2VEM Isomerase date Oct 25, 2007
title Structure-Based Enzyme Engineering Efforts With An Inactive Tim Variant: The Importance Of A Single Point Mutation For An Active Site With Suitable Binding Properties
authors M.Alahuhta, M.Salin, M.G.Casteleijn, C.Kemmer, I.El-Sayed, K.Augu P.Neubauer, R.K.Wierenga
compound source
Molecule: Glycosomal Triosephosphate Isomerase
Chain: A, B
Fragment: Residues 2-13,15-72,80-234,238-250
Synonym: Triosephosphate Isomerase, Tim, Triose-Phosphate I
Ec: 5.3.1.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Trypanosoma Brucei Brucei
Organism_taxid: 5702
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Pet3a
symmetry Space Group: P 1 21 1
R_factor 0.193 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.800 86.900 56.400 90.00 97.20 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand BBR, TBU enzyme Isomerase E.C.5.3.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure-based protein engineering efforts with a monomeric TIM variant: the importance of a single point mutation for generating an active site with suitable binding properties., Alahuhta M, Salin M, Casteleijn MG, Kemmer C, El-Sayed I, Augustyns K, Neubauer P, Wierenga RK, Protein Eng Des Sel. 2008 Jan 31;. PMID:18239072
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (2vem.pdb1.gz) 37 Kb
  • Biological Unit Coordinates (2vem.pdb2.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 2VEM
  • CSU: Contacts of Structural Units for 2VEM
  • Likely Quarternary Molecular Structure file(s) for 2VEM
  • Structure Factors (167 Kb)
  • Retrieve 2VEM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VEM from S2C, [Save to disk]
  • Re-refined 2vem structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VEM in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2VEM
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2VEM, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vem_A] [2vem] [2vem_B]
  • SWISS-PROT database: [P04789]
  • Domain organization of [TPIS_TRYBB] by SWISSPFAM
  • Other resources with information on 2VEM
  • Community annotation for 2VEM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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