PDBsum entry 4sli

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Enzyme PDB id
Protein chain
679 a.a. *
Waters ×560
* Residue conservation analysis
PDB id:
Name: Enzyme
Title: Leech intramolecular trans-sialidase complexed with 2- propenyl-neu5ac, an inactive substrate analogue
Structure: Intramolecular trans-sialidase. Chain: a. Fragment: devoid of n-terminal 28 residues. Engineered: yes
Source: Macrobdella decora. North american leech. Organism_taxid: 6405. Gene: t7. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: de3.
1.80Å     R-factor:   0.189     R-free:   0.229
Authors: Y.Luo,S.C.Li,Y.T.Li,M.Luo
Key ref:
Y.Luo et al. (1999). The 1.8 A structures of leech intramolecular trans-sialidase complexes: evidence of its enzymatic mechanism. J Mol Biol, 285, 323-332. PubMed id: 9878409 DOI: 10.1006/jmbi.1998.2345
04-Oct-98     Release date:   25-May-99    
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Protein chain
Pfam   ArchSchema ?
Q27701  (NANL_MACDE) -  Anhydrosialidase
762 a.a.
679 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Anhydrosialidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     hydrolase activity     5 terms  


DOI no: 10.1006/jmbi.1998.2345 J Mol Biol 285:323-332 (1999)
PubMed id: 9878409  
The 1.8 A structures of leech intramolecular trans-sialidase complexes: evidence of its enzymatic mechanism.
Y.Luo, S.C.Li, Y.T.Li, M.Luo.
Intramolecular trans-sialidase from leech (Macrobdella decora) is the first member of the sialidase superfamily found to exhibit strict specificity towards the cleavage of terminal Neu5Acalpha2-->3Gal linkage in sialoglycoconjugates. Its release of 2,7-anhydro-Neu5Ac instead of Neu5Ac indicates that it catalyzes an intramolecular trans-sialosyl reaction. Crystal structures of its complexes with an inactive substrate analogue 2-propenyl-Neu5Ac, and with the product 2,7-anhydro-Neu5Ac, have been determined to 1.8 A resolution. The boat conformation of the pyranose observed in the complexes supports the proposed enzymatic mechanism that O7 of an axial 6-glycerol group attacks the positively charged C2 of the intermediate. A generalized mechanism is proposed for the sialidase superfamily.
  Selected figure(s)  
Figure 4.
Figure 4. F[o] - F[c] maps contoured at 2.0 s for the leech IT-sialidase complexes with (a) inactive substrate analogue 2-propenyl-Neu5Ac (the terminal carbon in the 2-propenyl is not shown). There is no density for the two terminal carbon groups in 2-propenyl. In addition, 6-glycerol appears disordered with a bulk density. (b) Product 2,7-anhydro-Neu5Ac; (c) also product 2,7-anhydro-Neu5Ac, soaked with substrate 3'-sialyllactose.
Figure 6.
Figure 6. Alternate enzymatic pathways by hydrolytic sialidases/neuraminidases, trans-sialidases, and IT-sialidases. The favored substrate conformation (left) in the active site is always a boat conformation. The differences between each enzymatic mechanism are the nucleophilic attacking atoms. These are activated water molecule in sialidase, the 3-hydroxyl of the galactose intrans-sialidase, and the 7-hydroxyl of the substrate sialic acid in IT-sialidase. The proximity of the hydroxyl groups is enforced by the conformation restraints imposed by the active site.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 285, 323-332) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16510969 F.Fabiola, A.Korostelev, and M.S.Chapman (2006).
Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetry.
  Acta Crystallogr D Biol Crystallogr, 62, 227-238.  
14730352 C.P.Chiu, A.G.Watts, L.L.Lairson, M.Gilbert, D.Lim, W.W.Wakarchuk, S.G.Withers, and N.C.Strynadka (2004).
Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analog.
  Nat Struct Mol Biol, 11, 163-170.
PDB codes: 1ro7 1ro8
14580216 J.N.Watson, V.Dookhun, T.J.Borgford, and A.J.Bennet (2003).
Mutagenesis of the conserved active-site tyrosine changes a retaining sialidase into an inverting sialidase.
  Biochemistry, 42, 12682-12690.  
12732625 M.Wimmerova, E.Mitchell, J.F.Sanchez, C.Gautier, and A.Imberty (2003).
Crystal structure of fungal lectin: six-bladed beta-propeller fold and novel fucose recognition mode for Aleuria aurantia lectin.
  J Biol Chem, 278, 27059-27067.
PDB code: 1ofz
12419220 A.Buschiazzo, M.F.Amaya, M.L.Cremona, A.C.Frasch, and P.M.Alzari (2002).
The crystal structure and mode of action of trans-sialidase, a key enzyme in Trypanosoma cruzi pathogenesis.
  Mol Cell, 10, 757-768.
PDB codes: 1mr5 1ms0 1ms1 1ms3 1ms4 1ms5 1ms8 1ms9
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