4B4U

Crystal structure of Acinetobacter baumannii N5, N10- methylenetetrahydrofolate dehydrogenase-cyclohydrolase (FolD) complexed with NADP cofactor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

Acinetobacter Baumannii Fold Ligand Complexes; Potent Inhibitors of Folate Metabolism and a Re-Evaluation of the Ly374571 Structure.

Eadsforth, T.C., Maluf, F.V., Hunter, W.N.

(2012) FEBS J 279: 4350

  • DOI: https://doi.org/10.1111/febs.12025
  • Primary Citation of Related Structures:  
    4B4U, 4B4V, 4B4W

  • PubMed Abstract: 

    The bifunctional N(5),N(10)-methylenetetrahydrofolate dehydrogenase/cyclohydrolase (DHCH or FolD), which is widely distributed in prokaryotes and eukaryotes, is involved in the biosynthesis of folate cofactors that are essential for growth and cellular development. The enzyme activities represent a potential antimicrobial drug target. We have characterized the kinetic properties of FolD from the Gram-negative pathogen Acinetobacter baumanni and determined high-resolution crystal structures of complexes with a cofactor and two potent inhibitors. The data reveal new details with respect to the molecular basis of catalysis and potent inhibition. A unexpected finding was that our crystallographic data revealed a different structure for LY374571 (an inhibitor studied as an antifolate) than that previously published. The implications of this observation are discussed.

    • Organizational Affiliation: 

    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BIFUNCTIONAL PROTEIN FOLD
A, B
303Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
EC: 1.5.1.5 (PDB Primary Data), 3.5.4.9 (PDB Primary Data)
UniProt
Find proteins for D0CBC8 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
Explore D0CBC8 
Go to UniProtKB:  D0CBC8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0CBC8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]		NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
PEG
Query on PEG
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I [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO
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G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.036α = 90
b = 80.126β = 107.11
c = 68.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-10-24
    Changes: Database references
  • Version 1.2: 2012-12-05
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description