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PDBsum entry 1nf0

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protein ligands Protein-protein interface(s) links
Isomerase PDB id
1nf0
Jmol
Contents
Protein chains
247 a.a. *
Ligands
13P ×2
Waters ×419
* Residue conservation analysis
PDB id:
1nf0
Name: Isomerase
Title: Triosephosphate isomerase in complex with dhap
Structure: Triosephosphate isomerase. Chain: a, b. Synonym: tim. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: tpi1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.60Å     R-factor:   0.209     R-free:   0.268
Authors: G.Jogl,S.Rozovsky,A.E.Mcdermott,L.Tong
Key ref:
G.Jogl et al. (2003). Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution. Proc Natl Acad Sci U S A, 100, 50-55. PubMed id: 12509510 DOI: 10.1073/pnas.0233793100
Date:
12-Dec-02     Release date:   07-Jan-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00942  (TPIS_YEAST) -  Triosephosphate isomerase
Seq:
Struc:
248 a.a.
247 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 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 = 13P)
corresponds exactly
= glycerone phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1073/pnas.0233793100 Proc Natl Acad Sci U S A 100:50-55 (2003)
PubMed id: 12509510  
 
 
Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution.
G.Jogl, S.Rozovsky, A.E.McDermott, L.Tong.
 
  ABSTRACT  
 
In enzyme catalysis, where exquisitely positioned functionality is the sine qua non, atomic coordinates for a Michaelis complex can provide powerful insights into activation of the substrate. We focus here on the initial proton transfer of the isomerization reaction catalyzed by triosephosphate isomerase and present the crystal structure of its Michaelis complex with the substrate dihydroxyacetone phosphate at near-atomic resolution. The active site is highly compact, with unusually short and bifurcated hydrogen bonds for both catalytic Glu-165 and His-95 residues. The carboxylate oxygen of the catalytic base Glu-165 is positioned in an unprecedented close interaction with the ketone and the alpha-hydroxy carbons of the substrate (C em leader O approximately 3.0 A), which is optimal for the proton transfer involving these centers. The electrophile that polarizes the substrate, His-95, has close contacts to the substrate's O1 and O2 (N em leader O < or = 3.0 and 2.6 A, respectively). The substrate is conformationally relaxed in the Michaelis complex: the phosphate group is out of the plane of the ketone group, and the hydroxy and ketone oxygen atoms are not in the cisoid configuration. The epsilon ammonium group of the electrophilic Lys-12 is within hydrogen-bonding distance of the substrate's ketone oxygen, the bridging oxygen, and a terminal phosphate's oxygen, suggesting a role for this residue in both catalysis and in controlling the flexibility of active-site loop.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The isomerization reaction catalyzed by triosephosphate isomerase. (a) The reaction pathway from DHAP to GAP, including the putative reaction intermediate, an enediol(ate). The phosphate elimination side reaction produces a toxic compound, methylglyoxal. The catalytic base, Glu-165, extracts the pro-R proton on C1. Stabilization of the enediol(ate) is offered by the neutral His-95, as well as by Lys-12 and Asn-10 (5). (b) The atom-numbering scheme of DHAP and dihedral angles discussed throughout this paper are shown. (c) A molecular model of the previously proposed in-plane arrangement of the phosphate group. (d) The out-of-plane conformation of DHAP observed here in our structure of the Michaelis complex.
Figure 3.
Fig. 3. Structure of yeast TIM:DHAP complex. (a) Triosephosphate isomerase in complex with a tight-binding transition-state analog phosphoglycolohydroxamate [PDB entry 7TIM (9) in cyan and purple for carbon atoms in the enzyme and the analog, respectively] is overlaid with our structure of the actual substrate, DHAP (in yellow and green). The position of the substrate differs in fine details from that of the transition-state analog. (b) Omit electron density for the substrate and catalytic residues Glu-165, His-95, and Lys-12. (c) Omit electron density for the active site in the second molecule. (d) ORTEP representation displaying the anisotropic motion for the active-site atoms. The glutamic acid side chain and the substrate carbons (C3, C2, and less so, C1) as well as the oxygens undergoing isomerization (O1 and O2) are more dynamically flexible than the active-site residues and phosphate group. (e) A schematic drawing of the network of hydrogen bonds in the active site.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21308811 I.Pápai, A.Hamza, P.M.Pihko, and R.K.Wierenga (2011).
Stereoelectronic requirements for optimal hydrogen-bond-catalyzed enolization.
  Chemistry, 17, 2859-2866.  
21289039 M.Banerjee, H.Balaram, N.V.Joshi, and P.Balaram (2011).
Engineered dimer interface mutants of triosephosphate isomerase: the role of inter-subunit interactions in enzyme function and stability.
  Protein Eng Des Sel, 24, 463-472.  
  21447068 M.Samanta, M.Banerjee, M.R.Murthy, H.Balaram, and P.Balaram (2011).
Probing the role of the fully conserved Cys126 in triosephosphate isomerase by site-specific mutagenesis - distal effects on dimer stability.
  FEBS J, 278, 1932-1943.
PDB codes: 3pvf 3pwa 3py2
20694739 R.K.Wierenga, E.G.Kapetaniou, and R.Venkatesan (2010).
Triosephosphate isomerase: a highly evolved biocatalyst.
  Cell Mol Life Sci, 67, 3961-3982.  
19350589 G.F.Swiegers, J.Huang, R.Brimblecombe, J.Chen, G.C.Dismukes, U.T.Mueller-Westerhoff, L.Spiccia, and G.G.Wallace (2009).
Homogeneous catalysts with a mechanical ("machine-like") action.
  Chemistry, 15, 4746-4759.  
19583769 M.Banerjee, H.Balaram, and P.Balaram (2009).
Structural effects of a dimer interface mutation on catalytic activity of triosephosphate isomerase. The role of conserved residues and complementary mutations.
  FEBS J, 276, 4169-4183.  
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.  
19588901 N.Doucet, E.D.Watt, and J.P.Loria (2009).
The flexibility of a distant loop modulates active site motion and product release in ribonuclease A.
  Biochemistry, 48, 7160-7168.  
19622869 P.Gayathri, M.Banerjee, A.Vijayalakshmi, H.Balaram, P.Balaram, and M.R.Murthy (2009).
Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site.
  Acta Crystallogr D Biol Crystallogr, 65, 847-857.
PDB codes: 2vfd 2vfe 2vff 2vfg 2vfh 2vfi
18615422 X.Zhu, and L.Lai (2009).
A novel method for enzyme design.
  J Comput Chem, 30, 256-267.  
18772387 S.M.Sullivan, and T.Holyoak (2008).
Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection.
  Proc Natl Acad Sci U S A, 105, 13829-13834.
PDB codes: 3dt2 3dt4 3dt7 3dtb
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.  
17196220 M.Allert, M.A.Dwyer, and H.W.Hellinga (2007).
Local encoding of computationally designed enzyme activity.
  J Mol Biol, 366, 945-953.  
17287353 S.Rozovsky, and A.E.McDermott (2007).
Substrate product equilibrium on a reversible enzyme, triosephosphate isomerase.
  Proc Natl Acad Sci U S A, 104, 2080-2085.  
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.  
17075051 J.K.Lassila, H.K.Privett, B.D.Allen, and S.L.Mayo (2006).
Combinatorial methods for small-molecule placement in computational enzyme design.
  Proc Natl Acad Sci U S A, 103, 16710-16715.  
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.  
15796706 R.A.Friesner, and V.Guallar (2005).
Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis.
  Annu Rev Phys Chem, 56, 389-427.  
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.