Crystal structure of BioH from Klebsiella pneumonia

Experimental Data Snapshot

  • Resolution: 2.26 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 

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Structural insight into the carboxylesterase BioH from Klebsiella pneumoniae.

Wang, L.Chen, Y.Shang, F.Liu, W.Lan, J.Gao, P.Ha, N.C.Nam, K.H.Dong, Y.Quan, C.Xu, Y.

(2019) Biochem Biophys Res Commun 520: 538-543

  • DOI: https://doi.org/10.1016/j.bbrc.2019.10.050
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The BioH carboxylesterase which is a typical α/β-hydrolase enzyme involved in biotin synthetic pathway in most bacteria. BioH acts as a gatekeeper and blocks the further elongation of its substrate. In the pathogen Klebsiella pneumoniae, BioH plays a critical role in the biosynthesis of biotin. To better understand the molecular function of BioH, we determined the crystal structure of BioH from K. pneumoniae at 2.26 Å resolution using X-ray crystallography. The structure of KpBioH consists of an α-β-α sandwich domain and a cap domain. B-factor analysis revealed that the α-β-α sandwich domain is a rigid structure, while the loops in the cap domain shows the structural flexibility. The active site of KpBioH contains the catalytic triad (Ser82-Asp207-His235) on the interface of the α-β-α sandwich domain, which is surrounded by the cap domain. Size exclusion chromatography shows that KpBioH prefers the monomeric state in solution, whereas two-fold symmetric dimeric formation of KpBioH was observed in the asymmetric unit, the conserved Cys31-based disulfide bonds can maintain the irreversible dimeric formation of KpBioH. Our study provides important structural insight for understanding the molecular mechanisms of KpBioH and its homologous proteins.

  • Organizational Affiliation

    School of Life Science and Biotechnology, Dalian University of Technology, No 2 Linggong Road, Dalian, 116024, Liaoning, China; Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pimeloyl-[acyl-carrier protein] methyl ester esterase
A, B, C, D, E
A, B, C, D, E, F
257Klebsiella pneumoniaeMutation(s): 0 
Gene Names: bioH
Find proteins for A6TF35 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6TF35 
Go to UniProtKB:  A6TF35
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6TF35
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.26 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.642α = 90
b = 109.531β = 90
c = 292.857γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31200556
National Natural Science Foundation of ChinaChina21272031

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references