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- PDB-6pav: Structure of Human NMT1 with products CoA and myristoyl-lysine pe... -

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Basic information

Entry
Database: PDB / ID: 6pav
TitleStructure of Human NMT1 with products CoA and myristoyl-lysine peptide with acetylated N-terminus
Components
  • ARF6 peptide
  • Glycylpeptide N-tetradecanoyltransferase 1
  • acetyl-Arf6 peptide
KeywordsTRANSFERASE / lysine / myristoyl / myristoylation / n-myristoyl transferase
Function / homology
Function and homology information


erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / myristoyltransferase activity / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular ketone metabolic process / positive regulation of mitotic cytokinetic process / regulation of opsin-mediated signaling pathway ...erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / myristoyltransferase activity / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular ketone metabolic process / positive regulation of mitotic cytokinetic process / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / regulation of dendritic spine development / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of dendrite development / negative regulation of receptor-mediated endocytosis / regulation of Rac protein signal transduction / ruffle assembly / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / protein localization to membrane / MET receptor recycling / thioesterase binding / endocytic recycling / filopodium membrane / Flemming body / protein localization to cell surface / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / endocytic vesicle / signaling adaptor activity / vesicle-mediated transport / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / ruffle / small monomeric GTPase / cellular response to nerve growth factor stimulus / G protein activity / liver development / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / Inactivation, recovery and regulation of the phototransduction cascade / presynapse / Clathrin-mediated endocytosis / nervous system development / cell cortex / early endosome membrane / midbody / postsynapse / in utero embryonic development / cell differentiation / cell adhesion / endosome / cell cycle / cell division / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ADP-ribosylation factor 6 / Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain ...ADP-ribosylation factor 6 / Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Acyl-CoA N-acyltransferase / Aminopeptidase / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / MYRISTIC ACID / Glycylpeptide N-tetradecanoyltransferase 1 / ADP-ribosylation factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsPrice, I.R. / Lin, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1R01DK107868 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM086703-07 United States
CitationJournal: Nat Commun / Year: 2020
Title: NMT1 and NMT2 are lysine myristoyltransferases regulating the ARF6 GTPase cycle.
Authors: Kosciuk, T. / Price, I.R. / Zhang, X. / Zhu, C. / Johnson, K.N. / Zhang, S. / Halaby, S.L. / Komaniecki, G.P. / Yang, M. / DeHart, C.J. / Thomas, P.M. / Kelleher, N.L. / Christopher Fromme, J. / Lin, H.
History
DepositionJun 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glycylpeptide N-tetradecanoyltransferase 1
D: acetyl-Arf6 peptide
A: Glycylpeptide N-tetradecanoyltransferase 1
C: ARF6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,43712
Polymers92,0774
Non-polymers2,3608
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-16 kcal/mol
Surface area31320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.361, 58.217, 154.035
Angle α, β, γ (deg.)90.00, 90.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Glycylpeptide N-tetradecanoyltransferase 1 / Myristoyl-CoA:protein N-myristoyltransferase 1 / Type I N-myristoyltransferase / Peptide N- ...Myristoyl-CoA:protein N-myristoyltransferase 1 / Type I N-myristoyltransferase / Peptide N-myristoyltransferase 1


Mass: 45161.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Production host: Escherichia coli (E. coli)
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase

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Protein/peptide , 2 types, 2 molecules DC

#2: Protein/peptide acetyl-Arf6 peptide


Mass: 862.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62330*PLUS
#3: Protein/peptide ARF6 peptide


Mass: 893.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62330*PLUS

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Non-polymers , 4 types, 90 molecules

#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H28O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 7.5 mg/mL in 25 mM Tris-HCl pH 7.5, 120 mM NaCl, co-crystallized in the presence of 0.3 mM myristoyl-CoA and 0.3 mM AcKVLSKIF using a well solution of 18% PEG 8000, 100 mM NaCl, 100 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.52→77.012 Å / Num. obs: 27918 / % possible obs: 98.45 % / Redundancy: 3.8 % / CC1/2: 0.919 / Rmerge(I) obs: 0.3053 / Net I/σ(I): 4.98
Reflection shellResolution: 2.52→2.61 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.196 / Num. unique obs: 2722 / % possible all: 97.21

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→77.012 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2804 1467 5.32 %
Rwork0.2654 --
obs0.2663 27562 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→77.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6290 0 147 82 6519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136608
X-RAY DIFFRACTIONf_angle_d1.5758973
X-RAY DIFFRACTIONf_dihedral_angle_d24.1072469
X-RAY DIFFRACTIONf_chiral_restr0.309979
X-RAY DIFFRACTIONf_plane_restr0.0121117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.61010.43351580.42062561X-RAY DIFFRACTION97
2.6101-2.71460.40211330.38822619X-RAY DIFFRACTION99
2.7146-2.83820.40351600.34562584X-RAY DIFFRACTION99
2.8382-2.98780.32781200.31492642X-RAY DIFFRACTION99
2.9878-3.1750.3371370.31062627X-RAY DIFFRACTION99
3.175-3.42010.31771500.28612632X-RAY DIFFRACTION99
3.4201-3.76430.29721700.26522534X-RAY DIFFRACTION99
3.7643-4.3090.23631350.23072633X-RAY DIFFRACTION98
4.309-5.42870.21861550.20592572X-RAY DIFFRACTION96
5.4287-77.04840.24141490.2372691X-RAY DIFFRACTION98

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