Insights into a novel NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


A Secreted NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida Cleaves the Peptidoglycan of Potentially Competing Bacteria.

Lisboa, J.Pereira, C.Rifflet, A.Ayala, J.Terceti, M.S.Barca, A.V.Rodrigues, I.Pereira, P.J.B.Osorio, C.R.Garcia-Del Portillo, F.Gomperts Boneca, I.do Vale, A.Dos Santos, N.M.S.

(2021) mSphere 6

  • DOI: https://doi.org/10.1128/mSphere.00736-20
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Peptidoglycan (PG) is a major component of the bacterial cell wall, forming a mesh-like structure enwrapping the bacteria that is essential for maintaining structural integrity and providing support for anchoring other components of the cell envelope. PG biogenesis is highly dynamic and requires multiple enzymes, including several hydrolases that cleave glycosidic or amide bonds in the PG. This work describes the structural and functional characterization of an NlpC/P60-containing peptidase from Photobacterium damselae subsp. piscicida ( Phdp ), a Gram-negative bacterium that causes high mortality of warm-water marine fish with great impact for the aquaculture industry. PnpA ( P hotobacterium N lpC-like p rotein A ) has a four-domain structure with a hydrophobic and narrow access to the catalytic center and specificity for the γ-d-glutamyl- meso -diaminopimelic acid bond. However, PnpA does not cleave the PG of Phdp or PG of several Gram-negative and Gram-positive bacterial species. Interestingly, it is secreted by the Phdp type II secretion system and degrades the PG of Vibrio anguillarum and Vibrio vulnificus This suggests that PnpA is used by Phdp to gain an advantage over bacteria that compete for the same resources or to obtain nutrients in nutrient-scarce environments. Comparison of the muropeptide composition of PG susceptible and resistant to the catalytic activity of PnpA showed that the global content of muropeptides is similar, suggesting that susceptibility to PnpA is determined by the three-dimensional organization of the muropeptides in the PG. IMPORTANCE Peptidoglycan (PG) is a major component of the bacterial cell wall formed by long chains of two alternating sugars interconnected by short peptides, generating a mesh-like structure that enwraps the bacterial cell. Although PG provides structural integrity and support for anchoring other components of the cell envelope, it is constantly being remodeled through the action of specific enzymes that cleave or join its components. Here, it is shown that Photobacterium damselae subsp. piscicida , a bacterium that causes high mortality in warm-water marine fish, produces PnpA, an enzyme that is secreted into the environment and is able to cleave the PG of potentially competing bacteria, either to gain a competitive advantage and/or to obtain nutrients. The specificity of PnpA for the PG of some bacteria and its inability to cleave others may be explained by differences in the structure of the PG mesh and not by different muropeptide composition.

  • Organizational Affiliation

    Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal johnny.lisboa@ibmc.up.pt nsantos@ibmc.up.pt.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide-binding protein
A, B
499Photobacterium damselae subsp. piscicidaMutation(s): 0 
Gene Names: E4T26_07800FA893_15790PDPJ_2_00460
Find proteins for A0A1V1VDL8 (Photobacterium damsela subsp. piscicida)
Explore A0A1V1VDL8 
Go to UniProtKB:  A0A1V1VDL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1V1VDL8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PEG

Download Ideal Coordinates CCD File 
C4 H10 O3
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
U [auth A],
UA [auth B],
V [auth A]
C2 H6 O2
Query on BCT

Download Ideal Coordinates CCD File 
C H O3
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
X [auth B]
Y [auth B]
C [auth A],
D [auth A],
E [auth A],
X [auth B],
Y [auth B],
Z [auth B]
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on OCS
A, B
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.578α = 90
b = 109.966β = 90
c = 130.936γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalPTDC/CVT-CVT/30018/2017

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Structure summary
  • Version 1.2: 2021-02-24
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description