5HM3

2.25 Angstrom Resolution Crystal Structure of Long-chain-fatty-acid-AMP Ligase FadD32 from Mycobacterium tuberculosis in complex with Inhibitor 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the Essential Mtb FadD32 Enzyme: A Promising Drug Target for Treating Tuberculosis.

Kuhn, M.L.Alexander, E.Minasov, G.Page, H.J.Warwrzak, Z.Shuvalova, L.Flores, K.J.Wilson, D.J.Shi, C.Aldrich, C.C.Anderson, W.F.

(2016) Acs Infect Dis. 2: 579-591

  • DOI: 10.1021/acsinfecdis.6b00082

  • PubMed Abstract: 
  • Mycolic acids are indispensible lipids of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), and contribute to the distinctive architecture and impermeability of the mycobacterial cell envelope. FadD32 plays a pivotal role in ...

    Mycolic acids are indispensible lipids of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), and contribute to the distinctive architecture and impermeability of the mycobacterial cell envelope. FadD32 plays a pivotal role in mycolic acid biosynthesis by functionally linking fatty acid synthase (FAS) and polyketide synthase (PKS) biosynthetic pathways. FadD32, a fatty acyl-AMP ligase (FAAL), represents one of the best genetically and chemically validated new TB drug targets. We have determined the three-dimensional crystal structure of Mtb FadD32 in complex with a ligand specifically designed to stabilize the catalytically active adenylate-conformation, which provides a foundation for structure-based drug design efforts against this essential protein. The structure also captures the unique interactions of a FAAL-specific insertion sequence and provides insight into the specificity and mechanism of fatty acid transfer.


    Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States; Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Long-chain-fatty-acid--AMP ligase FadD32
A
657Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: fadD32
EC: 6.2.1.-
Find proteins for O53580 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  O53580
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
649
Query on 649

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Download CCD File 
A
5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine
C27 H38 N6 O8 S
VLRIGNDIFPKPGQ-ZCIWVVNKSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
649IC50: 6800 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 62.779α = 90.00
b = 74.558β = 90.00
c = 127.762γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-09-07
    Type: Database references