9HG0 | pdb_00009hg0

Crystal structure of M. smegmatis GMP reductase with XMP* intermidiate in complex with NADP+ and IMP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.248 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structural basis for allosteric regulation of mycobacterial guanosine 5 ́-monophosphate reductase by ATP and GTP.

Dolezal, M.Knejzlik, Z.Kouba, T.Filimonenko, A.Svachova, H.Dedola, M.Klima, M.Pichova, I.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-71657-9
  • Primary Citation Related Structures: 
    8RY0, 8RY1, 8RY3, 8RY4, 8RY5, 8RY6, 8RY7, 8RY8, 8RY9, 8RYA, 8RYB, 9HFZ, 9HG0, 9HG1, 9HG2, 9HG3

  • PubMed Abstract: 

    Guanosine 5'-monophosphate reductase (GMPR) is a crucial enzyme in the purine salvage pathway that catalyses the NADPH-dependent conversion of GMP to IMP, thereby contributing to purine nucleotide homeostasis. Mycobacterium smegmatis GMPR (MsmGMPR) contains a regulatory cystathionine β-synthase (CBS) domain, which mediates allosteric modulation by ATP and GTP. However, MsmGMPR exhibits an atypical tertiary structure that is incompatible with the acknowledged regulatory mechanisms of IMPDH/GMPR family enzymes. Here, we combine X-ray crystallography, cryogenic electron microscopy, and biochemical binding assays to elucidate the molecular basis of MsmGMPR regulation by ATP and GTP. We show that ATP stabilises a compressed conformation that inhibits the enzyme by restricting access to the active site and preventing NADPH binding. In contrast, GTP counteracts ATP binding, promoting an active conformation that enables catalysis. Our results provide insight into how MsmGMPR senses and responds to the purine nucleotide balance, revealing a distinct utilisation of the CBS domain compared with its typical role in IMPDH/GMPR enzymes.


  • 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
GMP reductase
A, B, C, D, E
A, B, C, D, E, F, G, H
496Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: guaB1MSMEG_3634MSMEI_3548
EC: 1.7.1.7
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth G]
J [auth A]
M [auth B]
P [auth C]
BA [auth G],
DA [auth G],
J [auth A],
M [auth B],
P [auth C],
S [auth D],
V [auth E],
Y [auth F]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
IMP (Subject of Investigation/LOI)
Query on IMP

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth G]
EA [auth H]
FA [auth H]
I [auth A]
AA [auth G],
CA [auth G],
EA [auth H],
FA [auth H],
I [auth A],
K [auth A],
L [auth B],
N [auth B],
O [auth C],
Q [auth C],
R [auth D],
T [auth D],
U [auth E],
W [auth E],
X [auth F],
Z [auth F]
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.248 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.8α = 90
b = 204.91β = 102.306
c = 116.15γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European UnionLX22NPO5103

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Database references