3HYK

2.31 Angstrom resolution crystal structure of a holo-(acyl-carrier-protein) synthase from Bacillus anthracis str. Ames in complex with CoA (3',5'-ADP)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 


Literature

Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria.

Halavaty, A.S., Kim, Y., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Zhou, M., Onopriyenko, O., Skarina, T., Papazisi, L., Kwon, K., Peterson, S.N., Joachimiak, A., Savchenko, A., Anderson, W.F.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1359-1370

  • DOI: https://doi.org/10.1107/S0907444912029101
  • Primary Citation of Related Structures:  
    3HYK, 3QMN, 4JM7

  • PubMed Abstract: 

    Some bacterial type II fatty-acid synthesis (FAS II) enzymes have been shown to be important candidates for drug discovery. The scientific and medical quest for new FAS II protein targets continues to stimulate research in this field. One of the possible additional candidates is the acyl-carrier-protein synthase (AcpS) enzyme. Its holo form post-translationally modifies the apo form of an acyl carrier protein (ACP), which assures the constant delivery of thioester intermediates to the discrete enzymes of FAS II. At the Center for Structural Genomics of Infectious Diseases (CSGID), AcpSs from Staphylococcus aureus (AcpS(SA)), Vibrio cholerae (AcpS(VC)) and Bacillus anthracis (AcpS(BA)) have been structurally characterized in their apo, holo and product-bound forms, respectively. The structure of AcpS(BA) is emphasized because of the two 3',5'-adenosine diphosphate (3',5'-ADP) product molecules that are found in each of the three coenzyme A (CoA) binding sites of the trimeric protein. One 3',5'-ADP is bound as the 3',5'-ADP part of CoA in the known structures of the CoA-AcpS and 3',5'-ADP-AcpS binary complexes. The position of the second 3',5'-ADP has never been described before. It is in close proximity to the first 3',5'-ADP and the ACP-binding site. The coordination of two ADPs in AcpS(BA) may possibly be exploited for the design of AcpS inhibitors that can block binding of both CoA and ACP.

    • Organizational Affiliation: 

    Center for Structural Genomics of Infectious Diseases, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Holo-[acyl-carrier-protein] synthase
A, B, C
122Bacillus anthracisMutation(s): 0 
Gene Names: acpS, BA_0250, GBAA_0250, BAS0236
EC: 2.7.8.7
UniProt
Find proteins for Q81JG3 (Bacillus anthracis)
Explore Q81JG3 
Go to UniProtKB:  Q81JG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ81JG3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A3P
Query on A3P
Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
P [auth B]
Q [auth B]
W [auth C]
H [auth A],
I [auth A],
P [auth B],
Q [auth B],
W [auth C],
X [auth C]
ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
F [auth A]
L [auth B]
N [auth B]
O [auth B]
T [auth C]
F [auth A],
L [auth B],
N [auth B],
O [auth B],
T [auth C],
V [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
G [auth A]
J [auth B]
K [auth B]
D [auth A],
E [auth A],
G [auth A],
J [auth B],
K [auth B],
M [auth B],
R [auth C],
S [auth C],
U [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.526α = 90
b = 77.526β = 90
c = 122.965γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-09-26
    Changes: Database references
  • Version 1.3: 2012-12-05
    Changes: Database references
  • Version 1.4: 2017-11-01
    Changes: Refinement description
  • Version 1.5: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2023-11-22
    Changes: Data collection