An artificially constructed dimer through deformation of a short zinc-binding loop

Jimin Park, Mi Sun Kim, Keehyoung Joo, Jooyoung Lee, Dong Hae Shin

Research output: Contribution to journalArticlepeer-review


We have analyzed the crystal structure of the dimeric form of D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase from Burkholderia thailandensis (BtGmhB), catalyzing the removal of the phosphate at the 7 position of D-glycero-D-manno-heptose-1,7-bisphosphate. The crystal structure of BtGmhB revealed a dimeric form caused by a disruption of a short zinc-binding loop. The dimeric BtGmhB structure was induced by triggering the loss of Zn2 + via the protonation of cysteine residues at pH 4.8 of the crystallization condition. Similarly, the addition of EDTA also causes the dimerization of BtGmhB. It appears there are two dimeric forms in solution with and without the disulfide bridge mediated by Cys95. The disulfide-free dimer produced by the loss of Zn2 + in the short zinc-binding loop is further converted to a stable disulfide-bonded dimer in vitro. Though the two dimeric forms are reversible, both of them are inactive due to a deformation of the active site. Single and triple mutant experiments confirmed the presence of two dimeric forms in vitro. Phosphatase assay results showed that only a zinc-bound monomeric form contains catalytic activity in contrast to the inactive zinc-free dimeric forms. The monomer-to-dimer transition caused by the loss of Zn2 + observed in this study is an example of reversal phenomenon caused by artificial proteins containing protein engineered zinc-finger motifs where the monomer-to-dimer transitions occurred in the presence of Zn2 +. Therefore, this unusual dimerization process may be applicable to designing proteins possessing a short zinc-binding loop with a novel regulatory role.

Original languageEnglish
Pages (from-to)205-213
Number of pages9
JournalBiochimica et Biophysica Acta - Proteins and Proteomics
Issue number2
StatePublished - Feb 2018

Bibliographical note

Funding Information:
We are grateful to the staffs at both Pohang Light Source and Advanced Light Source. We thank KIAS Center for Advanced Computation for providing computing resources. We also thank Dr. Andrew Brooks for manuscript editing. This work was supported by the Basic Science Research Program ( 2015R1D1A1A01058942 , 2016R1A6A3A11935354 ) and Creative Research Initiatives Center for in silico Protein Science ( 2008-0061987 ) funded by the National Research Foundation of Korea grant granted by the Ministry of Education, Science and Technology, Republic of Korea (MEST). J. Park was supported by Brain Korea 21 (BK21) Project.

Publisher Copyright:
© 2017 Elsevier B.V.


  • Artificial dimer
  • GmhB
  • Protein engineering
  • Zinc-binding loop


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