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PDBsum entry 2vel

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protein ligands metals Protein-protein interface(s) links
Isomerase PDB id
2vel
Jmol
Contents
Protein chains
238 a.a. *
Ligands
PGA ×2
Metals
_CL ×2
Waters ×366
* Residue conservation analysis
PDB id:
2vel
Name: Isomerase
Title: Structure-based enzyme engineering efforts with an inactive monomeric tim variant: the importance of a single point mutation for generating an active site with suitable binding properties
Structure: Glycosomal triosephosphate isomerase. Chain: a, b. Fragment: residues 2-13,15-72,80-234,238-250. Synonym: tim, triose-phosphate isomerase, triosephosphate isomerase. Engineered: yes. Mutation: yes
Source: Trypanosoma brucei brucei. Organism_taxid: 5702. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
2.30Å     R-factor:   0.184     R-free:   0.257
Authors: M.Alahuhta,M.Salin,M.G.Casteleijn,C.Kemmer,I.El-Sayed, K.Augustyns,P.Neubauer,R.K.Wierenga
Key ref: M.Alahuhta et al. (2008). Structure-based protein engineering efforts with a monomeric TIM variant: the importance of a single point mutation for generating an active site with suitable binding properties. Protein Eng Des Sel, 21, 257-266. PubMed id: 18239072 DOI: 10.1093/protein/gzn002
Date:
24-Oct-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.
238 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: 10.1093/protein/gzn002 Protein Eng Des Sel 21:257-266 (2008)
PubMed id: 18239072  
 
 
Structure-based protein engineering efforts with a monomeric TIM variant: the importance of a single point mutation for generating an active site with suitable binding properties.
M.Alahuhta, M.Salin, M.G.Casteleijn, C.Kemmer, I.El-Sayed, K.Augustyns, P.Neubauer, R.K.Wierenga.
 
  ABSTRACT  
 
A monomeric variant of triosephosphate isomerase (TIM) with a new engineered binding groove has been characterized further. In this variant (ml8bTIM), the phosphate binding loop had been shortened, causing the binding site to be much more extended. Here, it is reported that in the V233A variant of ml8bTIM (A-TIM), three important properties of the wild-type TIM active site have been restored: (i) the structural properties of loop-7, (ii) the binding site of a conserved water molecule between loop-7 and loop-8 and (iii) the binding site of the phosphate moiety. It is shown that the active site of A-TIM can bind TIM transition state analogs and suicide inhibitors competently. It is found that the active site geometry of the A-TIM complexes is less compact and more solvent exposed, as in wild-type TIM. This correlates with the observation that the catalytic efficiency of A-TIM for interconverting the TIM substrates is too low to be detected. It is also shown that the A-TIM active site can bind compounds which do not bind to wild-type TIM and which are completely different from the normal TIM substrate, like a citrate molecule. The binding of this citrate molecule is stabilized by hydrogen bonding interactions with the new binding groove.
 

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.  
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.