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- PDB-4xpd: Crystal structure of yeast N-terminal acetyltransferase NatE (ppG... -

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Basic information

Entry
Database: PDB / ID: 4xpd
TitleCrystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a bisubstrate
Components
  • (N-terminal acetyltransferase A complex subunit ...) x 2
  • N-terminal acetyltransferase A complex catalytic subunit ARD1
  • human ACTH8
KeywordsTRANSFERASE / N-terminal acetyltransferase / NatE / ppGpp / bisubstrate
Function / homology
Function and homology information


cellular pigmentation / positive regulation of oxytocin production / Peptide hormone biosynthesis / Defective ACTH causes obesity and POMCD / type 1 melanocortin receptor binding / type 3 melanocortin receptor binding / type 4 melanocortin receptor binding / regulation of corticosterone secretion / response to melanocyte-stimulating hormone / protein-N-terminal-glutamate acetyltransferase activity ...cellular pigmentation / positive regulation of oxytocin production / Peptide hormone biosynthesis / Defective ACTH causes obesity and POMCD / type 1 melanocortin receptor binding / type 3 melanocortin receptor binding / type 4 melanocortin receptor binding / regulation of corticosterone secretion / response to melanocyte-stimulating hormone / protein-N-terminal-glutamate acetyltransferase activity / N-terminal methionine Nalpha-acetyltransferase NatE / Opioid Signalling / N-terminal amino-acid Nalpha-acetyltransferase NatA / Androgen biosynthesis / NatA complex / protein N-terminal-methionine acetyltransferase activity / regulation of appetite / protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / regulation of glycogen metabolic process / Glucocorticoid biosynthesis / protein-N-terminal amino-acid acetyltransferase activity / acetyltransferase activator activity / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / mitotic sister chromatid cohesion / negative regulation of tumor necrosis factor production / neuropeptide signaling pathway / Endogenous sterols / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Transcriptional and post-translational regulation of MITF-M expression and activity / Peptide ligand-binding receptors / secretory granule / generation of precursor metabolites and energy / G protein-coupled receptor binding / calcium-mediated signaling / hormone activity / regulation of blood pressure / G-protein activation / glucose homeostasis / cell-cell signaling / ribosome binding / G alpha (i) signalling events / G alpha (s) signalling events / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / signaling receptor binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Opiodes neuropeptide / Pro-opiomelanocortin N-terminal / Opioids neuropeptide / Pro-opiomelanocortin, N-terminal region / Pro-opiomelanocortin, N-terminal region / Opioids neuropeptide / Pro-opiomelanocortin / Pro-opiomelanocortin/corticotropin, ACTH, central region / : / Corticotropin ACTH domain ...Opiodes neuropeptide / Pro-opiomelanocortin N-terminal / Opioids neuropeptide / Pro-opiomelanocortin, N-terminal region / Pro-opiomelanocortin, N-terminal region / Opioids neuropeptide / Pro-opiomelanocortin / Pro-opiomelanocortin/corticotropin, ACTH, central region / : / Corticotropin ACTH domain / Corticotropin ACTH domain / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / : / N-acetyltransferase Ard1-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Tetratricopeptide repeats / Aminopeptidase / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / CARBOXYMETHYL COENZYME *A / GUANOSINE-5',3'-TETRAPHOSPHATE / Pro-opiomelanocortin / N-terminal acetyltransferase A complex catalytic subunit ARD1 / N-terminal acetyltransferase A complex subunit NAT1 / N-alpha-acetyltransferase NAT5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.81 Å
AuthorsDong, J. / Wang, S. / York, J.D.
CitationJournal: To Be Published
Title: Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a bisubstrate
Authors: Dong, J. / Wang, S. / York, J.D.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-terminal acetyltransferase A complex subunit NAT1
B: N-terminal acetyltransferase A complex catalytic subunit ARD1
C: N-terminal acetyltransferase A complex subunit NAT5
F: human ACTH8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7357
Polymers147,4974
Non-polymers2,2383
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13140 Å2
ΔGint-49 kcal/mol
Surface area50240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.564, 113.649, 146.721
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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N-terminal acetyltransferase A complex subunit ... , 2 types, 2 molecules AC

#1: Protein N-terminal acetyltransferase A complex subunit NAT1 / NatA complex subunit NAT1 / Amino-terminal / alpha-amino / acetyltransferase 1


Mass: 99050.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P12945
#3: Protein N-terminal acetyltransferase A complex subunit NAT5 / NatA complex subunit NAT5


Mass: 19753.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
References: UniProt: Q08689, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Protein / Protein/peptide , 2 types, 2 molecules BF

#2: Protein N-terminal acetyltransferase A complex catalytic subunit ARD1 / NatA complex subunit ARD1 / Arrest-defective protein 1


Mass: 27635.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P07347, EC: 2.3.1.88
#4: Protein/peptide human ACTH8


Mass: 1058.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01189*PLUS

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Non-polymers , 4 types, 16 molecules

#5: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#6: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#7: Chemical ChemComp-CMC / CARBOXYMETHYL COENZYME *A


Mass: 825.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O18P3S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 17% PEG 550 MME, 0.1 M MES pH 6.5 / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 35928 / % possible obs: 99.5 % / Redundancy: 7.4 % / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.81→50 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.833 / SU B: 15.852 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29704 1560 5.1 %RANDOM
Rwork0.23637 ---
obs0.23943 29193 86.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.318 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--1.03 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9111 0 138 13 9262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0199448
X-RAY DIFFRACTIONr_bond_other_d0.0010.028953
X-RAY DIFFRACTIONr_angle_refined_deg0.9771.98412773
X-RAY DIFFRACTIONr_angle_other_deg0.707320593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.86751108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20224.505455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.281151676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5041546
X-RAY DIFFRACTIONr_chiral_restr0.0520.21386
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022195
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3934.8564475
X-RAY DIFFRACTIONr_mcbond_other1.3934.8564473
X-RAY DIFFRACTIONr_mcangle_it2.4567.2675568
X-RAY DIFFRACTIONr_mcangle_other2.4567.2685569
X-RAY DIFFRACTIONr_scbond_it1.0274.9134973
X-RAY DIFFRACTIONr_scbond_other1.0274.9134974
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8927.3427206
X-RAY DIFFRACTIONr_long_range_B_refined4.11637.73510742
X-RAY DIFFRACTIONr_long_range_B_other4.11637.7410742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.806→2.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 50 -
Rwork0.304 1080 -
obs--43.25 %

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