1QDD

CRYSTAL STRUCTURE OF HUMAN LITHOSTATHINE TO 1.3 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 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


  • 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 crys ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LITHOSTATHINE
A
144Homo sapiensMutation(s): 1 
Gene Names: REG1A (PSPS, PSPS1, REG)
Find proteins for P05451 (Homo sapiens)
Go to Gene View: REG1A
Go to UniProtKB:  P05451
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download SDF File 
Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
SIA
Query on SIA

Download SDF File 
Download CCD File 
A
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.159 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 48.000α = 90.00
b = 48.000β = 90.00
c = 111.000γ = 120.00
Software Package:
Software NamePurpose
SHELXL-97refinement
CCP4data scaling
DENZOdata reduction
AMoREphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance