6JN1

Structure of H247A mutant peptidoglycan peptidase complex with penta peptide

  • Classification: HYDROLASE
  • Organism(s): Campylobacter jejuni, synthetic construct
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2019-03-13 Released: 2020-01-15 
  • Deposition Author(s): Min, K.J., An, D.R., Yoon, H.J., Suh, S.W., Lee, H.H.
  • Funding Organization(s): National Research Foundation (Korea), Ministry of Science, ICT and Future Planning, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Peptidoglycan reshaping by a noncanonical peptidase for helical cell shape in Campylobacter jejuni.

Min, K., An, D.R., Yoon, H.J., Rana, N., Park, J.S., Kim, J., Lee, M., Hesek, D., Ryu, S., Kim, B.M., Mobashery, S., Suh, S.W., Lee, H.H.

(2020) Nat Commun 11: 458-458

  • DOI: https://doi.org/10.1038/s41467-019-13934-4
  • Primary Citation of Related Structures:  
    6JMX, 6JMY, 6JMZ, 6JN0, 6JN1, 6JN7, 6JN8, 6KV1

  • PubMed Abstract: 

    • Assembly of the peptidoglycan is crucial in maintaining viability of bacteria and in defining bacterial cell shapes, both of which are important for existence in the ecological niche that the organism occupies. Here, eight crystal structures for a member of the cell-shape-determining class of Campylobacter jejuni, the peptidoglycan peptidase 3 (Pgp3), are reported ...

    Assembly of the peptidoglycan is crucial in maintaining viability of bacteria and in defining bacterial cell shapes, both of which are important for existence in the ecological niche that the organism occupies. Here, eight crystal structures for a member of the cell-shape-determining class of Campylobacter jejuni, the peptidoglycan peptidase 3 (Pgp3), are reported. Characterization of the turnover chemistry of Pgp3 reveals cell wall D,D-endopeptidase and D,D-carboxypeptidase activities. Catalysis is accompanied by large conformational changes upon peptidoglycan binding, whereby a loop regulates access to the active site. Furthermore, prior hydrolysis of the crosslinked peptide stem from the saccharide backbone of the peptidoglycan on one side is a pre-requisite for its recognition and turnover by Pgp3. These analyses reveal the noncanonical nature of the transformations at the core of the events that define the morphological shape for C. jejuni as an intestinal pathogen.

    Organizational Affiliation: 

    Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea. hyungholee@snu.ac.kr.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidase M23254Campylobacter jejuniMutation(s): 1 
Gene Names: A8118_01115
UniProt
Find proteins for A0A1J6PWI8 (Campylobacter jejuni)
Explore A0A1J6PWI8 
Go to UniProtKB:  A0A1J6PWI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1J6PWI8
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
C0O-DAL-DAL3synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.256α = 90
b = 114.256β = 90
c = 55.88γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2015R1A5A1008958
National Research Foundation (Korea)Korea, Republic Of2015R1C1A1A01054842
National Research Foundation (Korea)Korea, Republic Of2018R1A2B2008142
Ministry of Science, ICT and Future PlanningKorea, Republic Of2014M1A8A1049296
Ministry of Science, ICT and Future PlanningKorea, Republic Of2013R1A2A1A05067303
National Research Foundation (Korea)Korea, Republic Of2018R1D1A1B07040808
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI090348
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM61629

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Database references
  • Version 1.2: 2022-03-23
    Changes: Author supporting evidence, Database references, Derived calculations