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Isomerase PDB id
1spq
Jmol
Contents
Protein chains
243 a.a. *
Ligands
PEG ×3
Waters ×352
* Residue conservation analysis
PDB id:
1spq
Name: Isomerase
Title: Understanding protein lids: structural analysis of active hi mutants in triosephosphate isomerase
Structure: Triosephosphate isomerase. Chain: a, b. Synonym: tim. Engineered: yes. Mutation: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Gene: tpi1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.16Å     R-factor:   0.162     R-free:   0.198
Authors: I.Kursula,M.Salin,J.Sun,B.V.Norledge,A.M.Haapalainen,N.S.Sam R.K.Wierenga
Key ref: I.Kursula et al. (2004). Understanding protein lids: structural analysis of active hinge mutants in triosephosphate isomerase. Protein Eng Des Sel, 17, 375-382. PubMed id: 15166315 DOI: 10.1093/protein/gzh048
Date:
17-Mar-04     Release date:   24-Aug-04    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00940  (TPIS_CHICK) -  Triosephosphate isomerase
Seq:
Struc: 		248 a.a.
243 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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!
  Biological process     metabolic process   10 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1093/protein/gzh048 Protein Eng Des Sel 17:375-382 (2004)
PubMed id: 15166315  
 
 
Understanding protein lids: structural analysis of active hinge mutants in triosephosphate isomerase.
I.Kursula, M.Salin, J.Sun, B.V.Norledge, A.M.Haapalainen, N.S.Sampson, R.K.Wierenga.
 
  ABSTRACT  
 
The conformational switch from open to closed of the flexible loop 6 of triosephosphate isomerase (TIM) is essential for the catalytic properties of TIM. Using a directed evolution approach, active variants of chicken TIM with a mutated C-terminal hinge tripeptide of loop 6 have been generated (Sun,J. and Sampson,N.S., Biochemistry, 1999, 38, 11474-11481). In chicken TIM, the wild-type C-terminal hinge tripeptide is KTA. Detailed enzymological characterization of six variants showed that some of these (LWA, NPN, YSL, KTK) have decreased catalytic efficiency, whereas others (KVA, NSS) are essentially identical with wild-type. The structural characterization of these six variants is reported. No significant structural differences compared with the wild-type are found for KVA, NSS and LWA, but substantial structural adaptations are seen for NPN, YSL and KTK. These structural differences can be understood from the buried position of the alanine side chain in the C-hinge position 3 in the open conformation of wild-type loop 6. Replacement of this alanine with a bulky side chain causes the closed conformation to be favored, which correlates with the decreased catalytic efficiency of these variants. The structural context of loop 6 and loop 7 and their sequence conservation in 133 wild-type sequences is also discussed.
 

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.  
20024078 M.Stein, R.R.Gabdoulline, and R.C.Wade (2010).
Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields.
  Mol Biosyst, 6, 152-164.  
20694739 R.K.Wierenga, E.G.Kapetaniou, and R.Venkatesan (2010).
Triosephosphate isomerase: a highly evolved biocatalyst.
  Cell Mol Life Sci, 67, 3961-3982.  
19425580 M.K.Go, T.L.Amyes, and J.P.Richard (2009).
Hydron transfer catalyzed by triosephosphate isomerase. Products of the direct and phosphite-activated isomerization of [1-(13)C]-glycolaldehyde in D(2)O.
  Biochemistry, 48, 5769-5778.  
19348462 Y.Wang, R.B.Berlow, and J.P.Loria (2009).
Role of loop-loop interactions in coordinating motions and enzymatic function in triosephosphate isomerase.
  Biochemistry, 48, 4548-4556.  
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
16323206 F.A.Konuklar, V.Aviyente, and T.Haliloğlu (2006).
Coupling of structural fluctuations to deamidation reaction in triosephosphate isomerase by Gaussian network model.
  Proteins, 62, 715-727.  
16741995 S.Donnini, G.Groenhof, R.K.Wierenga, and A.H.Juffer (2006).
The planar conformation of a strained proline ring: a QM/MM study.
  Proteins, 64, 700-710.  
15870208 M.Karplus, and J.Kuriyan (2005).
Molecular dynamics and protein function.
  Proc Natl Acad Sci U S A, 102, 6679-6685.  
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.