8THM

Beta carbonic anhydrase from the carboxysome of Cyanobium PCC 7001


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Cyanobacterial alpha-carboxysome carbonic anhydrase is allosterically regulated by the Rubisco substrate RuBP.

Pulsford, S.B.Outram, M.A.Forster, B.Rhodes, T.Williams, S.J.Badger, M.R.Price, G.D.Jackson, C.J.Long, B.M.

(2024) Sci Adv 10: eadk7283-eadk7283

  • DOI: https://doi.org/10.1126/sciadv.adk7283
  • Primary Citation of Related Structures:  
    8THM

  • PubMed Abstract: 

    Cyanobacterial CO 2 concentrating mechanisms (CCMs) sequester a globally consequential proportion of carbon into the biosphere. Proteinaceous microcompartments, called carboxysomes, play a critical role in CCM function, housing two enzymes to enhance CO 2 fixation: carbonic anhydrase (CA) and Rubisco. Despite its importance, our current understanding of the carboxysomal CAs found in α-cyanobacteria, CsoSCA, remains limited, particularly regarding the regulation of its activity. Here, we present a structural and biochemical study of CsoSCA from the cyanobacterium Cyanobium sp. PCC7001. Our results show that the Cyanobium CsoSCA is allosterically activated by the Rubisco substrate ribulose-1,5-bisphosphate and forms a hexameric trimer of dimers. Comprehensive phylogenetic and mutational analyses are consistent with this regulation appearing exclusively in cyanobacterial α-carboxysome CAs. These findings clarify the biologically relevant oligomeric state of α-carboxysomal CAs and advance our understanding of the regulation of photosynthesis in this globally dominant lineage.


  • Organizational Affiliation

    ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxysome shell carbonic anhydrase
A, B, C, D, E
A, B, C, D, E, F
462Cyanobium sp. PCC 7001Mutation(s): 0 
Gene Names: CPCC7001_23
EC: 4.2.1.1
UniProt
Find proteins for B5ILN4 (Cyanobium sp. PCC 7001)
Explore B5ILN4 
Go to UniProtKB:  B5ILN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5ILN4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RUB (Subject of Investigation/LOI)
Query on RUB

Download Ideal Coordinates CCD File 
BB [auth F]
FA [auth D]
N [auth A]
SA [auth E]
T [auth B]
BB [auth F],
FA [auth D],
N [auth A],
SA [auth E],
T [auth B],
Z [auth C]
RIBULOSE-1,5-DIPHOSPHATE
C5 H12 O11 P2
YAHZABJORDUQGO-NQXXGFSBSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
EA [auth D]
J [auth A]
K [auth A]
CA [auth D],
DA [auth D],
EA [auth D],
J [auth A],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
MA [auth E],
NA [auth E],
Q [auth B],
R [auth B],
UA [auth F],
VA [auth F],
W [auth C],
WA [auth F],
X [auth C],
XA [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
GA [auth D],
I [auth A],
U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth D]
G [auth A]
H [auth A]
JA [auth E]
O [auth B]
BA [auth D],
G [auth A],
H [auth A],
JA [auth E],
O [auth B],
P [auth B],
TA [auth F],
V [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth F]
M [auth A]
OA [auth E]
PA [auth E]
QA [auth E]
AB [auth F],
M [auth A],
OA [auth E],
PA [auth E],
QA [auth E],
RA [auth E],
S [auth B],
Y [auth C],
YA [auth F],
ZA [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
IA [auth D]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CO2
Query on CO2

Download Ideal Coordinates CCD File 
AA [auth C],
HA [auth D]
CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.314α = 90
b = 181.848β = 90
c = 190.057γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaCE200100029

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection
  • Version 1.2: 2024-08-28
    Changes: Database references