1F7T

HOLO-(ACYL CARRIER PROTEIN) SYNTHASE AT 1.8A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites.

Parris, K.D.Lin, L.Tam, A.Mathew, R.Hixon, J.Stahl, M.Fritz, C.C.Seehra, J.Somers, W.S.

(2000) Structure 8: 883-895

  • DOI: https://doi.org/10.1016/s0969-2126(00)00178-7
  • Primary Citation of Related Structures:  
    1F7L, 1F7T, 1F80

  • PubMed Abstract: 

    Holo-(acyl carrier protein) synthase (AcpS), a member of the phosphopantetheinyl transferase superfamily, plays a crucial role in the functional activation of acyl carrier protein (ACP) in the fatty acid biosynthesis pathway. AcpS catalyzes the attachment of the 4'-phosphopantetheinyl moiety of coenzyme A (CoA) to the sidechain of a conserved serine residue on apo-ACP. We describe here the first crystal structure of a type II ACP from Bacillus subtilis in complex with its activator AcpS at 2.3 A. We also have determined the structures of AcpS alone (at 1.8 A) and AcpS in complex with CoA (at 1.5 A). These structures reveal that AcpS exists as a trimer. A catalytic center is located at each of the solvent-exposed interfaces between AcpS molecules. Site-directed mutagenesis studies confirm the importance of trimer formation in AcpS activity. The active site in AcpS is only formed when two AcpS molecules dimerize. The addition of a third molecule allows for the formation of two additional active sites and also permits a large hydrophobic surface from each molecule of AcpS to be buried in the trimer. The mutations Ile5-->Arg, Gln113-->Glu and Gln113-->Arg show that AcpS is inactive when unable to form a trimer. The co-crystal structures of AcpS-CoA and AcpS-ACP allow us to propose a catalytic mechanism for this class of 4'-phosphopantetheinyl transferases.


  • Organizational Affiliation

    Biological Chemistry, Wyeth-Ayerst Research, Cambridge, MA 02140, USA. parrisk@war.wyeth.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
A, B, C, D, E
A, B, C, D, E, F
122Bacillus subtilisMutation(s): 1 
EC: 2.7.8.7
UniProt
Find proteins for P96618 (Bacillus subtilis (strain 168))
Explore P96618 
Go to UniProtKB:  P96618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP96618
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTT
Query on DTT

Download Ideal Coordinates CCD File 
FA [auth D],
GA [auth D],
M [auth A],
NA [auth F],
Y [auth C]
2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
HA [auth D],
R [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
I [auth A]
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
I [auth A],
J [auth A],
JA [auth E],
K [auth A],
KA [auth F],
L [auth A],
LA [auth F],
MA [auth F],
P [auth B],
Q [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth D]
G [auth A]
H [auth A]
IA [auth E]
N [auth B]
AA [auth D],
G [auth A],
H [auth A],
IA [auth E],
N [auth B],
O [auth B],
S [auth C],
Z [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.262α = 90
b = 76.16β = 93.32
c = 85.693γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2021-11-03
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-07
    Changes: Data collection