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TitleStructural snapshots of Mycobacterium tuberculosis enolase reveal dual mode of 2PG binding and its implication in enzyme catalysis.
Journal, issue, pagesIUCrJ, Vol. 10, Issue Pt 6, Page 738-753, Year 2023
Publish dateNov 1, 2023
AuthorsMohammed Ahmad / Bhavya Jha / Sucharita Bose / Satish Tiwari / Abhisek Dwivedy / Deepshikha Kar / Ravikant Pal / Richard Mariadasse / Tanya Parish / Jeyaraman Jeyakanthan / Kutti R Vinothkumar / Bichitra Kumar Biswal /
PubMed AbstractEnolase, a ubiquitous enzyme, catalyzes the reversible conversion of 2-phosphoglycerate (2PG) to phosphoenolpyruvate (PEP) in the glycolytic pathway of organisms of all three domains of life. The ...Enolase, a ubiquitous enzyme, catalyzes the reversible conversion of 2-phosphoglycerate (2PG) to phosphoenolpyruvate (PEP) in the glycolytic pathway of organisms of all three domains of life. The underlying mechanism of the 2PG to PEP conversion has been studied in great detail in previous work, however that of the reverse reaction remains to be explored. Here we present structural snapshots of Mycobacterium tuberculosis (Mtb) enolase in apo, PEP-bound and two 2PG-bound forms as it catalyzes the conversion of PEP to 2PG. The two 2PG-bound complex structures differed in the conformation of the bound product (2PG) viz the widely reported canonical conformation and a novel binding pose, which we refer to here as the alternate conformation. Notably, we observed two major differences compared with the forward reaction: the presence of Mg is non-obligatory for the reaction and 2PG assumes an alternate conformation that is likely to facilitate its dissociation from the active site. Molecular dynamics studies and binding free energy calculations further substantiate that the alternate conformation of 2PG causes distortions in both metal ion coordination and hydrogen-bonding interactions, resulting in an increased flexibility of the active-site loops and aiding product release. Taken together, this study presents a probable mechanism involved in PEP to 2PG catalysis that is likely to be mediated by the conformational change of 2PG at the active site.
External linksIUCrJ / PubMed:37860976 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.99 - 3.23 Å
Structure data

30988

7e4x

EMDB-30988, PDB-7e4x:
Structure of Enolase from Mycobacterium tuberculosis
Method: EM (single particle) / Resolution: 3.08 Å

30989

7e51

EMDB-30989, PDB-7e51:
Structure of PEP bound Enolase from Mycobacterium tuberculosis
Method: EM (single particle) / Resolution: 3.23 Å

PDB-6l7d:
Mycobacterium tuberculosis enolase mutant - S42A
Method: X-RAY DIFFRACTION / Resolution: 3 Å

PDB-7ckp:
Mycobacterium tuberculosis Enolase
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-7clk:
Mycobacterium tuberculosis enolase in complex with alternate 2-phosphoglycerate
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-7cll:
Mycobacterium tubeculosis enolase in complex with 2-Phosphoglycerate
Method: X-RAY DIFFRACTION / Resolution: 1.99 Å

PDB-7dlr:
Mycobacterium tuberculosis enolase mutant - E163A
Method: X-RAY DIFFRACTION / Resolution: 2.25 Å

PDB-7e4f:
Mycobacterium tuberculosis enolase mutant - E204A complex with phosphoenolpyruvate
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

Chemicals

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-2PG:
2-PHOSPHOGLYCERIC ACID

ChemComp-ACT:
ACETATE ION

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-MPD:
(4S)-2-METHYL-2,4-PENTANEDIOL / precipitant*YM

ChemComp-GOL:
GLYCEROL

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-CL:
Unknown entry

ChemComp-PEP:
PHOSPHOENOLPYRUVATE

Source
  • mycobacterium tuberculosis (bacteria)
  • mycobacterium tuberculosis h37rv (bacteria)
  • mycobacterium tuberculosis (strain atcc 25618 / h37rv) (bacteria)
KeywordsHYDROLASE / Mycobacterium tuberculosis / enolase / mutant / complex / LYASE / phosphoglycerate / phosphoenolpyuruvate / 2-phosphoglycerate / PEP / METAL BINDING PROTEIN

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