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 
  • R-Value Work: 0.216 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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]
DA [auth DDD],
EA [auth DDD],
G [auth AAA],
H [auth AAA],
M [auth BBB],
W [auth CCC]
(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]
CA [auth DDD],
F [auth AAA],
FA [auth DDD],
I [auth AAA],
L [auth BBB],
O [auth BBB],
P [auth BBB],
Q [auth BBB],
V [auth CCC],
X [auth CCC],
Y [auth CCC]
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]
AA [auth CCC],
GA [auth DDD],
HA [auth DDD],
J [auth AAA],
K [auth AAA],
R [auth BBB],
S [auth BBB],
Z [auth CCC]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • 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

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Ligand Structure Quality Assessment 


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