2NMT

MYRISTOYL-COA:PROTEIN N-MYRISTOYLTRANSFERASE BOUND TO MYRISTOYL-COA AND PEPTIDE ANALOGS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of N-myristoyltransferase with bound myristoylCoA and peptide substrate analogs.

Bhatnagar, R.S.Futterer, K.Farazi, T.A.Korolev, S.Murray, C.L.Jackson-Machelski, E.Gokel, G.W.Gordon, J.I.Waksman, G.

(1998) Nat.Struct.Mol.Biol. 5: 1091-1097

  • DOI: 10.1038/4202

  • PubMed Abstract: 
  • N-myristoyltransferase (Nmt) attaches myristate to the N-terminal glycine of many important eukaryotic and viral proteins. It is a target for anti-fungal and anti-viral therapy. We have determined the structure, to 2.9 A resolution, of a ternary comp ...

    N-myristoyltransferase (Nmt) attaches myristate to the N-terminal glycine of many important eukaryotic and viral proteins. It is a target for anti-fungal and anti-viral therapy. We have determined the structure, to 2.9 A resolution, of a ternary complex of Saccharomyces cerevisiae Nmt1p with bound myristoylCoA and peptide substrate analogs. The model reveals structural features that define the enzyme's substrate specificities and regulate the ordered binding and release of substrates and products. A novel catalytic mechanism is proposed involving deprotonation of the N-terminal ammonium of a peptide substrate by the enzyme's C-terminal backbone carboxylate.


    Organizational Affiliation

    Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYRISTOYL-COA\:PROTEIN N-MYRISTOYLTRANSFERASE
A
422Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NMT1 (CDC72)
EC: 2.3.1.97
Find proteins for P14743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: NMT1
Go to UniProtKB:  P14743
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MIM
Query on MIM

Download SDF File 
Download CCD File 
A
[CYCLOHEXYLETHYL]-[[[[4-[2-METHYL-1-IMIDAZOLYL-BUTYL]PHENYL]ACETYL]-SERYL]-LYSINYL]-AMINE
C33 H52 N6 O4
WHLPIOSHBKQGHA-KYJUHHDHSA-N
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A
S-(2-OXO)PENTADECYLCOA
C36 H64 N7 O17 P3 S
JKWHUJMJVNMKEF-SXKLBCNJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MIMIC50: 24 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.228 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.400α = 90.00
b = 105.400β = 90.00
c = 106.700γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-06
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance