5D6J

Crystal structure of a mycobacterial protein

• PDB DOI: https://doi.org/10.2210/pdb5D6J/pdb

• Classification: LIGASE/PROTEIN BINDING
• Organism(s): Mycolicibacterium smegmatis MC2 155, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


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

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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 

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

• PubMed: 26628098 
• DOI: https://doi.org/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 2.4 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 77.53 kDa 
• Atom Count: 5,943 
• Modelled Residue Count: 704 
• Deposited Residue Count: 704 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA synthase	A	630	Mycolicibacterium smegmatis MC2 155	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3	B	74	Saccharomyces cerevisiae S288C	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 122.211	α = 90
b = 122.211	β = 90
c = 142.588	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Li, W.J., Bi, L.J.

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Funding Organization	Location	Grant Number
	China	--

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations