5ZJM

Crystal structure of N-acetylneuraminate lyase from Fusobacterium nucleatum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.323 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structures and kinetics of N-acetylneuraminate lyase from Fusobacterium nucleatum

Kumar, J.P.Rao, H.Nayak, V.Ramaswamy, S.

(2018) Acta Crystallogr F Struct Biol Commun 74: 725-732

  • DOI: 10.1107/S2053230X18012992
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N-Acetyl-D-neuraminic acid lyase (NanA) catalyzes the breakdown of sialic acid (Neu5Ac) to N-acetyl-D-mannosamine (ManNAc) and pyruvate. NanA plays a key role in Neu5Ac catabolism in many pathogenic and bacterial commensals where sialic acid is avail ...

    N-Acetyl-D-neuraminic acid lyase (NanA) catalyzes the breakdown of sialic acid (Neu5Ac) to N-acetyl-D-mannosamine (ManNAc) and pyruvate. NanA plays a key role in Neu5Ac catabolism in many pathogenic and bacterial commensals where sialic acid is available as a carbon and nitrogen source. Several pathogens or commensals decorate their surfaces with sialic acids as a strategy to escape host innate immunity. Catabolism of sialic acid is key to a range of host-pathogen interactions. In this study, atomic resolution structures of NanA from Fusobacterium nucleatum (FnNanA) in ligand-free and ligand-bound forms are reported at 2.32 and 1.76 Å resolution, respectively. F. nucleatum is a Gram-negative pathogen that causes gingival and periodontal diseases in human hosts. Like other bacterial N-acetylneuraminate lyases, FnNanA also shares the triosephosphate isomerase (TIM)-barrel fold. As observed in other homologous enzymes, FnNanA forms a tetramer. In order to characterize the structure-function relationship, the steady-state kinetic parameters of the enzyme are also reported.


    Organizational Affiliation

    Technologies for the Advancement of Science, Institute for Stem Cell Biology and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka 560 065, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetylneuraminate lyase
A, B, C, D
291Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131)Mutation(s): 0 
Gene Names: nanA
EC: 4.1.3.3
Find proteins for Q8RDN6 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131))
Go to UniProtKB:  Q8RDN6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.323 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.165α = 90.00
b = 108.977β = 96.88
c = 141.137γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
IndiaBT/IN/SWEDEN/41/SR/2013
IndiaBT/PR5081/INF/156/2012
IndiaBT/PR12422/MED/31/287/214
IndiaBT/INF/22/SP22660/2017

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release