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- PDB-9omw: Crystal structure of E. coli ApaH in complex with Ap4U -

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Basic information

Entry
Database: PDB / ID: 9omw
TitleCrystal structure of E. coli ApaH in complex with Ap4U
ComponentsBis(5'-nucleosyl)-tetraphosphatase [symmetrical]
KeywordsHYDROLASE / ApaH / symmetrical hydrolase / RNA decapping
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase activity / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) / RNA decapping / nucleobase-containing small molecule interconversion / phosphatase activity / response to X-ray / hydrolase activity / cytoplasm
Similarity search - Function
Bis(5'-nucleosyl)-tetraphosphatase, symmetrical / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / : / Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsNuthanakanti, A. / Serganov, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM112940 United States
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: ApaH decaps Np 4 N-capped RNAs in two alternative orientations.
Authors: Nuthanakanti, A. / Korn, M. / Levenson-Palmer, R. / Wu, Y. / Babu, N.R. / Huang, X. / Banh, R.S. / Belasco, J.G. / Serganov, A.
History
DepositionMay 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,63913
Polymers64,3212
Non-polymers2,31811
Water11,566642
1
A: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1085
Polymers32,1611
Non-polymers9484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bis(5'-nucleosyl)-tetraphosphatase [symmetrical]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5318
Polymers32,1611
Non-polymers1,3707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.772, 55.107, 120.622
Angle α, β, γ (deg.)90.00, 129.89, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bis(5'-nucleosyl)-tetraphosphatase [symmetrical] / Ap4A hydrolase / Diadenosine 5' / 5'''-P1 / P4-tetraphosphate pyrophosphohydrolase / Diadenosine ...Ap4A hydrolase / Diadenosine 5' / 5'''-P1 / P4-tetraphosphate pyrophosphohydrolase / Diadenosine tetraphosphatase


Mass: 32160.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: apaH, b0049, JW0048 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P05637, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)

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Non-polymers , 6 types, 653 molecules

#2: Chemical ChemComp-A1L89 / P1-(5'-Adenosyl) P4-(5'-uridyl) tetraphosphate / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate / Adenosine(5')tetraphosphate uridine / Ap4U


Mass: 813.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H27N7O21P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 642 / 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: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Conditions: 0.3 mM ApaH (10 mg/mL), 1 mM DTT, 3 mM MgCl2, 10 mM Ca(OAc)2, 25 mM Hepes (pH 7.5), 0.2 M NaCl and soaked with Ap4U. Well solution: 0.2 M trisodium citrate, 20% PEG3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.56→29 Å / Num. obs: 118483 / % possible obs: 99.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 23.09 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.093 / Net I/σ(I): 94.9
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5844 / CC1/2: 0.701 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
HKL-2000data scaling
HKL-2000data reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→28.4 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 3773 1.69 %
Rwork0.1777 --
obs0.1781 118483 95.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.56→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4209 0 103 642 4954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074435
X-RAY DIFFRACTIONf_angle_d1.0996060
X-RAY DIFFRACTIONf_dihedral_angle_d17.022629
X-RAY DIFFRACTIONf_chiral_restr0.062645
X-RAY DIFFRACTIONf_plane_restr0.009770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.580.33811120.3217343X-RAY DIFFRACTION86
1.58-1.60.28421520.30827974X-RAY DIFFRACTION94
1.6-1.620.26491220.27178180X-RAY DIFFRACTION95
1.62-1.650.30021500.24968128X-RAY DIFFRACTION96
1.65-1.670.28551570.24638217X-RAY DIFFRACTION96
1.67-1.70.25431130.22958215X-RAY DIFFRACTION96
1.7-1.730.2381260.22818274X-RAY DIFFRACTION96
1.73-1.750.25571630.21688069X-RAY DIFFRACTION96
1.76-1.790.19311430.21018290X-RAY DIFFRACTION97
1.79-1.820.22881320.20888244X-RAY DIFFRACTION97
1.82-1.860.23241410.21018318X-RAY DIFFRACTION97
1.86-1.90.20331650.19288250X-RAY DIFFRACTION97
1.9-1.940.19461440.18528258X-RAY DIFFRACTION97
1.94-1.990.20681290.18548301X-RAY DIFFRACTION97
1.99-2.050.19111490.1828341X-RAY DIFFRACTION97
2.05-2.110.19161540.18158223X-RAY DIFFRACTION97
2.11-2.170.20181310.17558221X-RAY DIFFRACTION97
2.17-2.250.21031380.18088262X-RAY DIFFRACTION96
2.25-2.340.21961440.17938097X-RAY DIFFRACTION96
2.34-2.450.22021550.18458032X-RAY DIFFRACTION94
2.45-2.580.21481320.17818144X-RAY DIFFRACTION96
2.58-2.740.22391320.18578157X-RAY DIFFRACTION95
2.74-2.950.19041480.18228206X-RAY DIFFRACTION96
2.95-3.250.24151350.17718233X-RAY DIFFRACTION96
3.25-3.710.16591360.15648117X-RAY DIFFRACTION95
3.71-4.680.1711250.14137773X-RAY DIFFRACTION91
4.68-28.40.16091450.15558236X-RAY DIFFRACTION97

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