Structure of C. glutamicum GlnK

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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Crystal structures of adenylylated and unadenylylated P II protein GlnK from Corynebacterium glutamicum.

Grau, F.C.Burkovski, A.Muller, Y.A.

(2021) Acta Crystallogr D Struct Biol 77: 325-335

  • DOI: https://doi.org/10.1107/S2059798321000735
  • Primary Citation of Related Structures:  
    6YC6, 6YC7

  • PubMed Abstract: 

    P II proteins are ubiquitous signaling proteins that are involved in the regulation of the nitrogen/carbon balance in bacteria, archaea, and some plants and algae. Signal transduction via P II proteins is modulated by effector molecules and post-translational modifications in the P II T-loop. Whereas the binding of ADP, ATP and the concomitant binding of ATP and 2-oxoglutarate (2OG) engender two distinct conformations of the T-loop that either favor or disfavor the interaction with partner proteins, the structural consequences of post-translational modifications such as phosphorylation, uridylylation and adenylylation are far less well understood. In the present study, crystal structures of the P II protein GlnK from Corynebacterium glutamicum have been determined, namely of adenylylated GlnK (adGlnK) and unmodified unadenylylated GlnK (unGlnK). AdGlnK has been proposed to act as an inducer of the transcription repressor AmtR, and the adenylylation of Tyr51 in GlnK has been proposed to be a prerequisite for this function. The structures of unGlnK and adGlnK allow the first atomic insights into the structural implications of the covalent attachment of an AMP moiety to the T-loop. The overall GlnK fold remains unaltered upon adenylylation, and T-loop adenylylation does not appear to interfere with the formation of the two major functionally important T-loop conformations, namely the extended T-loop in the canonical ADP-bound state and the compacted T-loop that is adopted upon the simultaneous binding of Mg-ATP and 2OG. Thus, the P II -typical conformational switching mechanism appears to be preserved in GlnK from C. glutamicum, while at the same time the functional repertoire becomes expanded through the accommodation of a peculiar post-translational modification.

  • Organizational Affiliation

    Division of Biotechnology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestrasse 91, 91052 Erlangen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PII protein
A, B, C
119Corynebacterium glutamicumMutation(s): 0 
Gene Names: glnB
Find proteins for H7C694 (Corynebacterium glutamicum)
Explore H7C694 
Go to UniProtKB:  H7C694
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH7C694
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
I [auth B]
O4 P
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth C],
N [auth C]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.511α = 90
b = 82.511β = 90
c = 170.587γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description