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PDBsum entry 1vcu

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1vcu
Jmol
Contents
Protein chain
370 a.a. *
Ligands
DAN ×2
EPE ×4
Waters ×131
* Residue conservation analysis
PDB id:
1vcu
Name: Hydrolase
Title: Structure of the human cytosolic sialidase neu2 in complex with the inhibitor dana
Structure: Sialidase 2. Chain: a, b. Synonym: neu2, cytosolic sialidase, n-acetyl-alpha- neuraminidase 2. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Resolution:
2.85Å     R-factor:   0.195     R-free:   0.266
Authors: L.M.G.Chavas,P.Fusi,C.Tringali,B.Venerando,G.Tettamanti, R.Kato,E.Monti,S.Wakatsuki
Key ref:
L.M.Chavas et al. (2005). Crystal structure of the human cytosolic sialidase Neu2. Evidence for the dynamic nature of substrate recognition. J Biol Chem, 280, 469-475. PubMed id: 15501818 DOI: 10.1074/jbc.M411506200
Date:
12-Mar-04     Release date:   02-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9Y3R4  (NEUR2_HUMAN) -  Sialidase-2
Seq:
Struc:
380 a.a.
370 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.3.2.1.18  - 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!
  Cellular component     cytoplasm   2 terms 
  Biological process     metabolic process   9 terms 
  Biochemical function     exo-alpha-(2->3)-sialidase activity     6 terms  

 

 
DOI no: 10.1074/jbc.M411506200 J Biol Chem 280:469-475 (2005)
PubMed id: 15501818  
 
 
Crystal structure of the human cytosolic sialidase Neu2. Evidence for the dynamic nature of substrate recognition.
L.M.Chavas, C.Tringali, P.Fusi, B.Venerando, G.Tettamanti, R.Kato, E.Monti, S.Wakatsuki.
 
  ABSTRACT  
 
Gangliosides play key roles in cell differentiation, cell-cell interactions, and transmembrane signaling. Sialidases hydrolyze sialic acids to produce asialo compounds, which is the first step of degradation processes of glycoproteins and gangliosides. Sialidase involvement has been implicated in some lysosomal storage disorders such as sialidosis and galactosialidosis. Neu2 is a recently identified human cytosolic sialidase. Here we report the first high resolution x-ray structures of mammalian sialidase, human Neu2, in its apo form and in complex with an inhibitor, 2-deoxy-2,3-dehydro-N-acetylneuraminic acid (DANA). The structure shows the canonical six-blade beta-propeller observed in viral and bacterial sialidases with its active site in a shallow crevice. In the complex structure, the inhibitor lies in the catalytic crevice surrounded by ten amino acids. In particular, the arginine triad, conserved among sialidases, aids in the proper positioning of the carboxylate group of DANA within the active site region. The tyrosine residue, Tyr(334), conserved among mammalian and bacterial sialidases as well as in viral neuraminidases, facilitates the enzymatic reaction by stabilizing a putative carbonium ion in the transition state. The loops containing Glu(111) and the catalytic aspartate Asp(46) are disordered in the apo form but upon binding of DANA become ordered to adopt two short alpha-helices to cover the inhibitor, illustrating the dynamic nature of substrate recognition. The N-acetyl and glycerol moieties of DANA are recognized by Neu2 residues not shared by bacterial sialidases and viral neuraminidases, which can be regarded as a key structural difference for potential drug design against bacteria, influenza, and other viruses.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Sialic acid and inhibitors. Schematic structure of a sialylgalactose (a), NANA (b), and DANA (c). In the case of the sialylgalactose, the dotted line indicates the bond hydrolyzed by the sialidase.
Figure 4.
FIG. 4. Structural changes of Neu2 upon maltose and DANA binding. a, ribbon diagram of Neu2 apo form, viewed from the side. The active site is located on the top part of the protein. Secondary elements are colored as in Fig. 2. b, Neu2 sugar-induced form in the same orientation as in a. The arrow indicates the loop containing Glu111 that becomes ordered and forms helix 2. c, Neu2-DANA complex in the same orientation as in a. DANA is represented as a ball-and-stick model. The arrows indicate two helices ( 1 and 2) that are formed upon inhibitor binding.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 469-475) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21489803 A.Albohy, S.Mohan, R.B.Zheng, B.M.Pinto, and C.W.Cairo (2011).
Inhibitor selectivity of a new class of oseltamivir analogs against viral neuraminidase over human neuraminidase enzymes.
  Bioorg Med Chem, 19, 2817-2822.  
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.  
21305698 H.Hinou, R.Miyoshi, Y.Takasu, H.Kai, M.Kurogochi, S.Arioka, X.D.Gao, N.Miura, N.Fujitani, S.Omoto, T.Yoshinaga, T.Fujiwara, T.Noshi, H.Togame, H.Takemoto, and S.Nishimura (2011).
A strategy for neuraminidase inhibitors using mechanism-based labeling information.
  Chem Asian J, 6, 1048-1056.  
21472809 R.Bilyy, A.Tomin, I.Mahorivska, O.Shalay, V.Lohinskyy, R.Stoika, and Y.Kit (2011).
Antibody-mediated sialidase activity in blood serum of patients with multiple myeloma.
  J Mol Recognit, 24, 576-584.  
21206954 Y.Li, H.Cao, H.Yu, Y.Chen, K.Lau, J.Qu, V.Thon, G.Sugiarto, and X.Chen (2011).
Identifying selective inhibitors against the human cytosolic sialidase NEU2 by substrate specificity studies.
  Mol Biosyst, 7, 1060-1072.  
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.  
19797320 A.Bigi, L.Morosi, C.Pozzi, M.Forcella, G.Tettamanti, B.Venerando, E.Monti, and P.Fusi (2010).
Human sialidase NEU4 long and short are extrinsic proteins bound to outer mitochondrial membrane and the endoplasmic reticulum, respectively.
  Glycobiology, 20, 148-157.  
20213245 T.M.Finlay, P.Jayanth, S.R.Amith, A.Gilmour, C.Guzzo, K.Gee, R.Beyaert, and M.R.Szewczuk (2010).
Thymoquinone from nutraceutical black cumin oil activates Neu4 sialidase in live macrophage, dendritic, and normal and type I sialidosis human fibroblast cells via GPCR Galphai proteins and matrix metalloproteinase-9.
  Glycoconj J, 27, 329-348.  
20552664 T.V.Vuong, and D.B.Wilson (2010).
Glycoside hydrolases: catalytic base/nucleophile diversity.
  Biotechnol Bioeng, 107, 195-205.  
19554265 A.S.Bayden, M.Fornabaio, J.N.Scarsdale, and G.E.Kellogg (2009).
Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT.
  J Comput Aided Mol Des, 23, 621-632.  
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.  
19269961 R.Carapito, A.Imberty, J.M.Jeltsch, S.C.Byrns, P.H.Tam, T.L.Lowary, A.Varrot, and V.Phalip (2009).
Molecular basis of arabinobio-hydrolase activity in phytopathogenic fungi: crystal structure and catalytic mechanism of Fusarium graminearum GH93 exo-alpha-L-arabinanase.
  J Biol Chem, 284, 12285-12296.
PDB codes: 2w5n 2w5o
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.  
18694948 K.Hata, K.Koseki, K.Yamaguchi, S.Moriya, Y.Suzuki, S.Yingsakmongkon, G.Hirai, M.Sodeoka, M.von Itzstein, and T.Miyagi (2008).
Limited inhibitory effects of oseltamivir and zanamivir on human sialidases.
  Antimicrob Agents Chemother, 52, 3484-3491.  
18218621 S.L.Newstead, J.A.Potter, J.C.Wilson, G.Xu, C.H.Chien, A.G.Watts, S.G.Withers, and G.L.Taylor (2008).
The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates.
  J Biol Chem, 283, 9080-9088.
PDB codes: 2bf6 2vk5 2vk6 2vk7
19075514 T.Miyagi (2008).
Aberrant expression of sialidase and cancer progression.
  Proc Jpn Acad Ser B Phys Biol Sci, 84, 407-418.  
18758138 Y.Ikegaya (2008).
Large-scale recordings for drug screening in neural circuit systems.
  Yakugaku Zasshi, 128, 1251-1257.  
17426694 C.Y.Li, Q.Yu, Z.Q.Ye, Y.Sun, Q.He, X.M.Li, W.Zhang, J.Luo, X.Gu, X.Zheng, and L.Wei (2007).
A nonsynonymous SNP in human cytosolic sialidase in a small Asian population results in reduced enzyme activity: potential link with severe adverse reactions to oseltamivir.
  Cell Res, 17, 357-362.  
17435775 M.Long (2007).
Side effects of Tamiflu: clues from an Asian single nucleotide polymorphism.
  Cell Res, 17, 309-310.  
16929107 M.Hiraki, R.Kato, M.Nagai, T.Satoh, S.Hirano, K.Ihara, N.Kudo, M.Nagae, M.Kobayashi, M.Inoue, T.Uejima, S.Oda, L.M.Chavas, M.Akutsu, Y.Yamada, M.Kawasaki, N.Matsugaki, N.Igarashi, M.Suzuki, and S.Wakatsuki (2006).
Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses.
  Acta Crystallogr D Biol Crystallogr, 62, 1058-1065.  
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.