4SLI | pdb_00004sli

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

• PDB DOI: https://doi.org/10.2210/pdb4SLI/pdb

• Classification: ENZYME
• Organism(s): Macrobdella decora
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-10-04 Released: 1999-05-25 
• Deposition Author(s): Luo, Y., Li, S.C., Li, Y.T., Luo, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.229 (Depositor) 
• R-Value Work: 
  0.189 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

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 Biology 285: 323-332

• PubMed: 9878409 
• DOI: https://doi.org/10.1006/jmbi.1998.2345
• Primary Citation 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.

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Organizational Affiliation: 
• Center for Macromolecular Crystallography, University of Alabama at Birmingham, AL, 35294, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.9 kDa 
• Atom Count: 5,840 
• Modeled Residue Count: 679 
• Deposited Residue Count: 679 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTRAMOLECULAR TRANS-SIALIDASE	A	679	Macrobdella decora	Mutation(s): 0  Gene Names: T7 EC: 3.2.1.18 (PDB Primary Data), 4.2.2.15 (UniProt)
UniProt
Find proteins for Q27701 (Macrobdella decora) Explore Q27701  Go to UniProtKB:  Q27701

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CNP	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 (Depositor) 
• R-Value Work:  0.189 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.264	α = 112.93
b = 69.437	β = 95.6
c = 72.319	γ = 106.86

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-25 
Deposition Author(s): Luo, Y., Li, S.C., Li, Y.T., Luo, M.

Revision History  

• 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
• Version 1.5: 2024-04-03
  Changes: Refinement description