1NM2 | pdb_00001nm2

Malonyl-CoA:ACP Transacylase

• PDB DOI: https://doi.org/10.2210/pdb1NM2/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces coelicolor A3(2)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-01-08 Released: 2003-01-21 
• Deposition Author(s): Keatinge-Clay, A.T., Shelat, A.A., Savage, D.F., Tsai, S., Miercke, L.J.W., O'Connell III, J.D., Khosla, C., Stroud, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Catalysis, Specificity, and ACP Docking Site of Streptomyces coelicolor Malonyl-CoA:ACP Transacylase

Keatinge-Clay, A.T., Shelat, A.A., Savage, D.F., Tsai, S., Miercke, L.J.W., O'Connell III, J.D., Khosla, C., Stroud, R.M.

(2003) Structure 11: 147-154

• PubMed: 12575934 
• DOI: https://doi.org/10.1016/s0969-2126(03)00004-2
• Primary Citation Related Structures: 
  1NM2


• PubMed Abstract: 
  

  Malonyl-CoA:ACP transacylase (MAT), the fabD gene product of Streptomyces coelicolor A3(2), participates in both fatty acid and polyketide synthesis pathways, transferring malonyl groups that are used as extender units in chain growth from malonyl-CoA to pathway-specific acyl carrier proteins (ACPs). Here, the 2.0 A structure reveals an invariant arginine bound to an acetate that mimics the malonyl carboxylate and helps define the extender unit binding site. Catalysis may only occur when the oxyanion hole is formed through substrate binding, preventing hydrolysis of the acyl-enzyme intermediate. Macromolecular docking simulations with actinorhodin ACP suggest that the majority of the ACP docking surface is formed by a helical flap. These results should help to engineer polyketide synthases (PKSs) that produce novel polyketides.

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Organizational Affiliation: 
• Graduate Group in Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.43 kDa 
• Atom Count: 2,300 
• Modeled Residue Count: 305 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
malonyl CoA:acyl carrier protein malonyltransferase	A	317	Streptomyces coelicolor A3(2)	Mutation(s): 0  Gene Names: FABD EC: 2.3.1.39
UniProt
Find proteins for P72391 (Streptomyces coelicolor) Explore P72391  Go to UniProtKB:  P72391

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	C [auth A], D [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.067	α = 90
b = 54.486	β = 90
c = 109.88	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-21 
Deposition Author(s): Keatinge-Clay, A.T., Shelat, A.A., Savage, D.F., Tsai, S., Miercke, L.J.W., O'Connell III, J.D., Khosla, C., Stroud, R.M.

Revision History  

• Version 1.0: 2003-01-21
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2018-09-05
  Changes: Data collection, Structure summary
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description