5ZJM | pdb_00005zjm

Crystal structure of N-acetylneuraminate lyase from Fusobacterium nucleatum

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.245 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 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: https://doi.org/10.1107/S2053230X18012992
  • Primary Citation Related Structures: 
    5ZJM, 5ZKA

  • 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. 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.

Macromolecule Content 

  • Total Structure Weight: 131.92 kDa 
  • Atom Count: 8,907 
  • Modeled Residue Count: 1,162 
  • Deposited Residue Count: 1,164 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N-acetylneuraminate lyase
A, B, C, D
291Fusobacterium nucleatum subsp. nucleatum ATCC 25586Mutation(s): 0 
Gene Names: nanA
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RDN6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.165α = 90
b = 108.977β = 96.88
c = 141.137γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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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: 2019-01-23
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description