6IK4

A Novel M23 Metalloprotease Pseudoalterin from Deep-sea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A predator-prey interaction between a marine Pseudoalteromonas sp. and Gram-positive bacteria.

Tang, B.L.Yang, J.Chen, X.L.Wang, P.Zhao, H.L.Su, H.N.Li, C.Y.Yu, Y.Zhong, S.Wang, L.Lidbury, I.Ding, H.Wang, M.McMinn, A.Zhang, X.Y.Chen, Y.Zhang, Y.Z.

(2020) Nat Commun 11: 285-285

  • DOI: https://doi.org/10.1038/s41467-019-14133-x
  • Primary Citation of Related Structures:  
    6IK4

  • PubMed Abstract: 

    Predator-prey interactions play important roles in the cycling of marine organic matter. Here we show that a Gram-negative bacterium isolated from marine sediments (Pseudoalteromonas sp. strain CF6-2) can kill Gram-positive bacteria of diverse peptidoglycan (PG) chemotypes by secreting the metalloprotease pseudoalterin. Secretion of the enzyme requires a Type II secretion system. Pseudoalterin binds to the glycan strands of Gram positive bacterial PG and degrades the PG peptide chains, leading to cell death. The released nutrients, including PG-derived D-amino acids, can then be utilized by strain CF6-2 for growth. Pseudoalterin synthesis is induced by PG degradation products such as glycine and glycine-rich oligopeptides. Genes encoding putative pseudoalterin-like proteins are found in many other marine bacteria. This study reveals a new microbial interaction in the ocean.


  • Organizational Affiliation

    State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elastinolytic metalloprotease173Pseudoalteromonas sp. CF6-2Mutation(s): 0 
UniProt
Find proteins for E7D102 (Pseudoalteromonas sp. CF6-2)
Explore E7D102 
Go to UniProtKB:  E7D102
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE7D102
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.841α = 90
b = 82.443β = 90
c = 73.419γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31670063
National Natural Science Foundation of ChinaChinaU1706207

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description