1LSS | pdb_00001lss

KTN Mja218 CRYSTAL STRUCTURE IN COMPLEX WITH NAD+

• PDB DOI: https://doi.org/10.2210/pdb1LSS/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-05-18 Released: 2002-07-03 
• Deposition Author(s): Roosild, T.P., Miller, S., Booth, I.R., Choe, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.269 (Depositor) 
• R-Value Work: 
  0.220 (Depositor) 

Literature

A mechanism of regulating transmembrane potassium flux through a ligand-mediated conformational switch.

Roosild, T.P., Miller, S., Booth, I.R., Choe, S.

(2002) Cell 109: 781-791

• PubMed: 12086676 
• DOI: https://doi.org/10.1016/s0092-8674(02)00768-7
• Primary Citation Related Structures: 
  1LSS, 1LSU


• PubMed Abstract: 
  

  The regulation of cation content is critical for cell growth. However, the molecular mechanisms that gate the systems that control K+ movements remain unclear. KTN is a highly conserved cytoplasmic domain present ubiquitously in a variety of prokaryotic and eukaryotic K+ channels and transporters. Here we report crystal structures for two representative KTN domains that reveal a dimeric hinged assembly. Alternative ligands NAD+ and NADH block or vacate, respectively, the hinge region affecting the dimer's conformational flexibility. Conserved, surface-exposed hydrophobic patches that become coplanar upon hinge closure provide an assembly interface for KTN tetramerization. Mutational analysis using the KefC system demonstrates that this domain directly interacts with its respective transmembrane constituent, coupling ligand-mediated KTN conformational changes to the permease's activity.

---

Organizational Affiliation: 
• Structural Biology Laboratory, Salk Institute and Division of Biology, University of California, San Diego, 92037, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.52 kDa 
• Atom Count: 4,507 
• Modeled Residue Count: 528 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trk system potassium uptake protein trkA homolog	A, B, C, D	140	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: KtrA
UniProt
Find proteins for Q58505 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58505  Go to UniProtKB:  Q58505

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.269 (Depositor) 
• R-Value Work:  0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92	α = 90
b = 74.4	β = 90
c = 86	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-07-03 
Deposition Author(s): Roosild, T.P., Miller, S., Booth, I.R., Choe, S.

Revision History  

• Version 1.0: 2002-07-03
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-11-12
  Changes: Structure summary
• Version 1.4: 2020-03-18
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations