9GLG | pdb_00009glg

X-ray structure of the Thermus thermophilus Q218E mutant of the PilF-GSPIIB domain in the c-di-GMP bound state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.203 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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Literature

Protonated Glutamate and Aspartate Side Chains Can Recognize Phosphodiester Groups via Strong and Short Hydrogen Bonds in Biomacromolecular Complexes.

Neissner, K.Duchardt-Ferner, E.Wiedemann, C.Kraus, J.Hellmich, U.A.Wohnert, J.

(2025) Angew Chem Int Ed Engl 64: e202501589-e202501589

  • DOI: https://doi.org/10.1002/anie.202501589
  • Primary Citation of Related Structures:  
    9GL5, 9GLG

  • PubMed Abstract: 

    Phosphodiester groups occur ubiquitously in nature, e.g. in nucleic acids or in cyclic (di-)nucleotides important for signal transduction. Proteins often use polar or positively charged amino acids to interact with the negatively charged phosphodiester groups via hydrogen bonds and salt bridges. In contrast, the acidic amino acids aspartate and glutamate are generally not considered as important determinants for phosphodiester group recognition. Instead, they are regarded as detrimental to such interactions due to the assumed charge repulsion between their deprotonated, negatively charged side chain carboxylate groups and the phosphodiester. Accordingly, acidic amino acids are often purposefully introduced into proteins to abrogate nucleic acid interactions in functional studies. Here, we show that in appropriate structural contexts, glutamate side chains are readily protonated even at neutral pH and act as hydrogen bond donors to phosphodiester groups using a c-di-GMP binding protein - the GSPII-B domain of PilF from Thermus thermophilus - as an example. Surveying available RNA-protein and DNA-protein complex structures in the PDB, we found that hydrogen bonds between apparently protonated carboxylate groups of glutamate and aspartate and phosphodiester groups occur frequently in many different functional protein classes. Thus, the functional role of acidic amino acids in phosphodiester group recognition needs to be re-evaluated.


  • Organizational Affiliation

    Institute for Molecular Biosciences, Goethe-University Frankfurt/M., Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-binding motif-containing protein pilF
A, B
146Thermus thermophilus HB27Mutation(s): 1 
Gene Names: pilFTT_C1622
UniProt
Find proteins for Q72H73 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72H73 
Go to UniProtKB:  Q72H73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72H73
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E (Subject of Investigation/LOI)
Query on C2E

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
I [auth B]
J [auth B]
K [auth B]
D [auth A],
E [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.203 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.099α = 90
b = 108.099β = 90
c = 86.183γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
autoPROCdata processing
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Database references