2REF | pdb_00002ref

Crystal structure of the loading GNATL domain of CurA from Lyngbya majuscula soaked with malonyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.251 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

GNAT-like strategy for polyketide chain initiation.

Gu, L.Geders, T.W.Wang, B.Gerwick, W.H.Hakansson, K.Smith, J.L.Sherman, D.H.

(2007) Science 318: 970-974

  • DOI: https://doi.org/10.1126/science.1148790
  • Primary Citation Related Structures: 
    2REE, 2REF

  • PubMed Abstract: 

    An unexpected biochemical strategy for chain initiation is described for the loading module of the polyketide synthase of curacin A, an anticancer lead derived from the marine cyanobacterium Lyngbya majuscula. A central GCN5-related N-acetyltransferase (GNAT) domain bears bifunctional decarboxylase/S-acetyltransferase activity, both unprecedented for the GNAT superfamily. A CurA loading tridomain, consisting of an adaptor domain, the GNAT domain, and an acyl carrier protein, was assessed biochemically, revealing that a domain showing homology to GNAT (GNAT(L)) catalyzes (i) decarboxylation of malonyl-coenzyme A (malonyl-CoA) to acetyl-CoA and (ii) direct S-acetyl transfer from acetyl-CoA to load an adjacent acyl carrier protein domain (ACP(L)). Moreover, the N-terminal adapter domain was shown to facilitate acetyl-group transfer. Crystal structures of GNAT(L) were solved at 1.95 angstroms (ligand-free form) and 2.75 angstroms (acyl-CoA complex), showing distinct substrate tunnels for acyl-CoA and holo-ACP(L) binding. Modeling and site-directed mutagenesis experiments demonstrated that histidine-389 and threonine-355, at the convergence of the CoA and ACP tunnels, participate in malonyl-CoA decarboxylation but not in acetyl-group transfer. Decarboxylation precedes acetyl-group transfer, leading to acetyl-ACP(L) as the key curacin A starter unit.


  • Organizational Affiliation
    • Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.

Macromolecule Content 

  • Total Structure Weight: 53.45 kDa 
  • Atom Count: 3,510 
  • Modeled Residue Count: 406 
  • Deposited Residue Count: 448 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CurA
A, B
224Moorena producens 19LMutation(s): 0 
Gene Names: curA
EC: 2.3.1.38 (PDB Primary Data), 4.1.1.9 (PDB Primary Data)
UniProt
Find proteins for Q6DNF2 (Lyngbya majuscula)
Explore Q6DNF2 
Go to UniProtKB:  Q6DNF2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DNF2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.251 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.886α = 90
b = 91.886β = 90
c = 139.486γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-04-03
    Changes: Refinement description