Crystal structure of the soluble domain of LipC, a membrane fusion protein of a type I secretion system

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 

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Structural Basis for the Serratia marcescens Lipase Secretion System: Crystal Structures of the Membrane Fusion Protein and Nucleotide-Binding Domain.

Murata, D.Okano, H.Angkawidjaja, C.Akutsu, M.Tanaka, S.I.Kitahara, K.Yoshizawa, T.Matsumura, H.Kado, Y.Mizohata, E.Inoue, T.Sano, S.Koga, Y.Kanaya, S.Takano, K.

(2017) Biochemistry 56: 6281-6291

  • DOI: https://doi.org/10.1021/acs.biochem.7b00985
  • Primary Citation of Related Structures:  
    5NEN, 5X7K

  • PubMed Abstract: 

    Serratia marcescens secretes a lipase, LipA, through a type I secretion system (T1SS). The T1SS for LipA, the Lip system, is composed of an inner membrane ABC transporter with its nucleotide-binding domains (NBD), LipB, a membrane fusion protein, LipC, and an outer membrane channel protein, LipD. Passenger protein secreted by this system has been functionally and structurally characterized well, but relatively little information about the transporter complex is available. Here, we report the crystallographic studies of LipC without the membrane anchor region, LipC-, and the NBD of LipB (LipB-NBD). LipC- crystallographic analysis has led to the determination of the structure of the long α-helical and lipoyl domains, but not the area where it interacts with LipB, suggesting that the region is flexible without LipB. The long α-helical domain has three α-helices, which interacts with LipD in the periplasm. LipB-NBD has the common overall architecture and ATP hydrolysis activity of ABC transporter NBDs. Using the predicted models of full-length LipB and LipD, the overall structural insight into the Lip system is discussed.

  • Organizational Affiliation

    Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipase C
A, B
448Serratia marcescensMutation(s): 0 
Gene Names: lipC
Find proteins for Q54457 (Serratia marcescens)
Explore Q54457 
Go to UniProtKB:  Q54457
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54457
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.314α = 90
b = 126.314β = 90
c = 71.405γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection