PDBsum entry 2vk5

Go to PDB code: 
protein ligands metals links
Hydrolase PDB id
Protein chain
449 a.a. *
GOL ×2
_CA ×2
Waters ×1030
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: The structure of clostridium perfringens nani sialidase and its catalytic intermediates
Structure: Exo-alpha-sialidase. Chain: a. Fragment: catalytic domain, residues 243-694. Synonym: sialidase. Engineered: yes
Source: Clostridium perfringens. Organism_taxid: 1502. Expressed in: escherichia coli. Expression_system_taxid: 562
0.97Å     R-factor:   not given    
Authors: S.L.Newstead,J.A.Potter,J.C.Wilson,G.Xu,C.H.Chien,A.G.Watts, S.G.Withers,G.L.Taylor
Key ref:
S.L.Newstead et al. (2008). The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates. J Biol Chem, 283, 9080-9088. PubMed id: 18218621 DOI: 10.1074/jbc.M710247200
17-Dec-07     Release date:   22-Jan-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q59310  (Q59310_CLOPF) -  Exo-alpha-sialidase
694 a.a.
449 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Exo-alpha-sialidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     exo-alpha-sialidase activity     1 term  


DOI no: 10.1074/jbc.M710247200 J Biol Chem 283:9080-9088 (2008)
PubMed id: 18218621  
The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates.
S.L.Newstead, J.A.Potter, J.C.Wilson, G.Xu, C.H.Chien, A.G.Watts, S.G.Withers, G.L.Taylor.
Clostridium perfringens is a Gram-positive bacterium responsible for bacteremia, gas gangrene, and occasionally food poisoning. Its genome encodes three sialidases, nanH, nanI, and nanJ, that are involved in the removal of sialic acids from a variety of glycoconjugates and that play a role in bacterial nutrition and pathogenesis. Recent studies on trypanosomal (trans-) sialidases have suggested that catalysis in all sialidases may proceed via a covalent intermediate similar to that of other retaining glycosidases. Here we provide further evidence to support this suggestion by reporting the 0.97A resolution atomic structure of the catalytic domain of the C. perfringens NanI sialidase, and complexes with its substrate sialic acid (N-acetylneuramic acid) also to 0.97A resolution, with a transition-state analogue (2-deoxy-2,3-dehydro-N-acetylneuraminic acid) to 1.5A resolution, and with a covalent intermediate formed using a fluorinated sialic acid analogue to 1.2A resolution. Together, these structures provide high resolution snapshots along the catalytic pathway. The crystal structures suggested that NanI is able to hydrate 2-deoxy-2,3-dehydro-N-acetylneuraminic acid to N-acetylneuramic acid. This was confirmed by NMR, and a mechanism for this activity is suggested.
  Selected figure(s)  
Figure 4.
FIGURE 4. Stereo views of the NanI active site. A, complex with Neu5Ac showing the hydrogen-bonding interactions as green dotted lines. B, superposition of the three ligand complexes and ligand free structure: Neu5Ac with yellow carbons, Neu5Ac2en with magenta carbons, and the covalent fluorinated ligand with cyan carbons.
Figure 6.
FIGURE 6. Proposed mechanism for the hydration of Neu5Ac2en to Neu5Ac.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 9080-9088) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20978010 D.C.Watson, S.Leclerc, W.W.Wakarchuk, and N.M.Young (2011).
Enzymatic synthesis and properties of glycoconjugates with legionaminic acid as a replacement for neuraminic acid.
  Glycobiology, 21, 99.  
20511247 A.Albohy, M.D.Li, R.B.Zheng, C.Zou, and C.W.Cairo (2010).
Insight into substrate recognition and catalysis by the human neuraminidase 3 (NEU3) through molecular modeling and site-directed mutagenesis.
  Glycobiology, 20, 1127-1138.  
20659292 C.M.Stead, J.Zhao, C.R.Raetz, and M.S.Trent (2010).
Removal of the outer Kdo from Helicobacter pylori lipopolysaccharide and its impact on the bacterial surface.
  Mol Microbiol, 78, 837-852.  
20662782 J.Zhao, and C.R.Raetz (2010).
A two-component Kdo hydrolase in the inner membrane of Francisella novicida.
  Mol Microbiol, 78, 820-836.  
20007980 S.Kim, D.B.Oh, O.Kwon, and H.A.Kang (2010).
Identification and functional characterization of the NanH extracellular sialidase from Corynebacterium diphtheriae.
  J Biochem, 147, 523-533.  
19564377 D.Parker, G.Soong, P.Planet, J.Brower, A.J.Ratner, and A.Prince (2009).
The NanA neuraminidase of Streptococcus pneumoniae is involved in biofilm formation.
  Infect Immun, 77, 3722-3730.  
19714866 D.Wang, S.Zaitsev, G.Taylor, A.d'Azzo, and E.Bonten (2009).
Protective protein/cathepsin A rescues N-glycosylation defects in neuraminidase-1.
  Biochim Biophys Acta, 1790, 275-282.  
19594936 E.M.Quistgaard, and S.S.Thirup (2009).
Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families.
  BMC Struct Biol, 9, 46.  
19651873 M.Chiarezza, D.Lyras, S.J.Pidot, M.Flores-Díaz, M.M.Awad, C.L.Kennedy, L.M.Cordner, T.Phumoonna, R.Poon, M.L.Hughes, J.J.Emmins, A.Alape-Girón, and J.I.Rood (2009).
The NanI and NanJ sialidases of Clostridium perfringens are not essential for virulence.
  Infect Immun, 77, 4421-4428.  
19329630 M.May, and D.R.Brown (2009).
Diversifying and stabilizing selection of sialidase and N-acetylneuraminate catabolism in Mycoplasma synoviae.
  J Bacteriol, 191, 3588-3593.  
19279191 R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, and A.Kuno (2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
  J Biochem, 146, 61-70.
PDB codes: 2d1z 2d20 2d22 2d23 2d24
19411257 T.J.Morley, L.M.Willis, C.Whitfield, W.W.Wakarchuk, and S.G.Withers (2009).
A new sialidase mechanism: bacteriophage K1F endo-sialidase is an inverting glycosidase.
  J Biol Chem, 284, 17404-17410.  
18625334 A.Buschiazzo, and P.M.Alzari (2008).
Structural insights into sialic acid enzymology.
  Curr Opin Chem Biol, 12, 565-572.  
  18772331 A.Hinek, T.D.Bodnaruk, S.Bunda, Y.Wang, and K.Liu (2008).
Neuraminidase-1, a subunit of the cell surface elastin receptor, desialylates and functionally inactivates adjacent receptors interacting with the mitogenic growth factors PDGF-BB and IGF-2.
  Am J Pathol, 173, 1042-1056.  
  19727327 D.B.Berkowitz, K.R.Karukurichi, la Salud-Bea, D.L.Nelson, and C.D.McCune (2008).
Use of Fluorinated Functionality in Enzyme Inhibitor Development: Mechanistic and Analytical Advantages.
  J Fluor Chem, 129, 731-742.  
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
  18765901 G.Xu, X.Li, P.W.Andrew, and G.L.Taylor (2008).
Structure of the catalytic domain of Streptococcus pneumoniae sialidase NanA.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 772-775.
PDB codes: 2vvz 2w20
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.