8P37

Structure a catalytically inactive mutant of the IMP dehydrogenase related protein GUAB3 from Synechocystis PCC 6803


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

GuaB3, an overlooked enzyme in cyanobacteria's toolbox that sheds light on IMP dehydrogenase evolution.

Hernandez-Gomez, A.Irisarri, I.Fernandez-Justel, D.Pelaez, R.Jimenez, A.Revuelta, J.L.Balsera, M.Buey, R.M.

(2023) Structure 31: 1526-1534.e4

  • DOI: https://doi.org/10.1016/j.str.2023.09.014
  • Primary Citation of Related Structures:  
    8P37, 8P4Q

  • PubMed Abstract: 

    IMP dehydrogenase and GMP reductase are enzymes from the same protein family with analogous structures and catalytic mechanisms that have gained attention because of their essential roles in nucleotide metabolism and as potential drug targets. This study focusses on GuaB3, a less-explored enzyme within this family. Phylogenetic analysis uncovers GuaB3's independent evolution from other members of the family and it predominantly occurs in Cyanobacteria. Within this group, GuaB3 functions as a unique IMP dehydrogenase, while its counterpart in Actinobacteria has a yet unknown function. Synechocystis sp. PCC6803 GuaB3 structures demonstrate differences in the active site compared to canonical IMP dehydrogenases, despite shared catalytic mechanisms. These findings highlight the essential role of GuaB3 in Cyanobacteria, provide insights into the diversity and evolution of the IMP dehydrogenase protein family, and reveal a distinctive characteristic in nucleotide metabolism, potentially aiding in combating harmful cyanobacterial blooms-a growing concern for humans and wildlife.


  • Organizational Affiliation

    Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMP dehydrogenase subunit390Synechocystis sp. PCC 6803Mutation(s): 1 
Gene Names: guaB
UniProt
Find proteins for P73853 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P73853 
Go to UniProtKB:  P73853
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP73853
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
XMP
Query on XMP

Download Ideal Coordinates CCD File 
B [auth A]XANTHOSINE-5'-MONOPHOSPHATE
C10 H14 N4 O9 P
DCTLYFZHFGENCW-UUOKFMHZSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.867α = 90
b = 112.867β = 90
c = 54.119γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
autoPROCdata processing
Aimlessdata scaling
autoPROCdata processing
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2019-109671GB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release