4SLI

LEECH INTRAMOLECULAR TRANS-SIALIDASE COMPLEXED WITH 2-PROPENYL-NEU5AC, AN INACTIVE SUBSTRATE ANALOGUE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The 1.8 A structures of leech intramolecular trans-sialidase complexes: evidence of its enzymatic mechanism.

Luo, Y.Li, S.C.Li, Y.T.Luo, M.

(1999) J Mol Biol 285: 323-332

  • DOI: https://doi.org/10.1006/jmbi.1998.2345
  • Primary Citation of Related Structures:  
    2SLI, 3SLI, 4SLI

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Center for Macromolecular Crystallography, University of Alabama at Birmingham, AL, 35294, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INTRAMOLECULAR TRANS-SIALIDASE679Macrobdella decoraMutation(s): 0 
Gene Names: T7
EC: 3.2.1.18
UniProt
Find proteins for Q27701 (Macrobdella decora)
Explore Q27701 
Go to UniProtKB:  Q27701
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ27701
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CNP
Query on CNP

Download Ideal Coordinates CCD File 
B [auth A]2-propenyl-N-acetyl-neuraminic acid
C14 H23 N O8
IUGVDRFIVSPVGO-KXEMTNKZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.264α = 112.93
b = 69.437β = 95.6
c = 72.319γ = 106.86
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-25
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Other, Structure summary
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Structure summary