5ZKA

Crystal structure of N-acetylneuraminate lyase from Fusobacterium nucleatum complexed with Pyruvate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 

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.


    Related Citations: 
    • Structural basis for substrate specificity and mechanism of N-acetyl-D-neuraminic acid lyase from Pasteurella multocida.
      Huynh, N.,Aye, A.,Li, Y.,Yu, H.,Cao, H.,Tiwari, V.K.,Shin, D.W.,Chen, X.,Fisher, A.J.
      (2013) Biochemistry 52: 8570


    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
307Fusobacterium 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
N-acetylneuraminate lyase
B
296Fusobacterium 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KPI
Query on KPI
A
L-peptide linkingC9 H16 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 82.676α = 90.00
b = 86.568β = 90.00
c = 89.987γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

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: 2018-12-05
    Type: Initial release