6A0N | pdb_00006a0n

The crystal structure of apo-Lpg2622


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.233 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.195 (Depositor) 
  • R-Value Observed: 
    0.197 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6A0N

This is version 1.1 of the entry. See complete history

Literature

Structural characterization of the hypothetical protein Lpg2622, a new member of the C1 family peptidases from Legionella pneumophila

Gong, X.Zhao, X.Zhang, W.Wang, J.Chen, X.Hameed, M.F.Zhang, N.Ge, H.

(2018) FEBS Lett 592: 2798-2810

  • DOI: https://doi.org/10.1002/1873-3468.13210
  • Primary Citation Related Structures: 
    6A0N, 6A0Q

  • PubMed Abstract: 

    The Legionella pneumophila type II secretion system can promote bacterial growth under a wide variety of conditions and mediates the secretion of more than 25 proteins, including the uncharacterized effector Lpg2622. Here, we determined the crystal structures of apo-Lpg2622 and Lpg2622 in complex with the cysteine protease inhibitor E64. Structural analysis suggests that Lpg2622 belongs to the C1 family peptidases. Interestingly, unlike the other structurally resolved papain-like cysteine proteases, the propeptide of Lpg2622 forms a novel super-secondary structural fold (hairpin-turn-helix) and can be categorized into a new group. In addition, the N-terminal β-sheet of the Lpg2622 propeptide plays a regulatory role on enzymatic activity. This study enhances our understanding of the classification and regulatory mechanisms of the C1 family peptidases.


  • Organizational Affiliation
    • School of Life Sciences, Anhui University, Hefei, China.

Macromolecule Content 

  • Total Structure Weight: 76.16 kDa 
  • Atom Count: 5,226 
  • Modeled Residue Count: 649 
  • Deposited Residue Count: 686 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lpg2622
A, B
343Legionella pneumophila subsp. pneumophila str. Philadelphia 1Mutation(s): 0 
Gene Names: lpg2622
UniProt
Find proteins for Q5ZS97 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZS97 
Go to UniProtKB:  Q5ZS97
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZS97
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.233 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.195 (Depositor) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.628α = 90
b = 178.628β = 90
c = 113.227γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31270770
National Natural Science Foundation of ChinaChina31400641

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary