PDBsum entry 1tpf

Isomerase(intramolecular oxidoreductase)

PDB id: 1tpf

Contents

Protein chains

250 a.a. *

Ligands

DMS ×4

Waters ×158

* Residue conservation analysis

PDB id:

1tpf

Name:

Isomerase(intramolecular oxidoreductase)

Title:

Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms

Structure:

Triosephosphate isomerase. Chain: a, b. Engineered: yes

Source:

Trypanosoma brucei brucei. Organism_taxid: 5702. Strain: brucei

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.199

Authors:

K.V.Radha Kishan,J.Ph.Zeelen,R.K.Wierenga

Key ref:

K.V.Kishan et al. (1994). Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms. Protein Sci, 3, 779-787. PubMed id: 8061607 DOI: 10.1002/pro.5560030507

Date:

28-Feb-94 Release date: 31-May-94

Protein chains

P04789  (TPIS_TRYBB) -  Triosephosphate isomerase, glycosomal from Trypanosoma brucei brucei

Seq: 250 a.a.

Struc: 250 a.a.

Enzyme reactions

• Enzyme class: E.C.5.3.1.1 - triose-phosphate isomerase.
• Reaction: D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1002/pro.5560030507

Protein Sci 3:779-787 (1994)

PubMed id: 8061607

Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms.

K.V.Kishan, J.P.Zeelen, M.E.Noble, T.V.Borchert, R.K.Wierenga.

ABSTRACT

Triosephosphate isomerase (TIM) is a dimeric enzyme consisting of 2 identical subunits. Trypanosomal TIM can be crystallized in 4 different spacegroups: P2(1)2(1)2(1), C2(big cell), C2(small cell), and P1. The P1 crystal form only grows in the presence of 1.4 M DMSO; there are 2 DMSO binding sites per subunit. The structures have been refined at a resolution of 1.83 A, 2.10 A, 2.13 A, and 1.80 A, respectively. In the 4 different spacegroups the TIM subunit can be observed in the context of 7 different crystallographic environments. In the C2 cells, the dimer 2-fold axis coincides with a crystallographic 2-fold axis. The similarities and differences of the 7 subunits are discussed. In 6 subunits the flexible loop (loop 6) is open, whereas in the P2(1)2(1)2(1) cell, the flexible loop of subunit 2 is in an almost closed conformation. The crystal contacts in the 4 different crystal forms are predominantly generated by polar residues in loops. A statistical analysis of the residues involved in crystal contacts shows that, in particular, serines are frequently involved in these interactions; 19% of the exposed serines are involved in crystal contacts.

Selected figure(s)

Figure 2.
Fig. 2. Superposition of the7different loop 6structures.Thedeviating loop 6 structureisthe closed structure as ob- servedinsubunit of theP212121form. Glu 167is one of theactivesiteresdues. Residues172-175 move asarigid ody (Wierengaet al., 1991a).

Figure 3.
Fig. 3. Residuesinvolvedin crystal con- tacts in the 4 different crysta! forms. The cut-off value usedwas 3.5 A, therefore only tight crystal contact interactions have been considered. The labeled secondary structure elements identify the@-strands and a-helics of the 8 (&)-units. At the bottom f he figure: Ntot(residues) counts the total number ofresiduesin the 4 different secondary structure elements. Ntot(contacts)countsthe accumulated number of crystal contact residues per type of secondary structure. The loops be- forethe @-strands are located at he back side of thesubunit,far frm the active site; theloopsafterthe@-strandsare at thefront side of thesubunit, near the ac- tivesite (loop 1-loop 8) and near the di- mer interface (loop 1-loop 4).

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1994, 3, 779-787) copyright 1994.