spacer
spacer

PDBsum entry 1ml1

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Isomerase PDB id
1ml1
Jmol
Contents
Protein chains
(+ 0 more) 241 a.a. *
Ligands
PGA ×6
Waters ×53
* Residue conservation analysis
PDB id:
1ml1
Name: Isomerase
Title: Protein engineering with monomeric triosephosphate isomerase: the modelling and structure verification of a seven residue loop
Structure: Triosephosphate isomerase. Chain: a, c, e, g, i, k. Synonym: monotim. Engineered: yes
Source: Trypanosoma brucei brucei. Organism_taxid: 5702. Strain: brucei. Cell_line: xl1-blue. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_cell_line: xl1-blue.
Biol. unit: Trimer (from PQS)
Resolution:
2.60Å     R-factor:   0.231     R-free:   0.247
Authors: N.Thanki,J.P.Zeelen,M.Mathieu,R.Jaenicke,R.A.Abagyan, R.Wierenga,W.Schliebs
Key ref: N.Thanki et al. (1997). Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop. Protein Eng, 10, 159-167. PubMed id: 9089815
Date:
27-Sep-96     Release date:   12-Mar-97    
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 11 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    
 
 
Protein Eng 10:159-167 (1997)
PubMed id: 9089815  
 
 
Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop.
N.Thanki, J.P.Zeelen, M.Mathieu, R.Jaenicke, R.A.Abagyan, R.K.Wierenga, W.Schliebs.
 
  ABSTRACT  
 
Protein engineering experiments have been carried out with loop-1 of monomeric triosephosphate isomerase (monoTIM). Loop-1 of monoTIM is disordered in every crystal structure of liganded monoTIM, but in the wild-type TIM it is a very rigid dimer interface loop. This loop connects the first beta-strand with the first alpha-helix of the TIM-barrel scaffold. The first residue of this loop, Lys13, is a conserved catalytic residue. The protein design studies with loop-1 were aimed at rigidifying this loop such that the Lys13 side chain points in the same direction as seen in wild type. The modelling suggested that the loop should be made one residue shorter. With the modelling package ICM the optimal sequence of a new seven-residue loop-1 was determined and its structure was predicted. The new variant could be expressed and purified and has been characterized. The catalytic activity and stability are very similar to those of monoTIM. The crystal structure (at 2.6 A resolution) shows that the experimental loop-1 structure agrees well with the modelled loop-1 structure. The direct superposition of the seven loop residues of the modelled and experimental structures results in an r.m.s. difference of 0.5 A for the 28 main chain atoms. The good agreement between the predicted structure and the crystal structure shows that the described modelling protocol can be used successfully for the reliable prediction of loop structures.
 

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.  
19167403 S.D.Pegan, K.Rukseree, S.G.Franzblau, and A.D.Mesecar (2009).
Structural basis for catalysis of a tetrameric class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis.
  J Mol Biol, 386, 1038-1053.
PDB codes: 3ekl 3ekz 3elf
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
17971437 X.Hu, H.Wang, H.Ke, and B.Kuhlman (2007).
High-resolution design of a protein loop.
  Proc Natl Acad Sci U S A, 104, 17668-17673.
PDB codes: 2rb8 2rbl
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
  11045621 A.Fiser, R.K.Do, and A.Sali (2000).
Modeling of loops in protein structures.
  Protein Sci, 9, 1753-1773.  
10940251 M.A.Martí-Renom, A.C.Stuart, A.Fiser, R.Sánchez, F.Melo, and A.Sali (2000).
Comparative protein structure modeling of genes and genomes.
  Annu Rev Biophys Biomol Struct, 29, 291-325.  
9914192 G.A.Lazar, and T.M.Handel (1998).
Hydrophobic core packing and protein design.
  Curr Opin Chem Biol, 2, 675-679.  
9245397 W.Schliebs, N.Thanki, R.Jaenicke, and R.K.Wierenga (1997).
A double mutation at the tip of the dimer interface loop of triosephosphate isomerase generates active monomers with reduced stability.
  Biochemistry, 36, 9655-9662.  
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.