spacer
spacer

PDBsum entry 1trd

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Intramolecular oxidoreductase PDB id
1trd
Jmol
Contents
Protein chains
249 a.a. *
Ligands
PGH
Waters ×61
* Residue conservation analysis
PDB id:
1trd
Name: Intramolecular oxidoreductase
Title: The influence of crystal packing on crystallographic binding a new crystal form of trypanosomal tim
Structure: Triosephosphate isomerase. Chain: a, b. Engineered: yes
Source: Trypanosoma brucei brucei. Organism_taxid: 5702. Strain: brucei
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.147    
Authors: M.E.M.Noble,R.K.Wierenga
Key ref: M.E.Noble et al. (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. PubMed id: 8356028
Date:
06-Oct-92     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04789  (TPIS_TRYBB) -  Triosephosphate isomerase, glycosomal
Seq:
Struc:
250 a.a.
249 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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 = PGH)
matches with 66.67% 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    
 
 
Proteins 16:311-326 (1993)
PubMed id: 8356028  
 
 
Structures of the "open" and "closed" state of trypanosomal triosephosphate isomerase, as observed in a new crystal form: implications for the reaction mechanism.
M.E.Noble, J.P.Zeelen, R.K.Wierenga.
 
  ABSTRACT  
 
The structure of trypanosomal triosephosphate isomerase (TIM) has been solved at a resolution of 2.1A in a new crystal form grown at pH 8.8 from PEG6000. In this new crystal form (space group C2, cell dimensions 94.8 A, 48.3 A, 131.0 A, 90.0 degrees, 100.3 degrees, 90.0 degrees), TIM is present in a ligand-free state. The asymmetric unit consists of two TIM subunits. Each of these subunits is part of a dimer which is sitting on a crystallographic twofold axis, such that the crystal packing is formed from two TIM dimers in two distinct environments. The two constituent monomers of a given dimer are, therefore, crystallographically equivalent. In the ligand-free state of TIM in this crystal form, the two types of dimer are very similar in structure, with the flexible loops in the "open" conformation. For one dimer (termed molecule-1), the flexible loop (loop-6) is involved in crystal contacts. Crystals of this type have been used in soaking experiments with 0.4 M ammonium sulphate (studied at 2.4 A resolution), and with 40 microM phosphoglycolohydroxamate (studied at 2.5 A resolution). It is found that transfer to 0.4 M ammonium sulphate (equal to 80 times the Ki of sulphate for TIM), gives rise to significant sulphate binding at the active site of one dimer (termed molecule-2), and less significant binding at the active site of the other. In neither dimer does sulphate induce a "closed" conformation. In a mother liquor containing 40 microM phosphoglycolohydroxamate (equal to 10 times the Ki of phosphoglycolohydroxamate for TIM), an inhibitor molecule binds at the active site of only that dimer of which the flexible loop is free from crystal contacts (molecule-2). In this dimer, it induces a closed conformation. These three structures are compared and discussed with respect to the mode of binding of ligand in the active site as well as with respect to the conformational changes resulting from ligand binding.
 

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
20694739 R.K.Wierenga, E.G.Kapetaniou, and R.Venkatesan (2010).
Triosephosphate isomerase: a highly evolved biocatalyst.
  Cell Mol Life Sci, 67, 3961-3982.  
18175010 A.C.O'Donoghue, T.L.Amyes, and J.P.Richard (2008).
Slow proton transfer from the hydrogen-labelled carboxylic acid side chain (Glu-165) of triosephosphate isomerase to imidazole buffer in D(2)O.
  Org Biomol Chem, 6, 391-396.  
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
17336327 J.G.Kempf, J.Y.Jung, C.Ragain, N.S.Sampson, and J.P.Loria (2007).
Dynamic requirements for a functional protein hinge.
  J Mol Biol, 368, 131-149.  
17646926 K.H.Kim (2007).
Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers?
  J Comput Aided Mol Des, 21, 421-435.  
17444661 T.L.Amyes, and J.P.Richard (2007).
Enzymatic catalysis of proton transfer at carbon: activation of triosephosphate isomerase by phosphite dianion.
  Biochemistry, 46, 5841-5854.  
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
11983887 D.Arsenieva, R.Hardre, L.Salmon, and C.J.Jeffery (2002).
The crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid.
  Proc Natl Acad Sci U S A, 99, 5872-5877.
PDB code: 1koj
11151009 B.V.Norledge, A.M.Lambeir, R.A.Abagyan, A.Rottmann, A.M.Fernandez, V.V.Filimonov, M.G.Peter, and R.K.Wierenga (2001).
Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: toward a new substrate specificity.
  Proteins, 42, 383-389.
PDB code: 1dkw
11589711 I.Kursula, S.Partanen, A.M.Lambeir, D.M.Antonov, K.Augustyns, and R.K.Wierenga (2001).
Structural determinants for ligand binding and catalysis of triosephosphate isomerase.
  Eur J Biochem, 268, 5189-5196.
PDB code: 1if2
10758003 F.M.McMillan, M.Cahoon, A.White, L.Hedstrom, G.A.Petsko, and D.Ringe (2000).
Crystal structure at 2.4 A resolution of Borrelia burgdorferi inosine 5'-monophosphate dehydrogenase: evidence of a substrate-induced hinged-lid motion by loop 6.
  Biochemistry, 39, 4533-4542.
PDB code: 1eep
10591103 D.Maes, J.P.Zeelen, N.Thanki, N.Beaucamp, M.Alvarez, M.H.Thi, J.Backmann, J.A.Martial, L.Wyns, R.Jaenicke, and R.K.Wierenga (1999).
The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures.
  Proteins, 37, 441-453.
PDB code: 1b9b
  9684881 J.Sun, and N.S.Sampson (1998).
Determination of the amino acid requirements for a protein hinge in triosephosphate isomerase.
  Protein Sci, 7, 1495-1505.  
9708979 J.Y.Choe, B.W.Poland, H.J.Fromm, and R.B.Honzatko (1998).
Role of a dynamic loop in cation activation and allosteric regulation of recombinant porcine fructose-1,6-bisphosphatase.
  Biochemistry, 37, 11441-11450.
PDB codes: 1bfl 1cnq
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
  9336838 N.Beaucamp, A.Hofmann, B.Kellerer, and R.Jaenicke (1997).
Dissection of the gene of the bifunctional PGK-TIM fusion protein from the hyperthermophilic bacterium Thermotoga maritima: design and characterization of the separate triosephosphate isomerase.
  Protein Sci, 6, 2159-2165.  
9261072 S.S.Velanker, S.S.Ray, R.S.Gokhale, S.Suma, H.Balaram, P.Balaram, and M.R.Murthy (1997).
Triosephosphate isomerase from Plasmodium falciparum: the crystal structure provides insights into antimalarial drug design.
  Structure, 5, 751-761.
PDB code: 1ydv
  8745400 W.Schliebs, N.Thanki, R.Eritja, and R.Wierenga (1996).
Active site properties of monomeric triosephosphate isomerase (monoTIM) as deduced from mutational and structural studies.
  Protein Sci, 5, 229-239.  
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.  
  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
  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
16100954 T.V.Borchert, R.Abagyan, K.V.Kishan, J.P.Zeelen, and R.K.Wierenga (1993).
The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop.
  Structure, 1, 205-213.
PDB code: 1tri
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.