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PDBsum entry 1ml1
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* Residue conservation analysis
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PDB id:
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Isomerase
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Title:
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Protein engineering with monomeric triosephosphate isomerase: the modelling and structure verification of a seven residue loop
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Structure:
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Triosephosphate isomerase. Chain: a, c, e, g, i, k. Synonym: monotim. Engineered: yes
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Source:
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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.
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Biol. unit:
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Trimer (from
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Resolution:
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2.60Å
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R-factor:
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0.231
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R-free:
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0.247
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Authors:
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N.Thanki,J.P.Zeelen,M.Mathieu,R.Jaenicke,R.A.Abagyan,R.Wierenga, W.Schliebs
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Key ref:
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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:
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Date:
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27-Sep-96
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Release date:
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12-Mar-97
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PROCHECK
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Headers
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References
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P04789
(TPIS_TRYBB) -
Triosephosphate isomerase, glycosomal from Trypanosoma brucei brucei
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Seq:
Struc:
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250 a.a.
241 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 11 residue positions (black
crosses)
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Enzyme class:
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E.C.5.3.1.1
- triose-phosphate isomerase.
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Reaction:
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D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate
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D-glyceraldehyde 3-phosphate
Bound ligand (Het Group name = )
matches with 72.73% similarity
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=
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dihydroxyacetone phosphate
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Protein Eng
10:159-167
(1997)
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PubMed id:
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Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop.
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N.Thanki,
J.P.Zeelen,
M.Mathieu,
R.Jaenicke,
R.A.Abagyan,
R.K.Wierenga,
W.Schliebs.
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ABSTRACT
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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.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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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.
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Acta Crystallogr D Biol Crystallogr,
66,
934-944.
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PDB codes:
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R.K.Wierenga,
E.G.Kapetaniou,
and
R.Venkatesan
(2010).
Triosephosphate isomerase: a highly evolved biocatalyst.
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Cell Mol Life Sci,
67,
3961-3982.
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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.
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J Mol Biol,
386,
1038-1053.
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PDB codes:
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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.
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Acta Crystallogr D Biol Crystallogr,
64,
178-188.
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PDB codes:
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X.Hu,
H.Wang,
H.Ke,
and
B.Kuhlman
(2007).
High-resolution design of a protein loop.
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Proc Natl Acad Sci U S A,
104,
17668-17673.
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PDB codes:
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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.
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Proteins,
42,
383-389.
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PDB code:
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A.Fiser,
R.K.Do,
and
A.Sali
(2000).
Modeling of loops in protein structures.
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Protein Sci,
9,
1753-1773.
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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.
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Annu Rev Biophys Biomol Struct,
29,
291-325.
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G.A.Lazar,
and
T.M.Handel
(1998).
Hydrophobic core packing and protein design.
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Curr Opin Chem Biol,
2,
675-679.
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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.
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Biochemistry,
36,
9655-9662.
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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.
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Links
