[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

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: 3.0 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 / Ethylene glycol

ChemComp-2PG:
2-PHOSPHOGLYCERIC ACID / 2-Phosphoglyceric acid

ChemComp-ACT:
ACETATE ION / Acetate

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER / Water

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

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / Diethylene glycol

ChemComp-CL:
Unknown entry / Chloride

ChemComp-PEP:
PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid

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

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more