6LK4 | pdb_00006lk4

Crystal structure of GMP reductase from Trypanosoma brucei in complex with guanosine 5'-triphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.244 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Allosteric regulation accompanied by oligomeric state changes of Trypanosoma brucei GMP reductase through cystathionine-beta-synthase domain.

Imamura, A.Okada, T.Mase, H.Otani, T.Kobayashi, T.Tamura, M.Kubata, B.K.Inoue, K.Rambo, R.P.Uchiyama, S.Ishii, K.Nishimura, S.Inui, T.

(2020) Nat Commun 11: 1837-1837

  • DOI: https://doi.org/10.1038/s41467-020-15611-3
  • Primary Citation Related Structures: 
    6JIG, 6JL8, 6LK4

  • PubMed Abstract: 

    Guanosine 5'-monophosphate reductase (GMPR) is involved in the purine salvage pathway and is conserved throughout evolution. Nonetheless, the GMPR of Trypanosoma brucei (TbGMPR) includes a unique structure known as the cystathionine-β-synthase (CBS) domain, though the role of this domain is not fully understood. Here, we show that guanine and adenine nucleotides exert positive and negative effects, respectively, on TbGMPR activity by binding allosterically to the CBS domain. The present structural analyses revealed that TbGMPR forms an octamer that shows a transition between relaxed and twisted conformations in the absence and presence of guanine nucleotides, respectively, whereas the TbGMPR octamer dissociates into two tetramers when ATP is available instead of guanine nucleotides. These findings demonstrate that the CBS domain plays a key role in the allosteric regulation of TbGMPR by facilitating the transition of its oligomeric state depending on ligand nucleotide availability.


  • Organizational Affiliation
    • Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan.

Macromolecule Content 

  • Total Structure Weight: 54.46 kDa 
  • Atom Count: 3,016 
  • Modeled Residue Count: 425 
  • Deposited Residue Count: 504 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanosine 5'-monophosphate Reductase504Trypanosoma brucei bruceiMutation(s): 0 
EC: 1.7.1.7 (PDB Primary Data), 1.1.1.205 (UniProt)
UniProt
Find proteins for Q57ZS7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q57ZS7 
Go to UniProtKB:  Q57ZS7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57ZS7
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.244 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.107α = 90
b = 144.107β = 90
c = 135.698γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan25660231
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan25242046
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan17K19329

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description