Database accession: MF7000893
Name: Rabbit muscle triosephosphate isomerase
PDB ID: 1r2t
Experimental method: X-ray (2.25 Å)
Assembly: Homodimer
Source organism: Oryctolagus cuniculus
Primary publication of the structure:
Aparicio R, Ferreira ST, Polikarpov I
Closed conformation of the active site loop of rabbit muscle triosephosphate isomerase in the absence of substrate: evidence of conformational heterogeneity.
(2003) J. Mol. Biol. 334: 1023-41
PMID: 14643664
Abstract:
The active site loop of triosephosphate isomerase (TIM) exhibits a hinged-lid motion, alternating between the two well defined "open" and "closed" conformations. Until now the closed conformation had only been observed in protein complexes with substrate analogues. Here, we present the first rabbit muscle apo TIM structure, refined to 1.5A resolution, in which the active site loop is either in the open or in the closed conformation in different subunits of the enzyme. In the closed conformation described here, the lid loop residues participate in stabilizing hydrogen bonds characteristic of holo TIM structures, whereas chemical interactions observed in the open loop conformation are similar to those found in the apo structures of TIM. In the closed conformation, a number of water molecules are observed at the projected ligand atom positions that are hydrogen bonded to the active site residues. Additives used during crystallization (DMSO and Tris molecules and magnesium atoms) were modeled in the electron density maps. However, no specific binding of these molecules is observed at, or close to, the active site and the lid loop. To further investigate this unusual closed conformation of the apo enzyme, two more rabbit muscle TIM structures, one in the same and another in a different crystal form, were determined. These structures present the open lid conformation only, indicating that the closed conformation cannot be explained by crystal contact effects. To rationalize why the active site loop is closed in the absence of ligand in one of the subunits, extensive comparison with previously solved TIM structures was carried out, supported by the bulk of available experimental information about enzyme kinetics and reaction mechanism of TIM. The observation of both open and closed lid conformations in TIM crystals might be related to a persistent conformational heterogeneity of this protein in solution.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
methylglyoxal synthase activity methylglyoxal synthase activity
protein homodimerization activity protein homodimerization activity
triose-phosphate isomerase activity triose-phosphate isomerase activity
ubiquitin protein ligase binding ubiquitin protein ligase binding
Biological process:
canonical glycolysis canonical glycolysis
gluconeogenesis gluconeogenesis
glyceraldehyde-3-phosphate biosynthetic process glyceraldehyde-3-phosphate biosynthetic process
glycerol catabolic process glycerol catabolic process
methylglyoxal biosynthetic process methylglyoxal biosynthetic process
Cellular component:
cytosol cytosol
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Triosephosphate isomerase
Source organism: Oryctolagus cuniculus
Length: 249 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAPSRKFFVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALSEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ
UniProtKB AC: P00939 (positions: 4-249)
Coverage: 98%
Name: Triosephosphate isomerase
Source organism: Oryctolagus cuniculus
Length: 249 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAPSRKFFVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALSEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ
UniProtKB AC: P00939 (positions: 3-249)
Coverage: 99%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Triosephosphate isomerase
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
Two-state unfolding behavior was proved experimentally for sveral members of the family. Isolated monomers are not stable at all. (PMID:15037083, PMID:10785370, PMID:26206330).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
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