8THM | pdb_00008thm

Beta carbonic anhydrase from the carboxysome of Cyanobium PCC 7001

PDB DOI: https://doi.org/10.2210/pdb8THM/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Cyanobium sp. PCC 7001
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-07-17 Released: 2023-08-09
Deposition Author(s): Pulsford, S.B., Jackson, C.J.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.247 (Depositor), 0.250 (DCC)
R-Value Work:
0.193 (Depositor), 0.190 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: in silico
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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

PubMed: 38728392 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 313.01 kDa
Atom Count: 23,011
Modelled Residue Count: 2,769
Deposited Residue Count: 2,772
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxysome shell carbonic anhydrase	A, B, C, D, E A, B, C, D, E, F	462	Cyanobium sp. PCC 7001	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5ILN4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RUB (Subject of Investigation/LOI) Query on RUB Download Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain FA [auth D] SDF format, chain N [auth A] SDF format, chain SA [auth E] SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain FA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain BB [auth F] mmCIF format, chain FA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain SA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth C]	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		Interactions Focus chain BB [auth F] Focus chain FA [auth D] Focus chain N [auth A] Focus chain SA [auth E] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain BB [auth F] Focus chain FA [auth D] Focus chain N [auth A] Focus chain SA [auth E] Focus chain T [auth B] Focus chain Z [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain UA [auth F] SDF format, chain VA [auth F] SDF format, chain W [auth C] SDF format, chain WA [auth F] SDF format, chain X [auth C] SDF format, chain XA [auth F] SDF format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth F] MOL2 format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain VA [auth F] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth F] mmCIF format, chain CA [auth D]	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		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain W [auth C] Focus chain WA [auth F] Focus chain X [auth C] Focus chain XA [auth F] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain Q [auth B] Focus chain R [auth B] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain W [auth C] Focus chain WA [auth F] Focus chain X [auth C] Focus chain XA [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain I [auth A] SDF format, chain U [auth B] MOL2 format, chain GA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain U [auth B] mmCIF format, chain GA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain U [auth B]	GA [auth D], I [auth A], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain I [auth A] Focus chain U [auth B] Interactions & Density Focus chain GA [auth D] Focus chain I [auth A] Focus chain U [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain JA [auth E] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain TA [auth F] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain V [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain V [auth C]	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		Interactions Focus chain BA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain JA [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain TA [auth F] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain JA [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain TA [auth F] Focus chain V [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain M [auth A] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain Y [auth C] SDF format, chain YA [auth F] SDF format, chain ZA [auth F] MOL2 format, chain AB [auth F] MOL2 format, chain M [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth F] mmCIF format, chain AB [auth F] mmCIF format, chain M [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain QA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth F] mmCIF format, chain ZA [auth F]	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		Interactions Focus chain AB [auth F] Focus chain M [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain S [auth B] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain M [auth A] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain S [auth B] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain ZA [auth F]
BCT Query on BCT Download Ideal Coordinates CCD File SDF format, chain IA [auth D] MOL2 format, chain IA [auth D] mmCIF format, chain IA [auth D]	IA [auth D]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain IA [auth D] Interactions & Density Focus chain IA [auth D]
CO2 Query on CO2 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain HA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain HA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain HA [auth D]	AA [auth C], HA [auth D]	CARBON DIOXIDE C O₂ CURLTUGMZLYLDI-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain HA [auth D] Interactions & Density Focus chain AA [auth C] Focus chain HA [auth D]