1ML1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop.

Thanki, N.Zeelen, J.P.Mathieu, M.Jaenicke, R.Abagyan, R.A.Wierenga, R.K.Schliebs, W.

(1997) Protein Eng. 10: 159-167


  • PubMed 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 inte ...

    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.


    Related Citations: 
    • Active Site Properties of Monomeric Triosephosphate Isomerase (Monotim) as Deduced from Mutational and Structural Studies
      Schliebs, W.,Thanki, N.,Eritja, R.,Wierenga, R.
      (1996) Protein Sci. 5: 229
    • The Crystal Structure of an Engineered Monomeric Triosephosphate Isomerase, Monotim: The Correct Modelling of an Eight-Residue Loop
      Borchert, T.V.,Abagyan, R.,Kishan, K.V.R.,Zeelen, J.P.,Wierenga, R.K.
      (1993) Structure 1: 205
    • Three New Crystal Structures of Point Mutation Variants of Monotim: Conformational Flexibility of Loop-1, Loop-4 and Loop-8
      Borchert, T.V.,Kishan, K.V.,Zeelen, J.P.,Schliebs, W.,Thanki, N.,Abagyan, R.,Jaenicke, R.,Wierenga, R.K.
      (1995) Structure 3: 669


    Organizational Affiliation

    Institut für Biophysik und Physikalische Biochemie, Universitt Regensburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIOSEPHOSPHATE ISOMERASE
A, C, E, G, I, K
243Trypanosoma brucei bruceiEC: 5.3.1.1
Find proteins for P04789 (Trypanosoma brucei brucei)
Go to UniProtKB:  P04789
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGA
Query on PGA

Download SDF File 
Download CCD File 
A, C, E, G, I, K
2-PHOSPHOGLYCOLIC ACID
C2 H5 O6 P
ASCFNMCAHFUBCO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PGAKi: 52000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.231 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 165.230α = 90.00
b = 165.230β = 90.00
c = 51.230γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
SCALEPACKdata scaling
X-PLORmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-03-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance