7R50

Crystal structure of GMP reductase from mycobacterium smegmatis in complex with GMP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The mycobacterial guaB1 gene encodes a guanosine 5'-monophosphate reductase with a cystathionine-beta-synthase domain.

Knejzlik, Z.Dolezal, M.Herkommerova, K.Clarova, K.Klima, M.Dedola, M.Zbornikova, E.Rejman, D.Pichova, I.

(2022) FEBS J 289: 5571-5598

  • DOI: https://doi.org/10.1111/febs.16448
  • Primary Citation of Related Structures:  
    7OY9, 7R50

  • PubMed Abstract: 

    Mycobacteria express enzymes from both the de novo and purine-salvage pathways. However, the regulation of these processes and the roles of individual metabolic enzymes have not been sufficiently detailed. Both Mycobacterium tuberculosis (Mtb) and Mycobacterium smegmatis (Msm) possess three guaB genes, but information is only available on guaB2, which encodes an essential inosine 5'-monophosphate dehydrogenase (IMPDH) involved in de novo purine biosynthesis. This study shows that guaB1, annotated in databases as a putative IMPDH, encodes a guanosine 5'-monophosphate reductase (GMPR), which recycles guanosine monophosphate to inosine monophosphate within the purine-salvage pathway and contains a cystathionine-β-synthase domain (CBS), which is essential for enzyme activity. GMPR activity is allosterically regulated by the ATP/GTP ratio in a pH-dependent manner. Bioinformatic analysis has indicated the presence of GMPRs containing CBS domains across the entire Actinobacteria phylum.


  • Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5-monophosphate dehydrogenase guaB1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
496Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: MSMEI_3548
EC: 1.1.1
UniProt
Find proteins for A0QYE8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QYE8 
Go to UniProtKB:  A0QYE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QYE8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5GP (Subject of Investigation/LOI)
Query on 5GP

Download Ideal Coordinates CCD File 
AA [auth K]
BA [auth L]
CA [auth M]
DA [auth N]
EA [auth O]
AA [auth K],
BA [auth L],
CA [auth M],
DA [auth N],
EA [auth O],
FA [auth P],
Q [auth A],
R [auth B],
S [auth C],
T [auth D],
U [auth E],
V [auth F],
W [auth G],
X [auth H],
Y [auth I],
Z [auth J]
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.788α = 76.916
b = 105.098β = 81.857
c = 170.468γ = 69.013
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicCZ.02.1.01/0.0/16_019/000729

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-27
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description