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- PDB-6o07: Structure and mechanism of acetylation by the N-terminal dual enz... -

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Basic information

Entry
Database: PDB / ID: 6o07
TitleStructure and mechanism of acetylation by the N-terminal dual enzyme NatA/Naa50 complex
Components
  • (N-terminal acetyltransferase A complex ...) x 2
  • Naa15
KeywordsTRANSFERASE / N-terminal acetylation / protein complex / NatA / Naa50 / NatE
Function / homology
Function and homology information


N-terminal protein amino acid propionylation / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal methionine Nalpha-acetyltransferase NatE / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / mitotic sister chromatid cohesion / ribosome binding ...N-terminal protein amino acid propionylation / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal methionine Nalpha-acetyltransferase NatE / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / mitotic sister chromatid cohesion / ribosome binding / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
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 / Tetratricopeptide repeats / Acyl-CoA N-acyltransferase / Tetratricopeptide repeat ...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 / Tetratricopeptide repeats / Acyl-CoA N-acyltransferase / Tetratricopeptide repeat / Aminopeptidase / Tetratricopeptide-like helical domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / INOSITOL HEXAKISPHOSPHATE / MALONATE ION / K7_Nat1p / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsDeng, S. / Marmorstein, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118090 United States
CitationJournal: Structure / Year: 2019
Title: Structure and Mechanism of Acetylation by the N-Terminal Dual Enzyme NatA/Naa50 Complex.
Authors: Deng, S. / Magin, R.S. / Wei, X. / Pan, B. / Petersson, E.J. / Marmorstein, R.
History
DepositionFeb 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.5Oct 11, 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
C: N-terminal acetyltransferase A complex subunit NAT5
A: Naa15
B: N-terminal acetyltransferase A complex catalytic subunit ARD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,94736
Polymers146,4563
Non-polymers3,49133
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15790 Å2
ΔGint-185 kcal/mol
Surface area48720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.437, 125.726, 145.924
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 ... , 2 types, 2 molecules CB

#1: Protein N-terminal acetyltransferase A complex subunit NAT5 / NatA complex subunit NAT5 / Naa50


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, N-terminal methionine Nalpha-acetyltransferase NatE
#3: Protein N-terminal acetyltransferase A complex catalytic subunit ARD1 / NatA complex subunit ARD1 / Arrest-defective protein 1 / Naa10


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, N-terminal amino-acid Nalpha-acetyltransferase NatA

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Protein , 1 types, 1 molecules A

#2: Protein Naa15 / / Nat1p


Mass: 99067.188 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: G2WCC0, UniProt: P12945*PLUS

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Non-polymers , 7 types, 221 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#7: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#8: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#9: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 10% PEG3350, 0.1 M sodium malonate, pH 5.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 2, 2018
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 43295 / % possible obs: 99.3 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.11
Reflection shellResolution: 2.7→3 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.18 / Num. unique obs: 3314 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XNH

4xnh


Resolution: 2.702→47.658 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.83
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 1709 4.92 %Random selection
Rwork0.2221 ---
obs0.2235 34760 80.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.702→47.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8652 0 196 188 9036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049017
X-RAY DIFFRACTIONf_angle_d0.68412203
X-RAY DIFFRACTIONf_dihedral_angle_d4.2235364
X-RAY DIFFRACTIONf_chiral_restr0.0411339
X-RAY DIFFRACTIONf_plane_restr0.0031552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7023-2.78180.3707430.294752X-RAY DIFFRACTION23
2.7818-2.87160.3409670.28631363X-RAY DIFFRACTION40
2.8716-2.97420.33861060.28031901X-RAY DIFFRACTION56
2.9742-3.09330.32361400.27992310X-RAY DIFFRACTION69
3.0933-3.2340.3011450.27712791X-RAY DIFFRACTION82
3.234-3.40450.31051710.25983236X-RAY DIFFRACTION96
3.4045-3.61770.28161560.2323396X-RAY DIFFRACTION99
3.6177-3.89690.25271580.21583418X-RAY DIFFRACTION100
3.8969-4.28880.24171650.19973442X-RAY DIFFRACTION100
4.2888-4.90890.20391720.18223405X-RAY DIFFRACTION99
4.9089-6.18260.25772030.22393444X-RAY DIFFRACTION100
6.1826-47.66570.20231830.20923593X-RAY DIFFRACTION99

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