Novel IMP Binding in Feedback Inhibition of Hypoxanthine-Guanine Phosphoribosyltransferase from Thermoanaerobacter tengcongensis

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.219 

wwPDB Validation   3D Report Full Report

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Alternative IMP Binding in Feedback Inhibition of Hypoxanthine-Guanine Phosphoribosyltransferase from Thermoanaerobacter tengcongensis.

Chen, Q.Liang, Y.Su, X.Gu, X.Zheng, X.Luo, M.

(2005) J Mol Biol 348: 1199-1210

  • DOI: https://doi.org/10.1016/j.jmb.2005.02.064
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Crystal structures of Thermoanaerobacter tengcongensis hypoxanthine-guanine phosphoribosyltransferase (HGPRT) apoenzyme and the enzyme-inosine monophosphate (IMP) complex have been determined to 2.5A and 2.2A resolution, respectively. The active form of the enzyme was identified as a tetramer in solution and the K(i) value of IMP was measured to be 45 microM for alpha-D-phosphoribosyl-1-pyrophosphate (PRPP). Conformation of the flexible loop in T.tengcongensis HGPRT, which is involved in substrate PRPP binding, is different from that observed in phosphoribosyltransferases (PRTs). It contains a 3-10 helix, and a unique double serine repeat. This loop is ordered even in the apoenzyme and assumes a half-closed conformation. The primary magnesium ion is directly coordinated by side-chains of Glu101 and Asp102, and water molecules in the apoenzyme, suggesting a possible prerequisite role for substrate PRPP binding. Most interestingly, an alternative IMP binding mode is found in the structure of T.tengcongensis HGPRT-IMP complex. The 5'-phosphate of IMP occupies the PPi position usually seen in PRT-PRPP complexes. This new observation is consistent with the lower K(i) value of IMP and may suggest a mechanism involving multiple modes of interactions between IMP and T.tengcongensis HGPRT in product release and feedback inhibition. The structure of T.tengcongensis HGPRT is compared with those of mesophilic HPRTs, and several possible features contributing to its thermostability are elucidated. Overall, T.tengcongensis HGPRT appears to be more diverged from other PRTs.

  • Organizational Affiliation

    Laboratory of Structural Biology, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypoxanthine-guanine phosphoribosyltransferase
A, B
205Caldanaerobacter subterraneus subsp. tengcongensis MB4Mutation(s): 2 
Gene Names: hgprtHptTTE2394
Find proteins for Q8R7L0 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4))
Explore Q8R7L0 
Go to UniProtKB:  Q8R7L0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8R7L0
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
IMP Binding MOAD:  1YFZ Ki: 4.50e+4 (nM) from 1 assay(s)
PDBBind:  1YFZ Ki: 4.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.219 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.77α = 90
b = 137.73β = 90
c = 95.27γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-23
    Changes: Data collection, Refinement description