UCR

Biochemistry Department



Fan Research Group


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Welcome to the Fan Research Group

Research

Our research focuses on proteins and enzymes playing key roles in important biological processes. We apply a multi-disciplinary approach including protein X-ray crystallography, biochemistry and molecular biology techniques to study the structure and function of these proteins as well as their interactions with substrates and/or protein partners. Three major projects are currently carried out in our lab: 

 

1.)  DNA repair and recombination: we currently focus on DNA helicases and translocases involved in DNA repair pathways.figure 1 XPB is a helicase required for both transcription and DNA repair. It was reported that XPB functions either as a molecular wrench or DNA translocase.We believe that domain rotation induced by ATP binding and hydrolysis plays a key role for XPB to open dsDNA at the promoter region in transcription initiation and around the lesion in DNA repair. Crystal structures of XPB homologs from archaeal Archaeoglobus fulgidus (AfXPB) and Sulfolobus tokodaii (StXPB2) reveal four different conformations (named open, A, B, and C in the figure on the left) showing various stages between the open and closed ATP-binding groove.  Small angle X-ray scattering data further support the domain rotation induced by ATP-binding.

 

2.)  Amino acid/peptide metabolism: we have collaborated with others to study enzymatic mechanisms of tryptophan synthase and aminopeptidases;
Figures
Left:
the cross-section view of tryptophan synthase to show the substrate channel that allows the delivery of indole from the active site A to the active site B for the b-reaction. One chemical (green) is trapped in the channel and at the active site A.
Right: stereo view of the active site of leucine-aminopeptidase from tomato with microginin FR1 (green) modeled to show substrate selection by the enzyme. 

3.)  Bacteria-host interactions: we are interested in the structure and functions of proteins encoded by hypothetical Xanthomonas genes associated with citrus canker. Crystal structure of the protein product encoded by Xanthomonas gene 2369 reveals the molecular basis for its FMN binding property.

figure 5

 

 

 

 

 

Selected Publications
  •  K. DuPrez, M. Scranton, L. Walling*, and Li Fan* (2016). “Structure insights for the chaperone activity enhancement by mutation K354E in tomato acidic leucine aminopeptidase”. Acta Cryst. D72: 694-702. doi:10.1107/S205979831600509X.  (impact factor: 2.512).  PMID: 27139632
  • E. Hilario, B. G. Caulkins, Y.M.M. Huang, Chang, Chia-en; M. F. Dunn*; L. J. Mueller*; Li Fan* (2016). “Visualizing the tunnel in tryptophan synthase with crystallography: Insights into a selective filter for accommodating indole and rejecting water” Biochimica et Biophysica Acta - Proteins and Proteomics 1864 (3): 268-279. (Impact factor: 3.191). PMID: 26708480 http://www.sciencedirect.com/science/article/pii/S1570963915003052

  • Catalytic roles of βLys87 in tryptophan synthase: 15N solid state NMR studies.Caulkins BG, Yang C, Hilario E, Fan L, Dunn MF, Mueller LJ.Biochim Biophys Acta. 2015 Feb 14. pii: S1570-9639(15)00039-4.doi: 10.1016/j.bbapap.2015.02.003. [Epub ahead of print] PMID: 25688830.(impact factor: 3.191)
  • XPB: An unconventional SF2 DNA helicase.Fan L, DuPrez KT.Prog Biophys Mol Biol. 2015 Mar;117(2-3):174-81.doi: 10.1016/j.pbiomolbio.2014.12.005. Epub 2015 Jan 30. Review.PMID: 25641424. (impact factor: 2.274)

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