3LP9

Crystal structure of LS24, A Seed Albumin from Lathyrus sativus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure and functional insights of hemopexin fold protein from grass pea

Gaur, V.Qureshi, I.A.Singh, A.Chanana, V.Salunke, D.M.

(2010) Plant Physiol 152: 1842-1850

  • DOI: https://doi.org/10.1104/pp.109.150680
  • Primary Citation of Related Structures:  
    3LP9

  • PubMed Abstract: 

    A regulatory protein from grass pea (Lathyrus sativus), LS-24, a close homolog of albumin 2 from garden pea (Pisum sativum) that is associated with polyamine biosynthesis, was characterized and the structure of a hemopexin-type fold among plant proteins illustrated. Crystal structure of LS-24 determined at 2.2 A resolution by multiple isomorphous replacement phasing showed four-bladed beta-propeller structure having a pseudo 4-fold molecular symmetry along a metal ion-binding central channel. The structure represents typical mammalian hemopexin fold with discernible features correlated with the possible functional variations. The protein was found to exist in the dimeric state. While LS-24 dimer binds to spermine in the crystal structure as well as in solution, binding of heme in solution resulted in the dissociation of the dimer into monomers with concomitant release of bound spermine. Interactions of heme and spermine with LS-24 bear physiological implications. While binding of spermine to LS-24 can be linked with polyamine biosynthesis that of heme correlates with oxidative stress. Mutually exclusive binding of heme and spermine in different oligomeric states suggest a role for LS-24 in sensing oxidative stress through a ligand-regulated monomer-dimer transition switch.


  • Organizational Affiliation

    National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LS-24
A, B, C, D
227Lathyrus sativusMutation(s): 0 
UniProt
Find proteins for D4AEP7 (Lathyrus sativus)
Explore D4AEP7 
Go to UniProtKB:  D4AEP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD4AEP7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download Ideal Coordinates CCD File 
Q [auth D]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.17α = 90
b = 88.14β = 90
c = 154.53γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
SOLVEphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations