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PDBsum entry 1dkw

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Isomerase PDB id
1dkw
Jmol
Contents
Protein chains
238 a.a. *
Ligands
TBU ×2
Waters ×145
* Residue conservation analysis
PDB id:
1dkw
Name: Isomerase
Title: Crystal structure of triose-phosphate isomerase with modified substrate binding site
Structure: Triosephosphate isomerase. Chain: a, b. Engineered: yes
Source: Trypanosoma brucei brucei. Organism_taxid: 5702. Strain: brucei. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.65Å     R-factor:   0.186     R-free:   0.242
Authors: B.V.Norledge,A.M.Lambeir,R.A.Abagyan,A.Rottman, A.M.Fernandez,V.V.Filimonov,M.G.Peter,R.K.Wierenga
Key ref:
B.V.Norledge et al. (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. PubMed id: 11151009 DOI: 10.1002/1097-0134(20010215)42:3<383::AID-PROT80>3.0.CO;2-G
Date:
08-Dec-99     Release date:   03-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04789  (TPIS_TRYBB) -  Triosephosphate isomerase, glycosomal
Seq:
Struc:
250 a.a.
238 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 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
= 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: 10.1002/1097-0134(20010215)42:3<383::AID-PROT80>3.0.CO;2-G Proteins 42:383-389 (2001)
PubMed id: 11151009  
 
 
Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: toward a new substrate specificity.
B.V.Norledge, A.M.Lambeir, R.A.Abagyan, A.Rottmann, A.M.Fernandez, V.V.Filimonov, M.G.Peter, R.K.Wierenga.
 
  ABSTRACT  
 
Loop 8 (residues 232-242) in triosephosphate isomerase (TIM) is a highly conserved loop that forms a tight binding pocket for the phosphate moiety of the substrate. Its sequence includes the fully conserved, solvent-exposed Leu238. The tight phosphate-binding pocket explains the high substrate specificity of TIM being limited to the in vivo substrates dihydroxyacetone-phosphate and D-glyceraldehyde-3-phosphate. Here we use the monomeric variant of trypanosomal TIM for exploring the structural consequences of shortening this loop. The mutagenesis, guided by extensive modeling calculations and followed up by crystallographic characterization, is aimed at widening the phosphate-binding pocket and, consequently, changing the substrate specificity. Two new variants were characterized. The crystal structures of these variants indicate that in monomeric forms of TIM, the Leu238 side-chain is nicely buried in a hydrophobic cluster. Monomeric forms of wild-type dimeric TIM are known to exist transiently as folding intermediates; our structural analysis suggests that in this monomeric form, Leu238 of loop 8 also adopts this completely buried conformation, which explains its full conservation across the evolution. The much wider phosphate-binding pocket of the new variant allows for the development of a new TIM variant with a different substrate specificity.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Reaction catalyzed by TIM and the structure of the substrate analog PGA.
Figure 3.
Figure 3. Temperature dependency of the molar heat capacity, as measured by DSC (upper panel), and of [222], as measured by CD at 222 nm (lower panel) for ml8bTIM at pH 7.0, 200 mM NaCl, without ligand (solid lines), and in the presence of 1 mM PGA (dashed lines).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2001, 42, 383-389) copyright 2001.  
  Figures were selected by an automated process.  

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.  
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
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.  
12497604 V.Katritch, M.Totrov, and R.Abagyan (2003).
ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field.
  J Comput Chem, 24, 254-265.  
11551466 B.Höcker, C.Jürgens, M.Wilmanns, and R.Sterner (2001).
Stability, catalytic versatility and evolution of the (beta alpha)(8)-barrel fold.
  Curr Opin Biotechnol, 12, 376-381.  
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
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.