2G0B | pdb_00002g0b

The structure of FeeM, an N-acyl amino acid synthase from uncultured soil microbes

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.292 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.245 (DCC) 

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This is version 1.3 of the entry. See complete history. 

Literature

FeeM, an N-Acyl Amino Acid Synthase from an Uncultured Soil Microbe: Structure, Mechanism, and Acyl Carrier Protein Binding.

Van Wagoner, R.M., Clardy, J.

(2006) Structure 14: 1425-1435

  • DOI: https://doi.org/10.1016/j.str.2006.07.005
  • Primary Citation Related Structures: 
    2G0B

  • PubMed Abstract: 

    Attempts to access antibiotics by capturing biosynthetic genes and pathways directly from environmental DNA, which is overwhelmingly derived from uncultured bacteria, have revealed a large and previously unknown family of N-acyl amino acid synthases (NASs). The structure of the NAS FeeM reveals structural similarity to the GCN5-related N-acyl transferases and acylhomoserine lactone synthases. The overall structure has a central beta sheet with alpha helices on both sides. A bound product at a cleft in the beta sheet identifies the active site and the structural basis for catalysis, and sequence conservation in this region indicates a bias for recognition over speed. FeeM interacts with an acyl carrier protein (FeeL), and the structure, mutagenesis, and enzymatic measurements reveal that a small hydrophobic pocket in alpha helix 5 dominates binding of FeeM to FeeL. The structural and mechanistic analyses suggest that the products of FeeM could be bacterial signaling agents.

    • Organizational Affiliation: 
    • Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

Macromolecule Content 

  • Total Structure Weight: 177.15 kDa 
  • Atom Count: 11,507 
  • Modeled Residue Count: 1,451 
  • Deposited Residue Count: 1,584 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FeeM
A, B, C, D, E
A, B, C, D, E, F, G, H
198uncultured bacteriumMutation(s): 0 
Gene Names: feem
EC: 2.3.1
UniProt
Find proteins for Q8KNZ7 (uncultured bacterium CSLC2)
Explore Q8KNZ7 
Go to UniProtKB:  Q8KNZ7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KNZ7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.292 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.245 (DCC) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.832α = 90
b = 182.832β = 90
c = 287.429γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary