1QR0 | pdb_00001qr0

CRYSTAL STRUCTURE OF THE 4'-PHOSPHOPANTETHEINYL TRANSFERASE SFP-COENZYME A COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.278 (Depositor) 
  • R-Value Work: 
    0.216 (Depositor) 
  • R-Value Observed: 
    0.216 (Depositor) 

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This is version 1.4 of the entry. See complete history

Literature

Crystal structure of the surfactin synthetase-activating enzyme sfp: a prototype of the 4'-phosphopantetheinyl transferase superfamily.

Reuter, K.Mofid, M.R.Marahiel, M.A.Ficner, R.

(1999) EMBO J 18: 6823-6831

  • DOI: https://doi.org/10.1093/emboj/18.23.6823
  • Primary Citation Related Structures: 
    1QR0

  • PubMed Abstract: 

    The Bacillus subtilis Sfp protein activates the peptidyl carrier protein (PCP) domains of surfactin synthetase by transferring the 4'-phosphopantetheinyl moiety of coenzyme A (CoA) to a serine residue conserved in all PCPs. Its wide PCP substrate spectrum renders Sfp a biotechnologically valuable enzyme for use in combinatorial non-ribosomal peptide synthesis. The structure of the Sfp-CoA complex determined at 1.8 A resolution reveals a novel alpha/beta-fold exhibiting an unexpected intramolecular 2-fold pseudosymmetry. This suggests a similar fold and dimerization mode for the homodimeric phosphopantetheinyl transferases such as acyl carrier protein synthase. The active site of Sfp accommodates a magnesium ion, which is complexed by the CoA pyrophosphate, the side chains of three acidic amino acids and one water molecule. CoA is bound in a fashion that differs in many aspects from all known CoA-protein complex structures. The structure reveals regions likely to be involved in the interaction with the PCP substrate.


  • Organizational Affiliation
    • Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Emil-Mannkopff-Strasse 2, D-35037 Marburg.

Macromolecule Content 

  • Total Structure Weight: 27.33 kDa 
  • Atom Count: 2,188 
  • Modeled Residue Count: 228 
  • Deposited Residue Count: 228 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
4'-PHOSPHOPANTETHEINYL TRANSFERASE SFP228Bacillus subtilisMutation(s): 0 
Gene Names: SFP
EC: 2.7.8.7
UniProt
Find proteins for P39135 (Bacillus subtilis (strain 168))
Explore P39135 
Go to UniProtKB:  P39135
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39135
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.278 (Depositor) 
  • R-Value Work:  0.216 (Depositor) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.3α = 90
b = 65.3β = 90
c = 150.3γ = 90
Software Package:
Software NamePurpose
SHARPphasing
X-PLORrefinement
MAR345data collection
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations