4OZL

GlnK2 from Haloferax mediterranei complexed with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1111/febs.12881
  • Structures With Same Primary Citation

  • 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, ...

    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.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrogen regulatory protein P-II
A
143Haloferax mediterranei ATCC 33500Mutation(s): 0 
Gene Names: glnK2HFX_0092C439_09930BM92_08825E6P09_03555
Find proteins for B8ZYW1 (Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4))
Go to UniProtKB:  B8ZYW1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.09α = 90
b = 89.09β = 90
c = 95.26γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish governmentSpainBFU2011_30407
Spanish governmentSpainBIO2008_00082
Valencian governmentSpainPrometeo 2009/51

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references