7A7E | pdb_00007a7e

Structure of a delta-N mutant - E232start - of PA1120 (TpbB or YfiN) from Pseudomonas aeruginosa (PAO1) comprising only the GGDEF domain

• PDB DOI: https://doi.org/10.2210/pdb7A7E/pdb

• Classification: LIGASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-08-28 Released: 2021-07-07 
• Deposition Author(s): Giardina, G., Rinaldo, S., Mantoni, F., Brunotti, P.
• Funding Organization(s): Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Studying GGDEF Domain in the Act: Minimize Conformational Frustration to Prevent Artefacts.

Mantoni, F., Scribani Rossi, C., Paiardini, A., Di Matteo, A., Cappellacci, L., Petrelli, R., Ricciutelli, M., Paone, A., Cutruzzola, F., Giardina, G., Rinaldo, S.

(2021) Life (Basel) 11

• PubMed: 33418960 
• DOI: https://doi.org/10.3390/life11010031
• Primary Citation Related Structures: 
  7A7E


• PubMed Abstract: 
  

  GGDEF-containing proteins respond to different environmental cues to finely modulate cyclic diguanylate (c-di-GMP) levels in time and space, making the allosteric control a distinctive trait of the corresponding proteins. The diguanylate cyclase mechanism is emblematic of this control: two GGDEF domains, each binding one GTP molecule, must dimerize to enter catalysis and yield c-di-GMP. The need for dimerization makes the GGDEF domain an ideal conformational switch in multidomain proteins. A re-evaluation of the kinetic profile of previously characterized GGDEF domains indicated that they are also able to convert GTP to GMP: this unexpected reactivity occurs when conformational issues hamper the cyclase activity. These results create new questions regarding the characterization and engineering of these proteins for in solution or structural studies.

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Organizational Affiliation: 
• Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy.
Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, 00185 Rome, Italy.
Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro, 5, 00185 Rome, Italy.
Medicinal Chemistry Unit, School of Pharmacy, University of Camerino, Via S. Agostino 1, 62032 Camerino, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.75 kDa 
• Atom Count: 3,809 
• Modeled Residue Count: 520 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diguanylate cyclase TpbB	A, B, C	206	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: tpbB, PA1120 EC: 2.7.7.65
UniProt
Find proteins for Q9I4L5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I4L5  Go to UniProtKB:  Q9I4L5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A], E [auth B], F [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.642	α = 90
b = 85.104	β = 90
c = 126.975	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Giardina, G., Rinaldo, S., Mantoni, F., Brunotti, P.

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Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	RBFR10LHD1

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description