1LST

THREE-DIMENSIONAL STRUCTURES OF THE PERIPLASMIC LYSINE-, ARGININE-, ORNITHINE-BINDING PROTEIN WITH AND WITHOUT A LIGAND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding protein with and without a ligand.

Oh, B.H.Pandit, J.Kang, C.H.Nikaido, K.Gokcen, S.Ames, G.F.Kim, S.H.

(1993) J.Biol.Chem. 268: 11348-11355

  • Primary Citation of Related Structures:  2LAO

  • PubMed Abstract: 
  • Many proteins exhibit a large-scale movement of rigid globular domains. Among these, bacterial periplasmic binding proteins involved in substrate transport, or transport and chemotaxis, can be used as prototypes for understanding the mechanism of the ...

    Many proteins exhibit a large-scale movement of rigid globular domains. Among these, bacterial periplasmic binding proteins involved in substrate transport, or transport and chemotaxis, can be used as prototypes for understanding the mechanism of the movement. Such movements have been found to be associated with specific functions, such as substrate binding, catalysis, and recognition by other biomolecules. We have determined the three-dimensional structures of the lysine/arginine/ornithine-binding protein (LAO) from Salmonella typhimurium with and without lysine by x-ray crystallographic methods at 1.8- and 1.9-A resolution, respectively. The structures are composed of two lobes held together by two short connecting strands. The two lobes are far apart in the unliganded structure, but in contact with each other in the lysine-liganded structure. The large movement of the lobes is a consequence of a 52 degrees rotation of a single backbone torsion angle in the first connecting strand and of distributed smaller changes of three backbone torsion angles of the second connecting strand. The absence of contact between the lysine and the connecting strands suggests that the ligand does not induce the conformational change directly. We instead propose that the unliganded protein undergoes a dynamic change between an "open" and a "closed" conformation and that the role of the ligand is to stabilize the closed conformation. We discuss the nature of a surface area which might be recognized by the membrane-bound complex of these amino acids transport systems.


    Related Citations: 
    • Crystal Structure of the Lysine-, Arginine-, Ornithine-Binding Protein from Salmonella Typhimurium at 2.7 Angstroms Resolution
      Kang, C.-H.,Shin, W.-C.,Yamagata, Y.,Gokcen, S.,Ames, G.F.-L.,Kim, S.-H.
      (1992) J.Biol.Chem. 266: 23893


    Organizational Affiliation

    Department of Chemistry, Lawrence Berkeley Laboratory, University of California, Berkeley 94720.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSINE, ARGININE, ORNITHINE-BINDING PROTEIN
A
239Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Gene Names: argT
Find proteins for P02911 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P02911
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LYS
Query on LYS

Download SDF File 
Download CCD File 
A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LYSKd: 14 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.790α = 90.00
b = 59.630β = 90.00
c = 115.930γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1993-02-25 
  • Released Date: 1994-06-22 
  • Deposition Author(s): Kim, S.-H., Oh, B.-H.

Revision History 

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other