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- PDB-5ygu: Crystal structure of Escherichia coli (strain K12) mRNA Decapping... -

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Basic information

Entry
Database: PDB / ID: 5ygu
TitleCrystal structure of Escherichia coli (strain K12) mRNA Decapping Complex RppH-DapF
Components
  • Diaminopimelate epimerase
  • RNA pyrophosphohydrolase
KeywordsISOMERASE/HYDROLASE / RppH-DapF / Decapping / Hydrolase / ISOMERASE-HYDROLASE complex
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / RNA destabilization / mRNA 5'-diphosphatase activity / NAD-cap decapping / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / lysine biosynthetic process via diaminopimelate / tRNA processing ...diaminopimelate epimerase / diaminopimelate epimerase activity / RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / RNA destabilization / mRNA 5'-diphosphatase activity / NAD-cap decapping / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / lysine biosynthetic process via diaminopimelate / tRNA processing / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / enzyme activator activity / magnesium ion binding / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
RNA pyrophosphohydrolase RppH / Diaminopimelate epimerase, active site / Diaminopimelate epimerase signature. / Diaminopimelate epimerase, DapF / Diaminopimelate epimerase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. ...RNA pyrophosphohydrolase RppH / Diaminopimelate epimerase, active site / Diaminopimelate epimerase signature. / Diaminopimelate epimerase, DapF / Diaminopimelate epimerase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / L(+)-TARTARIC ACID / Diaminopimelate epimerase / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å
AuthorsWang, Q. / Guan, Z.Y. / Zhang, D.L. / Zou, T.T. / Yin, P.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli.
Authors: Wang, Q. / Zhang, D. / Guan, Z. / Li, D. / Pei, K. / Liu, J. / Zou, T. / Yin, P.
History
DepositionSep 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diaminopimelate epimerase
B: RNA pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,98615
Polymers50,3132
Non-polymers1,67313
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-10 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.418, 86.418, 173.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Diaminopimelate epimerase / DAP epimerase / PLP-independent amino acid racemase


Mass: 30245.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dapF, b3809, JW5592 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6K1, diaminopimelate epimerase
#2: Protein RNA pyrophosphohydrolase / (Di)nucleoside polyphosphate hydrolase / Ap5A pyrophosphatase


Mass: 20067.920 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-158 / Mutation: C16S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rppH, nudH, ygdP, b2830, JW2798 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A776, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Potassium Sodium Tartrate, Sodium Iodine, Xylitol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 30026 / % possible obs: 99.8 % / Redundancy: 14 % / Net I/σ(I): 18.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2V, 4IJZ

4s2v

4ijz


Resolution: 2.298→47.985 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4
RfactorNum. reflection% reflection
Rfree0.2387 1513 5.05 %
Rwork0.206 --
obs0.2077 29950 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.298→47.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 22 79 3451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093433
X-RAY DIFFRACTIONf_angle_d1.034643
X-RAY DIFFRACTIONf_dihedral_angle_d25.5511257
X-RAY DIFFRACTIONf_chiral_restr0.057500
X-RAY DIFFRACTIONf_plane_restr0.007607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2976-2.37180.33931380.26992476X-RAY DIFFRACTION99
2.3718-2.45660.31581500.25582536X-RAY DIFFRACTION100
2.4566-2.55490.32841280.23742560X-RAY DIFFRACTION100
2.5549-2.67120.30281230.24082551X-RAY DIFFRACTION100
2.6712-2.8120.29871280.24592573X-RAY DIFFRACTION100
2.812-2.98820.26471240.23872572X-RAY DIFFRACTION100
2.9882-3.21880.28031410.24342590X-RAY DIFFRACTION100
3.2188-3.54270.27231550.2062545X-RAY DIFFRACTION100
3.5427-4.05510.231260.18812629X-RAY DIFFRACTION100
4.0551-5.1080.1791470.16092649X-RAY DIFFRACTION100
5.108-47.99580.21331530.20732756X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 4.2964 Å / Origin y: 5.6066 Å / Origin z: 21.3458 Å
111213212223313233
T0.5601 Å2-0.0659 Å20.0827 Å2-0.3763 Å20.0164 Å2--0.3487 Å2
L1.2135 °2-0.1188 °20.2274 °2-2.1666 °20.1131 °2--1.243 °2
S0.0652 Å °-0.2333 Å °-0.1831 Å °0.651 Å °-0.0956 Å °0.4041 Å °0.2083 Å °-0.2262 Å °0.0186 Å °
Refinement TLS groupSelection details: all

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