5D6J

Crystal structure of a mycobacterial protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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Literature

Crystal structure of FadD32, an enzyme essential for mycolic acid biosynthesis in mycobacteria.

Li, W., Gu, S., Fleming, J., Bi, L.

(2015) Sci Rep 5: 15493-15493

  • DOI: 10.1038/srep15493
  • Primary Citation of Related Structures:  
    5D6J, 5D6N

  • PubMed Abstract: 

    • Fatty acid degradation protein D32 (FadD32), an enzyme required for mycolic acid biosynthesis and essential for mycobacterial growth, has recently been identified as a valid and promising target for anti-tuberculosis drug development. Here we report the crystal structures of Mycobacterium smegmatis FadD32 in the apo and ATP-bound states at 2 ...

    Fatty acid degradation protein D32 (FadD32), an enzyme required for mycolic acid biosynthesis and essential for mycobacterial growth, has recently been identified as a valid and promising target for anti-tuberculosis drug development. Here we report the crystal structures of Mycobacterium smegmatis FadD32 in the apo and ATP-bound states at 2.4 Å and 2.25 Å resolution, respectively. FadD32 consists of two globular domains connected by a flexible linker. ATP binds in a cleft at the interface between the N- and C-terminal domains and its binding induces significant local conformational changes in FadD32. The binding sites of meromycolic acid and phosphopantetheine are identified by structural comparison with other members of the adenylating enzyme superfamily. These results will improve our understanding of the catalytic mechanism of FadD32 and help in the design of inhibitors of this essential enzyme.

    Organizational Affiliation: 

    Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl-CoA synthaseA630Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: fadD32, MSMEG_6393, MSMEI_6225
EC: 6.2.1.20
UniProt
Find proteins for A0R618 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R618 
Go to UniProtKB:  A0R618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R618
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3B74Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SMT3, YDR510W, D9719.15
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12306
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ATP Binding MOAD:  5D6J Kd: 3.60e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.211α = 90
b = 122.211β = 90
c = 142.588γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-08-12 
  • Released Date: 2016-03-02 
    • Deposition Author(s): Li, W.J., Bi, L.J.
Funding OrganizationLocationGrant Number
China--

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release