1LT4 | pdb_00001lt4

HEAT-LABILE ENTEROTOXIN MUTANT S63K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.255 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.3 of the entry. See complete history

Literature

Crystal structure of a non-toxic mutant of heat-labile enterotoxin, which is a potent mucosal adjuvant.

van den Akker, F.Pizza, M.Rappuoli, R.Hol, W.G.

(1997) Protein Sci 6: 2650-2654

  • DOI: https://doi.org/10.1002/pro.5560061220
  • Primary Citation Related Structures: 
    1LT4

  • PubMed Abstract: 

    Two closely related bacterial toxins, heat-labile enterotoxin (LT-I) and cholera toxin (CT), not only invoke a toxic activity that affects many victims worldwide but also contain a beneficial mucosal adjuvant activity that significantly enhances the potency of vaccines in general. For the purpose of vaccine design it is most interesting that the undesirable toxic activity of these toxins can be eliminated by the single-site mutation Ser63Lys in the A subunit while the mucosal adjuvant activity is still present. The crystal structure of the Ser63Lys mutant of LT-I is determined at 2.0 A resolution. Its structure appears to be essentially the same as the wild-type LT-I structure. The substitution Ser63Lys was designed, based on the wild-type LT-I crystal structure, to decrease toxicity by interfering with NAD binding and/or catalysis. In the mutant crystal structure, the newly introduced lysine side chain is indeed positioned such that it could potentially obstruct the productive binding mode of the substrate NAD while at the same time its positive charge could possibly interfere with the critical function of nearby charged groups in the active site of LT-I. The fact that the Ser63Lys mutant of LT-I does not disrupt the wild-type LT-I structure makes the non-toxic mutant potentially suitable, from a structural point of view, to be used as a vaccine to prevent enterotoxigenic E. coli infections. The structural similarity of mutant and wild-type toxin might also be the reason why the inactive Ser63Lys variant retains its adjuvant activity.


  • Organizational Affiliation
    • Department of Biochemistry, University of Washington, Seattle 98195-7420, USA.

Macromolecule Content 

  • Total Structure Weight: 89.4 kDa 
  • Atom Count: 6,452 
  • Modeled Residue Count: 741 
  • Deposited Residue Count: 762 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HEAT-LABILE ENTEROTOXINA [auth D],
B [auth E],
C [auth F],
D [auth G],
E [auth H]
103Escherichia coliMutation(s): 0 
UniProt
Find proteins for P32890 (Escherichia coli)
Explore P32890 
Go to UniProtKB:  P32890
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32890
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HEAT-LABILE ENTEROTOXINF [auth A]247Escherichia coliMutation(s): 1 
UniProt
Find proteins for P06717 (Escherichia coli)
Explore P06717 
Go to UniProtKB:  P06717
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06717
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseG [auth B],
H [auth C],
I,
J,
K
2N/A
Glycosylation Resources
GlyTouCan: G84224TW
GlyCosmos: G84224TW
GlyGen: G84224TW

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.255 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120α = 90
b = 101.9β = 90
c = 64.4γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-06-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-11-03
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-09
    Changes: Refinement description
  • Version 2.3: 2024-10-23
    Changes: Data collection, Structure summary