8T1Y

Crystal Structure of Porphyromonas gingivalis Sialidase (PG_0352) Bound to Neu5Ac2en (DANA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Functional and structural analyses reveal that a dual domain sialidase protects bacteria from complement killing through desialylation of complement factors.

Clark, N.D.Pham, C.Kurniyati, K.Sze, C.W.Coleman, L.Fu, Q.Zhang, S.Malkowski, M.G.Li, C.

(2023) PLoS Pathog 19: e1011674-e1011674

  • DOI: https://doi.org/10.1371/journal.ppat.1011674
  • Primary Citation of Related Structures:  
    8FEB, 8T1Y, 8T1Z, 8T24, 8T26, 8T27

  • PubMed Abstract: 

    The complement system is the first line of innate immune defense against microbial infections. To survive in humans and cause infections, bacterial pathogens have developed sophisticated mechanisms to subvert the complement-mediated bactericidal activity. There are reports that sialidases, also known as neuraminidases, are implicated in bacterial complement resistance; however, its underlying molecular mechanism remains elusive. Several complement proteins (e.g., C1q, C4, and C5) and regulators (e.g., factor H and C4bp) are modified by various sialoglycans (glycans with terminal sialic acids), which are essential for their functions. This report provides both functional and structural evidence that bacterial sialidases can disarm the complement system via desialylating key complement proteins and regulators. The oral bacterium Porphyromonas gingivalis, a "keystone" pathogen of periodontitis, produces a dual domain sialidase (PG0352). Biochemical analyses reveal that PG0352 can desialylate human serum and complement factors and thus protect bacteria from serum killing. Structural analyses show that PG0352 contains a N-terminal carbohydrate-binding module (CBM) and a C-terminal sialidase domain that exhibits a canonical six-bladed β-propeller sialidase fold with each blade composed of 3-4 antiparallel β-strands. Follow-up functional studies show that PG0352 forms monomers and is active in a broad range of pH. While PG0352 can remove both N-acetylneuraminic acid (Neu5Ac) and N-glycolyl-neuraminic acid (Neu5Gc), it has a higher affinity to Neu5Ac, the most abundant sialic acid in humans. Structural and functional analyses further demonstrate that the CBM binds to carbohydrates and serum glycoproteins. The results shown in this report provide new insights into understanding the role of sialidases in bacterial virulence and open a new avenue to investigate the molecular mechanisms of bacterial complement resistance.


  • Organizational Affiliation

    Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, the State University of New York, Buffalo, New York, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sialidase509Porphyromonas gingivalisMutation(s): 0 
Gene Names: PG_0352
UniProt
Find proteins for Q7MX62 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore Q7MX62 
Go to UniProtKB:  Q7MX62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MX62
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DAN (Subject of Investigation/LOI)
Query on DAN

Download Ideal Coordinates CCD File 
B [auth A]2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H17 N O8
JINJZWSZQKHCIP-UFGQHTETSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
H [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
C [auth A],
E [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
G [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.517α = 90
b = 55.9β = 115.49
c = 84.478γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
xia2data scaling
DIALSdata reduction
xia2data reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United States5R01DE023080-10

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Database references