6IK4 | pdb_00006ik4

A Novel M23 Metalloprotease Pseudoalterin from Deep-sea

• PDB DOI: https://doi.org/10.2210/pdb6IK4/pdb

• Classification: HYDROLASE
• Organism(s): Pseudoalteromonas sp. CF6-2
• Mutation(s): No 


• Deposited: 2018-10-14 Released: 2019-10-16 
• Deposition Author(s): Zhao, H.L., Tang, B.L., Yang, J., Chen, X.L., Zhang, Y.Z.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

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

• PubMed: 31941905 
• DOI: https://doi.org/10.1038/s41467-019-14133-x
• Primary Citation 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.

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Organizational Affiliation: 
• State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.
College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.
Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China.
School of Life Sciences, University of Warwick, Coventry, UK.
SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, 200136, China.
Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia.
State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China. [e-mail].
College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China. [e-mail].
Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.55 kDa 
• Atom Count: 1,557 
• Modeled Residue Count: 173 
• Deposited Residue Count: 173 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elastinolytic metalloprotease	A	173	Pseudoalteromonas sp. CF6-2	Mutation(s): 0
UniProt
Find proteins for E7D102 (Pseudoalteromonas sp. CF6-2) Explore E7D102  Go to UniProtKB:  E7D102

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.841	α = 90
b = 82.443	β = 90
c = 73.419	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-16 
Deposition Author(s): Zhao, H.L., Tang, B.L., Yang, J., Chen, X.L., Zhang, Y.Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31670063
National Natural Science Foundation of China	China	U1706207

Revision History  

• 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
• Version 1.3: 2024-10-09
  Changes: Structure summary