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PDBsum entry 2v2h

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protein ligands metals Protein-protein interface(s) links
Isomerase PDB id
2v2h
Jmol
Contents
Protein chains
241 a.a. *
Ligands
PGA ×3
Metals
_CL ×3
Waters ×848
* Residue conservation analysis
PDB id:
2v2h
Name: Isomerase
Title: The a178l mutation in thE C-terminal hinge of the flexible loop-6 of triosephosphate isomerase (tim) induces a more closed conformation of this hinge region in dimeric and monomeric tim
Structure: Triosephosphate isomerase glycosomal. Chain: a, b, c. Synonym: triosephosphate isomerase, tim, triose-phosphate isomerase. Engineered: yes. Mutation: yes
Source: Trypanosoma brucei brucei. Organism_taxid: 5702. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
1.18Å     R-factor:   0.139     R-free:   0.186
Authors: M.Alahuhta,M.G.Casteleijn,P.Neubauer,R.K.Wierenga
Key ref:
M.Alahuhta et al. (2008). Structural studies show that the A178L mutation in the C-terminal hinge of the catalytic loop-6 of triosephosphate isomerase (TIM) induces a closed-like conformation in dimeric and monomeric TIM. Acta Crystallogr D Biol Crystallogr, 64, 178-188. PubMed id: 18219118 DOI: 10.1107/S0907444907059021
Date:
06-Jun-07     Release date:   19-Feb-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04789  (TPIS_TRYBB) -  Triosephosphate isomerase, glycosomal
Seq:
Struc:
250 a.a.
241 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.5.3.1.1  - Triose-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate
D-glyceraldehyde 3-phosphate
Bound ligand (Het Group name = PGA)
matches with 72.00% similarity
= glycerone phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     glycosome   2 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S0907444907059021 Acta Crystallogr D Biol Crystallogr 64:178-188 (2008)
PubMed id: 18219118  
 
 
Structural studies show that the A178L mutation in the C-terminal hinge of the catalytic loop-6 of triosephosphate isomerase (TIM) induces a closed-like conformation in dimeric and monomeric TIM.
M.Alahuhta, M.G.Casteleijn, P.Neubauer, R.K.Wierenga.
 
  ABSTRACT  
 
The flexible catalytic loop, loop-6, of TIM has evolved to preferably be open in the unliganded state and to preferably be closed in the liganded state. The N-terminal and C-terminal hinges of this loop are important for its opening/closing mechanism. In this study, a small conserved C-terminal hinge residue, Ala178, has been mutated into a residue with a larger side chain, Leu178. This mutation has been made in the dimeric trypanosomal wild-type TIM (wtTIM) and in its mutated catalytically competent monomeric variant (ml1TIM). The variants are referred to as A178L and ml1A178L, respectively. Crystal structures have been determined of unliganded A178L (at 2.2 A), liganded A178L (at 1.89 A), unliganded ml1A178L (at 2.3 A) and liganded ml1A178L (at 1.18 A) using the transition-state analogue 2-phosphoglycolate as a ligand. Structural characterization of the two variants shows that this mutation favours the closed conformation of the C-terminal hinge region, even in the absence of ligand. In the structure of the unliganded A178L variant a range of new loop-6 conformations are observed, including subunits in which the tip of loop-6 is completely disordered. The catalytic efficiency of A178L is lower than that of wtTIM, which correlates with the structural differences between the apo forms of wtTIM and A178L, in particular the more disordered loop-6 in the structure of unliganded A178L. In the liganded structures of A178L and ml1A178L the structural differences induced by the mutation are minimal. Structural characterization of the ml1A178L variant highlights its structural plasticity.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Comparison of the open (unliganded, 5tim , cyan) and closed (liganded, 1n55 , magenta) structures of wild-type TIM (top view). (a) The open structure of loop-6 is coloured cyan; the closed structure is coloured magenta. (b) Stereo picture, showing the environment of Ala178 in the open (cyan) and closed (magenta) conformation.
Figure 3.
Figure 3 Comparison of the structures of liganded wtTIM (1n55 ) and liganded ml1TIM (1ml1 ). (a) Schematic view. (b) Stereo picture. The wtTIM structure is coloured magenta and the ml1TIM structure is coloured gold. In wtTIM the carboxyl moiety of the ligand has a double conformation (up and down). The up conformation is the major conformation. In the structure of the ml1TIM-2PG complex only the down conformation is observed.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 178-188) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21396445 J.Moraes, R.Arreola, N.Cabrera, L.Saramago, D.Freitas, A.Masuda, I.da Silva Vaz, M.Tuena de Gomez-Puyou, R.Perez-Montfort, A.Gomez-Puyou, and C.Logullo (2011).
Structural and biochemical characterization of a recombinant triosephosphate isomerase from Rhipicephalus (Boophilus) microplus.
  Insect Biochem Mol Biol, 41, 400-409.
PDB code: 3th6
20693693 M.Salin, E.G.Kapetaniou, M.Vaismaa, M.Lajunen, M.G.Casteleijn, P.Neubauer, L.Salmon, and R.K.Wierenga (2010).
Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase.
  Acta Crystallogr D Biol Crystallogr, 66, 934-944.
PDB codes: 2x16 2x1r 2x1s 2x1t 2x1u 2x2g
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