Database accession: MF7000210
Name: Chorismate mutase (Mycobacterium tuberculosis)
PDB ID: 5mpv
Experimental method: X-ray (1.49 Å)
Assembly: Homodimer
Source organism: Mycobacterium tuberculosis
Primary publication of the structure:
Fahrig-Kamarauskait J, Würth-Roderer K, Thorbjørnsrud HV, Mailand S, Krengel U, Kast P
Evolving the naturally compromised chorismate mutase from Mycobacterium tuberculosis to top performance.
(2020) J. Biol. Chem. 295: 17514-17534
PMID: 33453995
Abstract:
Chorismate mutase (CM), an essential enzyme at the branch-point of the shikimate pathway, is required for the biosynthesis of phenylalanine and tyrosine in bacteria, archaea, plants, and fungi. MtCM, the CM from Mycobacterium tuberculosis, has less than 1% of the catalytic efficiency of a typical natural CM and requires complex formation with 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase for high activity. To explore the full potential of MtCM for catalyzing its native reaction, we applied diverse iterative cycles of mutagenesis and selection, thereby raising kcat/Km 270-fold to 5 × 105m-1s-1, which is even higher than for the complex. Moreover, the evolutionarily optimized autonomous MtCM, which had 11 of its 90 amino acids exchanged, was stabilized compared with its progenitor, as indicated by a 9 °C increase in melting temperature. The 1.5 Å crystal structure of the top-evolved MtCM variant reveals the molecular underpinnings of this activity boost. Some acquired residues (e.g. Pro52 and Asp55) are conserved in naturally efficient CMs, but most of them lie beyond the active site. Our evolutionary trajectories reached a plateau at the level of the best natural enzymes, suggesting that we have exhausted the potential of MtCM. Taken together, these findings show that the scaffold of MtCM, which naturally evolved for mediocrity to enable inter-enzyme allosteric regulation of the shikimate pathway, is inherently capable of high activity.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
chorismate mutase activity chorismate mutase activity
Biological process:
amino acid biosynthetic process amino acid biosynthetic process
aromatic amino acid family biosynthetic process, prephenate pathway aromatic amino acid family biosynthetic process, prephenate pathway
chorismate metabolic process chorismate metabolic process
salicylic acid biosynthetic process salicylic acid biosynthetic process
Cellular component:
cytoplasm cytoplasm
plasma membrane plasma membrane
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: D, D-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Intracellular chorismate mutase
Source organism: Mycobacterium tuberculosis
Length: 105 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMRPEPPHHENAELAAMNLEMLESQPVPEIDTLREEIDRLDAEILALVKRRAEVSKAIGKARMASGGTRLVHSREMKVIERYSELGPDGKDLAILLLRLGRGRLGH
UniProtKB AC: P9WIC1 (positions: 26-93)
Coverage: 64%
Name: Intracellular chorismate mutase
Source organism: Mycobacterium tuberculosis
Length: 105 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMRPEPPHHENAELAAMNLEMLESQPVPEIDTLREEIDRLDAEILALVKRRAEVSKAIGKARMASGGTRLVHSREMKVIERYSELGPDGKDLAILLLRLGRGRLGH
UniProtKB AC: P9WIC1 (positions: 26-93)
Coverage: 64%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Chorismate mutase type II
Evidence level: Indirect evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
The enzyme is an intertwined dimer of three helices with connecting loops. The N-terminal helices of the two monomers twine together to form an anti-parallel coiled-coil with a hydrophobic interaction surface. The loop between the first and second helices is disordered (PMID:16914555).
Chain D:
N/A
Chain D-2:
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)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
