5H5Y

Structure of Transferase mutant-C23S,C199S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for arginine glycosylation of host substrates by bacterial effector proteins.

Park, J.B.Kim, Y.H.Yoo, Y.Kim, J.Jun, S.H.Cho, J.W.El Qaidi, S.Walpole, S.Monaco, S.Garcia-Garcia, A.A.Wu, M.Hays, M.P.Hurtado-Guerrero, R.Angulo, J.Hardwidge, P.R.Shin, J.S.Cho, H.S.

(2018) Nat Commun 9: 4283-4283

  • DOI: 10.1038/s41467-018-06680-6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The bacterial effector proteins SseK and NleB glycosylate host proteins on arginine residues, leading to reduced NF-κB-dependent responses to infection. Salmonella SseK1 and SseK2 are E. coli NleB1 orthologs that behave as NleB1-like GTs, although th ...

    The bacterial effector proteins SseK and NleB glycosylate host proteins on arginine residues, leading to reduced NF-κB-dependent responses to infection. Salmonella SseK1 and SseK2 are E. coli NleB1 orthologs that behave as NleB1-like GTs, although they differ in protein substrate specificity. Here we report that these enzymes are retaining glycosyltransferases composed of a helix-loop-helix (HLH) domain, a lid domain, and a catalytic domain. A conserved HEN motif (His-Glu-Asn) in the active site is important for enzyme catalysis and bacterial virulence. We observe differences between SseK1 and SseK2 in interactions with substrates and identify substrate residues that are critical for enzyme recognition. Long Molecular Dynamics simulations suggest that the HLH domain determines substrate specificity and the lid-domain regulates the opening of the active site. Overall, our data suggest a front-face S N i mechanism, explain differences in activities among these effectors, and have implications for future drug development against enteric pathogens.


    Organizational Affiliation

    School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Fundación ARAID, 50018, Zaragoza, Spain. rhurtado@bifi.es.,College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA.,BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain.,BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain. rhurtado@bifi.es.,Department of Microbiology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Severance Biomedical Science Institute and Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea. jsshin6203@yuhs.ac.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea. hscho8@yonsei.ac.kr.,Department of Microbiology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea. jsshin6203@yuhs.ac.,Center for Electron Microscopy Research, Korea Basic Science Institute, Ochang, Chungbuk, 28119, Republic of Korea.,School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK. j.angulo@uea.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Non-LEE encoded effector protein NleB
A, B
326Escherichia coliMutation(s): 2 
Gene Names: nleB_1 (nleB, nleB2, nleB_2)
Find proteins for A0A0D7C3R7 (Escherichia coli)
Go to UniProtKB:  A0A0D7C3R7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.219 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 67.830α = 90.00
b = 95.550β = 90.00
c = 120.180γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
iMOSFLMdata reduction
REFMACphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-09-19
    Type: Data collection, Database references
  • Version 1.2: 2018-10-24
    Type: Data collection, Database references
  • Version 1.3: 2018-10-31
    Type: Data collection, Database references