2F9Y | pdb_00002f9y

The Crystal Structure of The Carboxyltransferase Subunit of ACC from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.261 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.257 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.257 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2F9Y

This is version 1.5 of the entry. See complete history

Literature

The Structure of the Carboxyltransferase Component of Acetyl-CoA Carboxylase Reveals a Zinc-Binding Motif Unique to the Bacterial Enzyme(,).

Bilder, P.Lightle, S.Bainbridge, G.Ohren, J.Finzel, B.Sun, F.Holley, S.Al-Kassim, L.Spessard, C.Melnick, M.Newcomer, M.Waldrop, G.L.

(2006) Biochemistry 45: 1712-1722

  • DOI: https://doi.org/10.1021/bi0520479
  • Primary Citation Related Structures: 
    2F9I, 2F9Y

  • PubMed Abstract: 

    Acetyl-coA carboxylase (ACC) is a central metabolic enzyme that catalyzes the committed step in fatty acid biosynthesis: biotin-dependent conversion of acetyl-coA to malonyl-coA. The bacterial carboxyltransferase (CT) subunit of ACC is a target for the design of novel therapeutics that combat severe, hospital-acquired infections resistant to the established classes of frontline antimicrobials. Here, we present the structures of the bacterial CT subunits from two prevalent nosocomial pathogens, Staphylococcus aureus and Escherichia coli, at a resolution of 2.0 and 3.0 A, respectively. Both structures reveal a small, independent zinc-binding domain that lacks a complement in the primary sequence or structure of the eukaryotic homologue.


  • Organizational Affiliation
    • Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.

Macromolecule Content 

  • Total Structure Weight: 70.93 kDa 
  • Atom Count: 4,266 
  • Modeled Residue Count: 558 
  • Deposited Residue Count: 643 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetyl-CoA carboxylase, Carboxyltransferase alpha chain339Escherichia coliMutation(s): 0 
EC: 6.4.1.2 (PDB Primary Data), 2.1.3.15 (UniProt)
UniProt
Find proteins for P0ABD5 (Escherichia coli (strain K12))
Explore P0ABD5 
Go to UniProtKB:  P0ABD5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABD5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta304Escherichia coliMutation(s): 0 
Gene Names: accD
EC: 6.4.1.2 (PDB Primary Data), 2.1.3.15 (UniProt)
UniProt
Find proteins for P0A9Q5 (Escherichia coli (strain K12))
Explore P0A9Q5 
Go to UniProtKB:  P0A9Q5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9Q5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.261 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.257 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.257 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.729α = 90
b = 156.728β = 90
c = 192.824γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
MAR345data collection

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2006-12-12 
  • Deposition Author(s): Bilder, P.W.

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-08-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary