4OZJ

GlnK2 from Haloferax mediterranei complexed with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The structure of a PII signaling protein from a halophilic archaeon reveals novel traits and high-salt adaptations.

Palanca, C.Pedro-Roig, L.Llacer, J.L.Camacho, M.Bonete, M.J.Rubio, V.

(2014) FEBS J 281: 3299-3314

  • DOI: https://doi.org/10.1111/febs.12881
  • Primary Citation of Related Structures:  
    4OZJ, 4OZL, 4OZN

  • PubMed Abstract: 

    To obtain insights into archaeal nitrogen signaling and haloadaptation of the nitrogen/carbon/energy-signaling protein PII, we determined crystal structures of recombinantly produced GlnK2 from the extreme halophilic archaeon Haloferax mediterranei, complexed with AMP or with the PII effectors ADP or ATP, at respective resolutions of 1.49 Å, 1.45 Å, and 2.60 Å. A unique trait of these structures was a three-tongued crown protruding from the trimer body convex side, formed by an 11-residue, N-terminal, highly acidic extension that is absent from structurally studied PII proteins. This extension substantially contributed to the very low pI value, which is a haloadaptive trait of H. mediterranei GlnK2, and participated in hexamer-forming contacts in one crystal. Similar acidic N-extensions are shown here to be common among PII proteins from halophilic organisms. Additional haloadaptive traits prominently represented in H. mediterranei GlnK2 are a very high ratio of small residues to large hydrophobic aliphatic residues, and the highest ratio of polar to nonpolar exposed surface for any structurally characterized PII protein. The presence of a dense hydration layer in the region between the three T-loops might also be a haloadaptation. Other unique findings revealed by the GlnK2 structure that might have functional relevance are: the adoption by its T-loop of a three-turn α-helical conformation, perhaps related to the ability of GlnK2 to directly interact with glutamine synthetase; and the firm binding of AMP, confirmed by biochemical binding studies with ATP, ADP, and AMP, raising the possibility that AMP could be an important PII effector, at least in archaea. The atomic coordinates and structure factors have been deposited in the Protein Data Bank under the accession numbers 4OZL (hmGlnK2-AMP), 4OZJ (hmGlnK2-ADP), and 4OZN (hmGlnK2-ATP). hmGlnK2 and hmGlnK2 bind by x-ray crystallography (View interaction).


  • Organizational Affiliation

    Instituto de Biomedicina de Valencia of the CSIC (IBV-CSIC), Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogen regulatory protein P-II143Haloferax mediterranei ATCC 33500Mutation(s): 0 
Gene Names: glnK2HFX_0092C439_09930
UniProt
Find proteins for B8ZYW1 (Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4))
Explore B8ZYW1 
Go to UniProtKB:  B8ZYW1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8ZYW1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.185α = 90
b = 89.185β = 90
c = 96.349γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish governmentSpainBFU2011-30407
Spanish governmentSpainBIO2008_00082
Valencian governmentSpainPrometeo 2009/51

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy