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- PDB-9kpy: Structure of Phosphopantetheine adenylyltransferase (PPAT) from E... -

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Basic information

Entry
Database: PDB / ID: 9kpy
TitleStructure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.20 A resolution.
Components
  • Heptapeptide
  • Phosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / coaD / PPAT / COENZYME A biosynthesis / EXPRESSION TAG
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphopantetheine adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
PHOSPHONOACETIC ACID / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEnterobacter sp. 638 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAhmad, N. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchI-1251 India
CitationJournal: Protein Sci. / Year: 2025
Title: Protein-tags and their fragments as potent inhibitors of enzymes: Structure of the ternary complex of phosphopantetheine adenylyltransferase from Enterobacter spp. with tag-peptides and ...Title: Protein-tags and their fragments as potent inhibitors of enzymes: Structure of the ternary complex of phosphopantetheine adenylyltransferase from Enterobacter spp. with tag-peptides and phosphonoacetic acid at 2.20 angstrom resolution.
Authors: Ahmad, N. / Kumar, V. / Goel, V.K. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionNov 24, 2024Deposition site: PDBJ / Processing site: PDBJ
SupersessionDec 11, 2024ID: 8I8J
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
E: Phosphopantetheine adenylyltransferase
F: Phosphopantetheine adenylyltransferase
H: Heptapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,24018
Polymers115,7477
Non-polymers1,49211
Water10,106561
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8776
Polymers38,3652
Non-polymers5124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-39 kcal/mol
Surface area16190 Å2
MethodPISA
2
C: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
H: Heptapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5787
Polymers39,0183
Non-polymers5604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-45 kcal/mol
Surface area15160 Å2
MethodPISA
3
E: Phosphopantetheine adenylyltransferase
F: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7855
Polymers38,3652
Non-polymers4203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-39 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.966, 78.659, 107.027
Angle α, β, γ (deg.)90.000, 93.121, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT


Mass: 19182.268 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. 638 (bacteria) / Gene: coaD, Ent638_0105 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A4W515, pantetheine-phosphate adenylyltransferase
#2: Protein/peptide Heptapeptide


Mass: 653.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. 638 (bacteria) / Gene: coaD, Ent638_0105 / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-PAE / PHOSPHONOACETIC ACID


Mass: 140.032 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H5O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: BIS-TRIS propane pH 7.0, Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.2→41.581 Å / Num. obs: 56390 / % possible obs: 97.3 % / Redundancy: 2.1 % / Biso Wilson estimate: 33.7 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.132 / Rrim(I) all: 0.187 / Net I/σ(I): 3.6
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4680 / CC1/2: 0.395 / Rpim(I) all: 0.723 / Rrim(I) all: 1.024

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MxCuBEdata collection
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→41.581 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: FREE R-VALUE / ESU R: 0.289 / ESU R Free: 0.233
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.267 1135 2.013 %
Rwork0.207 55254 -
all0.208 --
obs-56389 96.847 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.442 Å2
Baniso -1Baniso -2Baniso -3
1-1.931 Å20 Å20.099 Å2
2--0.739 Å2-0 Å2
3----2.666 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7704 0 86 561 8351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0128004
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167674
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.82710830
X-RAY DIFFRACTIONr_angle_other_deg0.7321.74517676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.389550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.135101404
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.65210341
X-RAY DIFFRACTIONr_chiral_restr0.0630.21230
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029255
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021769
X-RAY DIFFRACTIONr_nbd_refined0.2090.21771
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.27132
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23924
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.23949
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2453
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0830.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.244
X-RAY DIFFRACTIONr_nbd_other0.2430.2182
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.217
X-RAY DIFFRACTIONr_mcbond_it3.0614.3233980
X-RAY DIFFRACTIONr_mcbond_other3.0594.3223979
X-RAY DIFFRACTIONr_mcangle_it4.8747.7474973
X-RAY DIFFRACTIONr_mcangle_other4.8747.7484974
X-RAY DIFFRACTIONr_scbond_it3.5894.7824024
X-RAY DIFFRACTIONr_scbond_other3.5884.7844025
X-RAY DIFFRACTIONr_scangle_it5.8138.6055854
X-RAY DIFFRACTIONr_scangle_other5.8128.6065855
X-RAY DIFFRACTIONr_lrange_it10.14252.86835901
X-RAY DIFFRACTIONr_lrange_other10.14252.86735901
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2570.4021040.30740950.30942550.9020.92798.68390.306
2.257-2.3190.34760.29640480.29741880.9270.93698.47180.293
2.319-2.3860.33710.29139000.29240430.9410.9498.21910.286
2.386-2.4590.332640.27138000.27239410.9270.94898.04620.265
2.459-2.5390.354890.26836420.2738060.9290.95198.02940.263
2.539-2.6280.346680.25835300.2636870.9390.95697.58610.253
2.628-2.7270.282650.23134040.23235730.9380.96597.08930.225
2.727-2.8380.259450.20932980.2134570.9580.97296.70230.206
2.838-2.9630.267650.2230900.22132750.9520.96896.33590.224
2.963-3.1070.326640.2229630.22231350.9120.9796.5550.223
3.107-3.2740.3490.19728880.19930210.9490.97797.21950.202
3.274-3.4710.222470.20327070.20328390.9770.97797.0060.213
3.471-3.7090.266660.19125210.19326720.9560.97996.81890.203
3.709-4.0040.239790.17523390.17725100.9620.98196.33470.194
4.004-4.3820.268460.15521550.15723040.9540.98595.52950.177
4.382-4.8920.166480.14919370.14920900.9830.98694.97610.176
4.892-5.6360.269410.20216910.20418560.960.97993.3190.242
5.636-6.8710.284120.21314610.21415710.9730.97893.76190.252
6.871-9.5870.154270.13311360.13412470.9860.9993.26380.173
9.587-41.5810.22490.1756490.1757450.9750.9888.32210.231

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