2NMT

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.228 
  • R-Value Observed: 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 Biol 5: 1091-1097

  • DOI: https://doi.org/10.1038/4202
  • Primary Citation of Related Structures:  
    2NMT

  • 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 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MYRISTOYL-COA\:PROTEIN N-MYRISTOYLTRANSFERASE422Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NMT1
EC: 2.3.1.97
UniProt
Find proteins for P14743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14743 
Go to UniProtKB:  P14743
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14743
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NHM
Query on NHM
Download Ideal Coordinates CCD File 
B [auth A]S-(2-OXO)PENTADECYLCOA
C36 H64 N7 O17 P3 S
JKWHUJMJVNMKEF-SXKLBCNJSA-N
MIM
Query on MIM
Download Ideal Coordinates CCD File 
C [auth A][CYCLOHEXYLETHYL]-[[[[4-[2-METHYL-1-IMIDAZOLYL-BUTYL]PHENYL]ACETYL]-SERYL]-LYSINYL]-AMINE
C33 H52 N6 O4
WHLPIOSHBKQGHA-KYJUHHDHSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [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],
M [auth A],
N [auth A],
O [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MIM BindingDB:  2NMT IC50: 24 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.4α = 90
b = 105.4β = 90
c = 106.7γ = 120
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

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