6PAU

Structure of Human NMT2 with myristoyl-lysine peptide and CoA products

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-06-11 Released: 2020-03-11 
  • Deposition Author(s): Price, I.R., Lin, H.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


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Literature

NMT1 and NMT2 are lysine myristoyltransferases regulating the ARF6 GTPase cycle.

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.

(2020) Nat Commun 11: 1067-1067

  • DOI: 10.1038/s41467-020-14893-x
  • Primary Citation of Related Structures:  
    6PAV, 6PAU

  • PubMed Abstract: 
  • Lysine fatty acylation in mammalian cells was discovered nearly three decades ago, yet the enzymes catalyzing it remain unknown. Unexpectedly, we find that human N-terminal glycine myristoyltransferases (NMT) 1 and 2 can efficiently myristoylate specific lysine residues ...

    Lysine fatty acylation in mammalian cells was discovered nearly three decades ago, yet the enzymes catalyzing it remain unknown. Unexpectedly, we find that human N-terminal glycine myristoyltransferases (NMT) 1 and 2 can efficiently myristoylate specific lysine residues. They modify ADP-ribosylation factor 6 (ARF6) on lysine 3 allowing it to remain on membranes during the GTPase cycle. We demonstrate that the NAD + -dependent deacylase SIRT2 removes the myristoyl group, and our evidence suggests that NMT prefers the GTP-bound while SIRT2 prefers the GDP-bound ARF6. This allows the lysine myrisotylation-demyristoylation cycle to couple to and promote the GTPase cycle of ARF6. Our study provides an explanation for the puzzling dissimilarity of ARF6 to other ARFs and suggests the existence of other substrates regulated by this previously unknown function of NMT. Furthermore, we identified a NMT/SIRT2-ARF6 regulatory axis, which may offer new ways to treat human diseases.


    Organizational Affiliation

    Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA. hl379@cornell.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase 2A383Homo sapiensMutation(s): 0 
Gene Names: NMT2
EC: 2.3.1.97
UniProt & NIH Common Fund Data Resources
Find proteins for O60551 (Homo sapiens)
Explore O60551 
Go to UniProtKB:  O60551
PHAROS:  O60551
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Arf6 peptideB [auth C]7Homo sapiensMutation(s): 0 
Gene Names: ARF6
UniProt & NIH Common Fund Data Resources
Find proteins for P62330 (Homo sapiens)
Explore P62330 
Go to UniProtKB:  P62330
PHAROS:  P62330
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4PS (Subject of Investigation/LOI)
Query on 4PS

Download Ideal Coordinates CCD File 
M [auth A]4'-diphospho pantetheine
C11 H24 N2 O10 P2 S
UQURMDBHCKDEJS-VIFPVBQESA-N
 Ligand Interaction
MYR (Subject of Investigation/LOI)
Query on MYR

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O [auth C]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
N [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , 
D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.162α = 90
b = 46.35β = 114.25
c = 74.395γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-06-11 
  • Released Date: 2020-03-11 
  • Deposition Author(s): Price, I.R., Lin, H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States1R01DK107868
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM086703-07

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release