1QDD

CRYSTAL STRUCTURE OF HUMAN LITHOSTATHINE TO 1.3 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.159 
  • R-Value Observed: 0.132 

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This is version 2.0 of the entry. See complete history


Literature

Mechanism of calcite crystal growth inhibition by the N-terminal undecapeptide of lithostathine.

Gerbaud, V.Pignol, D.Loret, E.Bertrand, J.A.Berland, Y.Fontecilla-Camps, J.C.Canselier, J.P.Gabas, N.Verdier, J.M.

(2000) J Biol Chem 275: 1057-1064

  • DOI: 10.1074/jbc.275.2.1057
  • Primary Citation of Related Structures:  
    1QDD

  • PubMed Abstract: 
  • Pancreatic juice is supersaturated with calcium carbonate. Calcite crystals therefore may occur, obstruct pancreatic ducts, and finally cause a lithiasis. Human lithostathine, a protein synthesized by the pancreas, inhibits the growth of calcite crystals by inducing a habit modification: the rhombohedral (10 14) usual habit is transformed into a needle-like habit through the (11 0) crystal form ...

    Pancreatic juice is supersaturated with calcium carbonate. Calcite crystals therefore may occur, obstruct pancreatic ducts, and finally cause a lithiasis. Human lithostathine, a protein synthesized by the pancreas, inhibits the growth of calcite crystals by inducing a habit modification: the rhombohedral (10 14) usual habit is transformed into a needle-like habit through the (11 0) crystal form. A similar observation was made with the N-terminal undecapeptide (pE(1)R(11)) of lithostathine. We therefore aimed at discovering how peptides inhibit calcium salt crystal growth. We solved the complete x-ray structure of lithostathine, including the flexible N-terminal domain, at 1.3 A. Docking studies of pE(1)R(11) with the (10 14) and (11 0) faces through molecular dynamics simulation resulted in three successive steps. First, the undecapeptide progressively unfolded as it approached the calcite surface. Second, mobile lateral chains of amino acids made hydrogen bonds with the calcite surface. Last, electrostatic bonds between calcium ions and peptide bonds stabilized and anchored pE(1)R(11) on the crystal surface. pE(1)R(11)-calcite interaction was stronger with the (11 0) face than with the (10 14) face, confirming earlier experimental observations. Energy contributions showed that the peptide backbone governed the binding more than did the lateral chains. The ability of peptides to inhibit crystal growth is therefore essentially based on backbone flexibility.


    Related Citations: 
    • Crystal structure of human lithostathine, the pancreatic inhibitor of stone formation
      Bertrand, J., Pignol, D., Bernard, J.P., Verdier, J.M., Dagorn, J.C., Fontecilla-Camps, J.C.
      (1996) EMBO J 15: 2678

    Organizational Affiliation

    Laboratoire de Génie Chimique, Unité Mixte de Recherche CNRS 5503, Ecole Nationale Supérieure de Génie Chimique-Institut National Polytechnique de Toulouse/Université Paul Sabatier, Toulouse, Cedex 4 31078, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LITHOSTATHINEA144Homo sapiensMutation(s): 1 
Gene Names: REG1APSPSPSPS1REG
UniProt & NIH Common Fund Data Resources
Find proteins for P05451 (Homo sapiens)
Explore P05451 
Go to UniProtKB:  P05451
PHAROS:  P05451
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-glucopyranoseB3O-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G43175RA
GlyCosmos:  G43175RA
GlyGen:  G43175RA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.159 
  • R-Value Observed: 0.132 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48α = 90
b = 48β = 90
c = 111γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
AMoREphasing
SHELXL-97refinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    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: Advisory, Atomic model, Data collection, Derived calculations, Structure summary