5O9U

HsNMT1 in complex with CoA and Myristoylated-GCSVSKKK octapeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern.

Castrec, B.Dian, C.Ciccone, S.Ebert, C.L.Bienvenut, W.V.Le Caer, J.P.Steyaert, J.M.Giglione, C.Meinnel, T.

(2018) Nat. Chem. Biol. 14: 671-679

  • DOI: 10.1038/s41589-018-0077-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An organism's entire protein modification repertoire has yet to be comprehensively mapped. N-myristoylation (MYR) is a crucial eukaryotic N-terminal protein modification. Here we mapped complete Homo sapiens and Arabidopsis thaliana myristoylomes. Th ...

    An organism's entire protein modification repertoire has yet to be comprehensively mapped. N-myristoylation (MYR) is a crucial eukaryotic N-terminal protein modification. Here we mapped complete Homo sapiens and Arabidopsis thaliana myristoylomes. The crystal structures of human modifier NMT1 complexed with reactive and nonreactive target-mimicking peptide ligands revealed unexpected binding clefts and a modifier recognition pattern. This information allowed integrated mapping of myristoylomes using peptide macroarrays, dedicated prediction algorithms, and in vivo mass spectrometry. Global MYR profiling at the genomic scale identified over a thousand novel, heterogeneous targets in both organisms. Surprisingly, MYR involved a non-negligible set of overlapping targets with N-acetylation, and the sequence signature marks for a third proximal acylation-S-palmitoylation-were genomically imprinted, allowing recognition of sequences exhibiting both acylations. Together, the data extend the N-end rule concept for Gly-starting proteins to subcellular compartmentalization and reveal the main neighbors influencing protein modification profiles and consequent cell fate.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Gif-sur-Yvette cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycylpeptide N-tetradecanoyltransferase 1
A, B
402Homo sapiensMutation(s): 0 
Gene Names: NMT1 (NMT)
EC: 2.3.1.97
Find proteins for P30419 (Homo sapiens)
Go to Gene View: NMT1
Go to UniProtKB:  P30419
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calcineurin B-like protein 4
C, D
8Arabidopsis thalianaMutation(s): 0 
Gene Names: CBL4 (SOS3)
Find proteins for O81223 (Arabidopsis thaliana)
Go to UniProtKB:  O81223
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
C, D
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A, B
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.155 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.236α = 90.00
b = 79.779β = 90.00
c = 178.751γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR PalmyProt
Fondation ARCFranceSFI2011120111203841

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-11-07
    Type: Data collection, Database references