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PDBsum entry 2tim

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Isomerase(intramolecular oxidoreductse) PDB id
2tim
Jmol
Contents
Protein chains
249 a.a.
Ligands
SO4 ×2
DTT
Waters ×292
Superseded by: 5tim
PDB id:
2tim
Name: Isomerase(intramolecular oxidoreductse)
Structure: Triosephosphate isomerase complex with sulphate
Source: (Trypanosoma brucei brucei)
Authors: R.K.Wierenga
Key ref: R.K.Wierenga et al. (1991). The crystal structure of the "open" and the "closed" conformation of the flexible loop of trypanosomal triosephosphate isomerase. Proteins, 10, 33-49. PubMed id: 2062827
Date:
15-May-90     Release date:   15-Oct-91    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 249 a.a.
Key:    Secondary structure  CATH domain

 

 
Proteins 10:33-49 (1991)
PubMed id: 2062827  
 
 
The crystal structure of the "open" and the "closed" conformation of the flexible loop of trypanosomal triosephosphate isomerase.
R.K.Wierenga, M.E.Noble, J.P.Postma, H.Groendijk, K.H.Kalk, W.G.Hol, F.R.Opperdoes.
 
  ABSTRACT  
 
Triosephosphate isomerase has an important loop near the active site which can exist in a "closed" and in an "open" conformation. Here we describe the structural properties of this "flexible" loop observed in two different structures of trypanosomal triosephosphate isomerase. Trypanosomal triosephosphate isomerase, crystallized in the presence of 2.4 M ammonium sulfate, packs as an asymmetric dimer of 54,000 Da in the crystallographic asymmetric unit. Due to different crystal contacts, peptide 167-180 (the flexible loop of subunit-1) is an open conformation, whereas in subunit-2, this peptide (residues 467-480) is in a closed conformation. In the closed conformation, a hydrogen bond exists between the tip of the loop and a well-defined sulfate ion which is bound to the active site of subunit-2. Such an active site sulfate is not present in subunit-1 due to crystal contacts. When the native (2.4 M ammonium sulfate) crystals are transferred to a sulfate-free mother liquor, the flexible loop of subunit-2 adopts the open conformation. From a closed starting model, this open conformation was discovered through molecular dynamics refinement without manual intervention, despite involving C alpha shifts of up to 7 A. The tip of the loop, residues 472, 473, 474, and 475, moves as a rigid body. Our analysis shows that in this crystal form the flexible loop of subunit-2 faces a solvent channel. Therefore the open and the closed conformations of this flexible loop are virtually unaffected by crystal contacts. The actual observed conformation depends only on the absence or presence of a suitable ligand in the active site.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
19343225 B.K.Ho, and D.A.Agard (2009).
Probing the flexibility of large conformational changes in protein structures through local perturbations.
  PLoS Comput Biol, 5, e1000343.  
  19342791 S.Mukherjee, D.Dutta, B.Saha, and A.K.Das (2009).
Expression, purification, crystallization and preliminary X-ray diffraction studies of triosephosphate isomerase from methicillin-resistant Staphylococcus aureus (MRSA252).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 398-401.  
17957775 C.H.Chu, Y.J.Lai, H.Huang, and Y.J.Sun (2008).
Kinetic and structural properties of triosephosphate isomerase from Helicobacter pylori.
  Proteins, 71, 396-406.
PDB code: 2jgq
18219118 M.Alahuhta, M.G.Casteleijn, P.Neubauer, and R.K.Wierenga (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.
PDB codes: 2v0t 2v2c 2v2d 2v2h
12509510 G.Jogl, S.Rozovsky, A.E.McDermott, and L.Tong (2003).
Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution.
  Proc Natl Acad Sci U S A, 100, 50-55.
PDB codes: 1ney 1nf0
12522213 I.Kursula, and R.K.Wierenga (2003).
Crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83-A resolution.
  J Biol Chem, 278, 9544-9551.
PDB code: 1n55
11512153 C.L.Verlinde, V.Hannaert, C.Blonski, M.Willson, J.J.Périé, L.A.Fothergill-Gilmore, F.R.Opperdoes, M.H.Gelb, W.G.Hol, and P.A.Michels (2001).
Glycolysis as a target for the design of new anti-trypanosome drugs.
  Drug Resist Updat, 4, 50-65.  
9442062 M.Alvarez, J.P.Zeelen, V.Mainfroid, F.Rentier-Delrue, J.A.Martial, L.Wyns, R.K.Wierenga, and D.Maes (1998).
Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. Kinetic and structural properties.
  J Biol Chem, 273, 2199-2206.
PDB codes: 1aw1 1aw2
9723162 R.W.Gracy, J.M.Talent, and A.I.Zvaigzne (1998).
Molecular wear and tear leads to terminal marking and the unstable isoforms of aging.
  J Exp Zool, 282, 18-27.  
  9568892 V.Chu, S.Freitag, I.Le Trong, R.E.Stenkamp, and P.S.Stayton (1998).
Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-biotin system.
  Protein Sci, 7, 848-859.
PDB codes: 1swf 1swg
  9154907 S.Kellenberger, J.W.West, W.A.Catterall, and T.Scheuer (1997).
Molecular analysis of potential hinge residues in the inactivation gate of brain type IIA Na+ channels.
  J Gen Physiol, 109, 607-617.  
7878054 A.Chilkoti, P.H.Tan, and P.S.Stayton (1995).
Site-directed mutagenesis studies of the high-affinity streptavidin-biotin complex: contributions of tryptophan residues 79, 108, and 120.
  Proc Natl Acad Sci U S A, 92, 1754-1758.  
8807818 A.Gómez-Puyou, E.Saavedra-Lira, I.Becker, R.A.Zubillaga, A.Rojo-Domínguez, and R.Pérez-Montfort (1995).
Using evolutionary changes to achieve species-specific inhibition of enzyme action--studies with triosephosphate isomerase.
  Chem Biol, 2, 847-855.  
8591049 A.Mattevi, G.Valentini, M.Rizzi, M.L.Speranza, M.Bolognesi, and A.Coda (1995).
Crystal structure of Escherichia coli pyruvate kinase type I: molecular basis of the allosteric transition.
  Structure, 3, 729-741.
PDB code: 1pky
  8580851 L.F.Delboni, S.C.Mande, F.Rentier-Delrue, V.Mainfroid, S.Turley, F.M.Vellieux, J.A.Martial, and W.G.Hol (1995).
Crystal structure of recombinant triosephosphate isomerase from Bacillus stearothermophilus. An analysis of potential thermostability factors in six isomerases with known three-dimensional structures points to the importance of hydrophobic interactions.
  Protein Sci, 4, 2594-2604.
PDB code: 1btm
  8061607 K.V.Kishan, J.P.Zeelen, M.E.Noble, T.V.Borchert, and R.K.Wierenga (1994).
Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms.
  Protein Sci, 3, 779-787.
PDB codes: 1tpe 1tpf
7656010 R.C.Wade, B.A.Luty, E.Demchuk, J.D.Madura, M.E.Davis, J.M.Briggs, and J.A.McCammon (1994).
Simulation of enzyme-substrate encounter with gated active sites.
  Nat Struct Biol, 1, 65-69.  
  8061610 S.C.Mande, V.Mainfroid, K.H.Kalk, K.Goraj, J.A.Martial, and W.G.Hol (1994).
Crystal structure of recombinant human triosephosphate isomerase at 2.8 A resolution. Triosephosphate isomerase-related human genetic disorders and comparison with the trypanosomal enzyme.
  Protein Sci, 3, 810-821.
PDB code: 1hti
8356028 M.E.Noble, J.P.Zeelen, and R.K.Wierenga (1993).
Structures of the "open" and "closed" state of trypanosomal triosephosphate isomerase, as observed in a new crystal form: implications for the reaction mechanism.
  Proteins, 16, 311-326.
PDB codes: 1tpd 1trd 2v5l
8431552 R.C.Wade, M.E.Davis, B.A.Luty, J.D.Madura, and J.A.McCammon (1993).
Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme.
  Biophys J, 64, 9.  
  1304889 C.L.Verlinde, C.J.Witmans, T.Pijning, K.H.Kalk, W.G.Hol, M.Callens, and F.R.Opperdoes (1992).
Structure of the complex between trypanosomal triosephosphate isomerase and N-hydroxy-4-phosphono-butanamide: binding at the active site despite an "open" flexible loop conformation.
  Protein Sci, 1, 1578-1584.
PDB code: 1tsi
1633802 D.A.Kuntz, R.Osowski, M.Schudok, R.K.Wierenga, K.Müller, H.Kessler, and F.R.Opperdoes (1992).
Inhibition of triosephosphate isomerase from Trypanosoma brucei with cyclic hexapeptides.
  Eur J Biochem, 207, 441-447.  
1521533 G.Garza-Ramos, M.Tuena de Gómez-Puyou, A.Gómez-Puyou, and R.W.Gracy (1992).
Dimerization and reactivation of triosephosphate isomerase in reverse micelles.
  Eur J Biochem, 208, 389-395.  
1639191 R.K.Wierenga, T.V.Borchert, and M.E.Noble (1992).
Crystallographic binding studies with triosephosphate isomerases: conformational changes induced by substrate and substrate-analogues.
  FEBS Lett, 307, 34-39.  
2065677 K.D.Schnackerz, and R.W.Gracy (1991).
Probing the catalytic sites of triosephosphate isomerase by 31P-NMR with reversibly and irreversibly binding substrate analogues.
  Eur J Biochem, 199, 231-238.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.