4DG9

Structure of holo-PA1221, an NRPS protein containing adenylation and PCP domains bound to vinylsulfonamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

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This is version 2.1 of the entry. See complete history


Literature

Structure of PA1221, a Nonribosomal Peptide Synthetase Containing Adenylation and Peptidyl Carrier Protein Domains.

Mitchell, C.A.Shi, C.Aldrich, C.C.Gulick, A.M.

(2012) Biochemistry 51: 3252-3263

  • DOI: https://doi.org/10.1021/bi300112e
  • Primary Citation of Related Structures:  
    4DG8, 4DG9

  • PubMed Abstract: 

    Many bacteria use large modular enzymes for the synthesis of polyketide and peptide natural products. These multidomain enzymes contain integrated carrier domains that deliver bound substrates to multiple catalytic domains, requiring coordination of these chemical steps. Nonribosomal peptide synthetases (NRPSs) load amino acids onto carrier domains through the activity of an upstream adenylation domain. Our lab recently determined the structure of an engineered two-domain NRPS containing fused adenylation and carrier domains. This structure adopted a domain-swapped dimer that illustrated the interface between these two domains. To continue our investigation, we now examine PA1221, a natural two-domain protein from Pseudomonas aeruginosa. We have determined the amino acid specificity of this new enzyme and used domain specific mutations to demonstrate that loading the downstream carrier domain within a single protein molecule occurs more quickly than loading of a nonfused carrier domain intermolecularly. Finally, we have determined crystal structures of both apo- and holo-PA1221 proteins, the latter using a valine-adenosine vinylsulfonamide inhibitor that traps the adenylation domain-carrier domain interaction. The protein adopts an interface similar to that seen with the prior adenylation domain-carrier protein construct. A comparison of these structures with previous structures of multidomain NRPSs suggests that a large conformational change within the NRPS adenylation domains guides the carrier domain into the active site for thioester formation.


  • Organizational Affiliation

    Hauptman-Woodward Institute and Department of Structural Biology, University at Buffalo, Buffalo, New York 14203, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PA1221620Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA1221
EC: 6.2.1
UniProt
Find proteins for Q9I4B7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I4B7 
Go to UniProtKB:  Q9I4B7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I4B7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DG9
Query on DG9

Download Ideal Coordinates CCD File 
B [auth A]5'-({[(2R,3R)-3-amino-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-{[oxido(oxo)phosphonio]oxy}butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-4-methylpentyl]sulfonyl}amino)-5'-deoxyadenosine
C27 H48 N9 O12 P S2
LAWRAYXGFUHBCH-AWSFPXBRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.19α = 90
b = 231.18β = 90
c = 122.05γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata 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: 2012-05-02
    Type: Initial release
  • Version 2.0: 2022-06-29
    Changes: Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Refinement description