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 
  • R-Value Observed: 0.188 

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:  
    5ZKA, 5ZJM

  • 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 available as a carbon and nitrogen source ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-acetylneuraminate lyaseA307Fusobacterium nucleatum subsp. nucleatum ATCC 25586Mutation(s): 0 
Gene Names: nanAFN1475
EC: 4.1.3.3
UniProt
Find proteins for Q8RDN6 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355))
Explore Q8RDN6 
Go to UniProtKB:  Q8RDN6
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N-acetylneuraminate lyaseB296Fusobacterium nucleatum subsp. nucleatum ATCC 25586Mutation(s): 0 
Gene Names: nanAFN1475
EC: 4.1.3.3
UniProt
Find proteins for Q8RDN6 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355))
Explore Q8RDN6 
Go to UniProtKB:  Q8RDN6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KPI
Query on KPI
AL-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 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.676α = 90
b = 86.568β = 90
c = 89.987γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report




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  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release