3WY7

Crystal structure of Mycobacterium smegmatis 7-Keto-8-aminopelargonic acid (KAPA) synthase BioF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


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Literature

Structure and function of Mycobacterium smegmatis 7-keto-8-aminopelargonic acid (KAPA) synthase

Fan, S.H.Li, D.F.Wang, D.C.Fleming, J.Zhang, H.T.Zhou, Y.Zhou, L.Zhou, J.Chen, T.Chen, G.J.Zhang, X.E.Bi, L.J.

(2014) Int.J.Biochem.Cell Biol. 58C: 71-80

  • DOI: 10.1016/j.biocel.2014.11.006

  • PubMed Abstract: 
  • The biotin biosynthesis pathway is an attractive target for development of novel drugs against mycobacterial pathogens, however there are as yet no suitable inhibitors that target this pathway in mycobacteria. 7-Keto-8-aminopelargonic acid synthase ( ...

    The biotin biosynthesis pathway is an attractive target for development of novel drugs against mycobacterial pathogens, however there are as yet no suitable inhibitors that target this pathway in mycobacteria. 7-Keto-8-aminopelargonic acid synthase (KAPA synthase, BioF) is the enzyme which catalyzes the first committed step of the biotin synthesis pathway, but both its structure and function in mycobacteria remain unresolved. Here we present the crystal structure of Mycobacterium smegmatis BioF (MsBioF). The structure reveals an incomplete dimer, and the active site organization is similar to, but distinct from Escherichia coli 8-amino-7-oxononanoate synthase (EcAONS), the E. coli homologue of BioF. To investigate the influence of structural characteristics on the function of MsBioF, we deleted bioF in M. smegmatis and confirmed that BioF is required for growth in the absence of exogenous biotin. Based on structural and mutagenesis studies, we confirmed that pyridoxal 5'-phosphate (PLP) binding site residues His129, Lys235 and His200 are essential for MsBioF activity in vivo and residue Glu171 plays an important, but not essential role in MsBioF activity. The N-terminus (residues 1-37) is also essential for MsBioF activity in vivo. The structure and function of MsBioF reported here provides further insights for developing new anti-tuberculosis inhibitors aimed at the biotin synthesis pathway.


    Organizational Affiliation

    State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, China. Electronic address: guanjun@sdu.edu.cn.,The 4th People's Hospital, Foshan, Guangdong 528000, China.,National Laboratory of Biomacromolecules and CAS Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: zhangxe@sun5.ibp.ac.cn.,State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, China.,National Laboratory of Biomacromolecules and CAS Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,Center for Tuberculosis Control of Guangdong Province, Guangdong 510630, China.,National Laboratory of Biomacromolecules and CAS Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: blj@ibp.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
8-amino-7-oxononanoate synthase
A, B, C, D
404Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: bioF
EC: 2.3.1.47
Find proteins for A0QX65 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QX65
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.880α = 90.00
b = 91.680β = 97.80
c = 109.840γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASESphasing
ADSCdata collection
MOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release