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / iron ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal ...ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Ribonucleoside-diphosphate reductase 1 subunit alpha / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsFunk, M.A. / Zimanyi, C.M. / Drennan, C.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM08334 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-ES002109 United States
National Science Foundation (NSF, United States)0645960 United States
CitationJournal: Biochemistry / Year: 2024
Title: How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase.
Authors: Funk, M.A. / Zimanyi, C.M. / Andree, G.A. / Hamilos, A.E. / Drennan, C.L.
History
DepositionJan 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion protein of Ribonucleoside-diphosphate reductase 1 subunits alpha and beta
B: Fusion protein of Ribonucleoside-diphosphate reductase 1 subunits alpha and beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,75516
Polymers181,8812
Non-polymers1,87414
Water24,4461357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-104 kcal/mol
Surface area53090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.214, 111.207, 209.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fusion protein of Ribonucleoside-diphosphate reductase 1 subunits alpha and beta


Mass: 90940.352 Da / Num. of mol.: 2
Mutation: Truncated final 8 residues of alpha,fused C-terminal 35 residues of beta
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: nrdA, dnaF, b2234, JW2228, nrdB, ftsB, b2235, JW2229 / Production host: Escherichia coli (E. coli)
References: UniProt: P00452, UniProt: P69924, ribonucleoside-diphosphate reductase

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Non-polymers , 6 types, 1371 molecules

#2: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1357 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.11 Å3/Da / Density % sol: 60.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 1.4M NaCl, 8% (w/vol) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 118973 / % possible obs: 98.7 % / Redundancy: 8.9 % / Biso Wilson estimate: 37.21 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 6.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.801 / Num. unique obs: 5892 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R1R

1r1r


Resolution: 2.1→49.15 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 3712 3.12 %
Rwork0.159 --
obs0.16 118834 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.45 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11659 0 106 1357 13122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.30911240.26133872X-RAY DIFFRACTION91
2.13-2.150.27841310.24574170X-RAY DIFFRACTION98
2.15-2.180.25751380.22494256X-RAY DIFFRACTION99
2.18-2.220.27391270.21984062X-RAY DIFFRACTION94
2.22-2.250.25231370.21054241X-RAY DIFFRACTION99
2.25-2.280.23351380.19964244X-RAY DIFFRACTION99
2.28-2.320.26141380.19864287X-RAY DIFFRACTION99
2.32-2.360.24111370.19394215X-RAY DIFFRACTION100
2.36-2.40.22511380.18914278X-RAY DIFFRACTION99
2.4-2.450.22611370.18494258X-RAY DIFFRACTION99
2.45-2.50.25791380.19324257X-RAY DIFFRACTION100
2.5-2.550.22141390.18254255X-RAY DIFFRACTION99
2.55-2.610.25281380.1754299X-RAY DIFFRACTION99
2.61-2.680.21821370.17834159X-RAY DIFFRACTION97
2.68-2.750.2031360.17464207X-RAY DIFFRACTION98
2.75-2.830.22581390.17134288X-RAY DIFFRACTION100
2.83-2.920.23751380.17674308X-RAY DIFFRACTION99
2.92-3.030.23221410.17764311X-RAY DIFFRACTION99
3.03-3.150.21231390.18644310X-RAY DIFFRACTION99
3.15-3.290.19981400.16154315X-RAY DIFFRACTION100
3.29-3.470.20731350.14944295X-RAY DIFFRACTION99
3.47-3.680.14791340.13834217X-RAY DIFFRACTION96
3.68-3.970.14671430.12694376X-RAY DIFFRACTION100
3.97-4.370.14971390.12054365X-RAY DIFFRACTION100
4.37-50.14571430.12014402X-RAY DIFFRACTION100
5-6.290.16581420.14734333X-RAY DIFFRACTION97
6.3-49.150.16971460.15574542X-RAY DIFFRACTION98
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)
14.32361.3405-1.36541.8157-0.9791.8795-0.0174-0.3697-0.39870.1787-0.0571-0.06090.08060.06560.06730.31680.019-0.01460.32840.04750.229-26.884930.65489.8595
21.0226-0.040.34910.5491-0.03453.05440.0040.18590.0976-0.04910.04520.00270.11970.0703-0.05490.1802-0.00990.01440.21330.02950.2273-23.971838.9057-28.1769
31.37220.03610.10110.896-0.08811.23670.03130.08890.23360.06250.02760.0805-0.1326-0.0873-0.05320.22510.01590.02670.19410.06020.2761-31.080850.7017-21.5277
42.08870.8604-0.1312.25-1.97492.01820.23483.0620.8286-2.3088-0.06560.49890.04750.2784-0.01781.02350.00970.00261.19420.130.6372-24.79329.4359-90.4259
52.8621.4032-2.75258.69972.65695.44430.31771.0062-0.3055-0.7537-0.170.44090.32290.3117-0.15030.4144-0.0015-0.06650.5704-0.06970.3602-29.41.6168-84.0005
65.30513.23090.88874.50030.9251.9993-0.0460.42980.7406-0.338-0.11320.4342-0.326-0.05970.15740.36110.04640.01140.50590.0340.4223-11.236317.3958-74.9002
70.5744-0.1373-0.19420.8760.25022.0551-0.0099-0.0356-0.01260.15840.0143-0.08190.0408-0.1211-0.01510.2563-0.0247-0.02840.2859-0.03810.2645-11.491510.402-35.7103
81.42360.05840.02250.78640.24211.0851-0.00730.0756-0.0738-0.04340.0712-0.14380.05510.1341-0.06120.2391-0.02380.0060.2457-0.09030.2639-0.5962.5204-48.6372
91.94220.07530.34860.99660.33514.82310.09180.1765-0.2584-0.0429-0.09120.15090.2655-0.5614-0.05990.2867-0.05810.00150.29-0.12630.3624-18.3105-6.1595-52.6913
104.20144.51645.62594.89656.07287.5494-0.4964-0.39312.2162-0.363-0.27031.83-0.6509-0.92960.76480.69510.1165-0.07620.99950.11681.3108-50.513454.1989-38.756
114.3352.1693-4.84741.3957-2.38545.5159-0.3373-0.4594-2.4160.5477-0.1710.33971.8138-0.27290.51851.3462-0.296-0.0180.93550.05231.0604-18.962-18.9288-28.9446
127.3401-3.5873-2.85762.87022.26941.7946-0.5453-2.1802-4.23281.0918-0.18860.60333.8195-1.62550.75871.5192-0.25140.04830.82110.2381.2748-9.1675-18.2686-32.5858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 5 THROUGH 168 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 169 THROUGH 371 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 372 THROUGH 737 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 20 THROUGH 29 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 30 THROUGH 46 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 58 THROUGH 188 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 189 THROUGH 390 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 391 THROUGH 624 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 625 THROUGH 737 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 1365 THROUGH 1375 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 1366 THROUGH 1370 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 1371 THROUGH 1375 )

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