1ml1: Difference between revisions

Revision as of 01:21, 3 May 2008

PROTEIN ENGINEERING WITH MONOMERIC TRIOSEPHOSPHATE ISOMERASE: THE MODELLING AND STRUCTURE VERIFICATION OF A SEVEN RESIDUE LOOP

OverviewOverview

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.

About this StructureAbout this Structure

1ML1 is a Single protein structure of sequence from Trypanosoma brucei brucei. Full crystallographic information is available from OCA.

ReferenceReference

Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop., Thanki N, Zeelen JP, Mathieu M, Jaenicke R, Abagyan RA, Wierenga RK, Schliebs W, Protein Eng. 1997 Feb;10(2):159-67. PMID:9089815 Page seeded by OCA on Sat May 3 01:20:58 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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 [[Image:1ml1.gif|left|200px]]
- {{Structure
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+The line below this paragraph, containing "STRUCTURE_1ml1", creates the "Structure Box" on the page.
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+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=PGA:2-PHOSPHOGLYCOLIC+ACID'>PGA</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </span>
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-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ml1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ml1 OCA], [http://www.ebi.ac.uk/pdbsum/1ml1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ml1 RCSB]</span>
-}}
 '''PROTEIN ENGINEERING WITH MONOMERIC TRIOSEPHOSPHATE ISOMERASE: THE MODELLING AND STRUCTURE VERIFICATION OF A SEVEN RESIDUE LOOP'''
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 [[Category: Wierenga, R.]]
 [[Category: Zeelen, J P.]]
-[[Category: complex (isomerase/phosphoglycolic acid)]]
+[[Category: Intramolecular oxidoreductase]]
-[[Category: intramolecular oxidoreductase]]
+[[Category: Loop design]]
-[[Category: loop design]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 01:20:58 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:17:29 2008''