2NMT | pdb_00002nmt

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

• PDB DOI: https://doi.org/10.2210/pdb2NMT/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-07-14 Released: 1999-01-06 
• Deposition Author(s): Fuetterer, K., Bhatnagar, R.S., Waksman, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.297 (Depositor) 
• R-Value Work: 
  0.228 (Depositor) 
• R-Value Observed: 
  0.228 (Depositor) 

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

• PubMed: 9846880 
• DOI: https://doi.org/10.1038/4202
• Primary Citation 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.71 kDa 
• Atom Count: 3,601 
• Modeled Residue Count: 422 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYRISTOYL-COA\:PROTEIN N-MYRISTOYLTRANSFERASE	A	422	Saccharomyces cerevisiae	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHM	B [auth A]	S-(2-OXO)PENTADECYLCOA C36 H64 N7 O17 P3 S JKWHUJMJVNMKEF-SXKLBCNJSA-N
MIM	C [auth A]	[CYCLOHEXYLETHYL]-[[[[4-[2-METHYL-1-IMIDAZOLYL-BUTYL]PHENYL]ACETYL]-SERYL]-LYSINYL]-AMINE C33 H52 N6 O4 WHLPIOSHBKQGHA-KYJUHHDHSA-N
GOL	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.297 (Depositor) 
• R-Value Work:  0.228 (Depositor) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.4	α = 90
b = 105.4	β = 90
c = 106.7	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-06 
Deposition Author(s): Fuetterer, K., Bhatnagar, R.S., Waksman, G.

Revision History  

• 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
• Version 1.3: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary