8ORU

cyclic 2,3-diphosphoglycerate synthetase from the hyperthermophilic archaeon Methanothermus fervidus bound to 2,3-diphosphoglycerate and ADP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 
    0.256 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.220 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view detailsBest fitted DG2Click on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Structural characterization of a novel cyclic 2,3-diphosphoglycerate synthetase involved in extremolyte production in the archaeon Methanothermus fervidus .

De Rose, S.A.Isupov, M.N.Worthy, H.L.Stracke, C.Harmer, N.J.Siebers, B.Littlechild, J.A.

(2023) Front Microbiol 14: 1267570-1267570

  • DOI: https://doi.org/10.3389/fmicb.2023.1267570
  • Primary Citation of Related Structures:  
    8ORK, 8ORU

  • PubMed Abstract: 

    The enzyme cyclic di-phosphoglycerate synthetase that is involved in the production of the osmolyte cyclic 2,3-diphosphoglycerate has been studied both biochemically and structurally. Cyclic 2,3-diphosphoglycerate is found exclusively in the hyperthermophilic archaeal methanogens, such as Methanothermus fervidus , Methanopyrus kandleri , and Methanothermobacter thermoautotrophicus . Its presence increases the thermostability of archaeal proteins and protects the DNA against oxidative damage caused by hydroxyl radicals. The cyclic 2,3-diphosphoglycerate synthetase enzyme has been crystallized and its structure solved to 1.7 Å resolution by experimental phasing. It has also been crystallized in complex with its substrate 2,3 diphosphoglycerate and the co-factor ADP and this structure has been solved to 2.2 Å resolution. The enzyme structure has two domains, the core domain shares some structural similarity with other NTP-dependent enzymes. A significant proportion of the structure, including a 127 amino acid N-terminal domain, has no structural similarity to other known enzyme structures. The structure of the complex shows a large conformational change that occurs in the enzyme during catalytic turnover. The reaction involves the transfer of the γ-phosphate group from ATP to the substrate 2,3 -diphosphoglycerate and the subsequent S N 2 attack to form a phosphoanhydride. This results in the production of the unusual extremolyte cyclic 2,3 -diphosphoglycerate which has important industrial applications.


  • Organizational Affiliation

    Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic 2,3-diphosphoglycerate synthetaseA [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
459Methanothermus fervidus DSM 2088Mutation(s): 0 
Gene Names: cpgSMfer_0077
EC: 6.5.1.9
UniProt
Find proteins for O93732 (Methanothermus fervidus (strain ATCC 43054 / DSM 2088 / JCM 10308 / V24 S))
Explore O93732 
Go to UniProtKB:  O93732
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO93732
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth DDD],
E [auth AAA],
N [auth BBB],
U [auth CCC]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
DG2 (Subject of Investigation/LOI)
Query on DG2

Download Ideal Coordinates CCD File 
DA [auth DDD]
EA [auth DDD]
G [auth AAA]
H [auth AAA]
M [auth BBB]
(2R)-2,3-diphosphoglyceric acid
C3 H8 O10 P2
XOHUEYCVLUUEJJ-UWTATZPHSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
T [auth BBB]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth DDD]
F [auth AAA]
FA [auth DDD]
I [auth AAA]
L [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth CCC]
GA [auth DDD]
HA [auth DDD]
J [auth AAA]
K [auth AAA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.234α = 97.015
b = 71.478β = 103.424
c = 103.543γ = 99.045
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view detailsBest fitted DG2Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Database references