7C5V

Crystal structure of the iota-carbonic anhydrase from cyanobacterium complexed with bicarbonate

PDB DOI: https://doi.org/10.2210/pdb7C5V/pdb

Classification: LYASE
Organism(s): Nostoc sp. PCC 7120 = FACHB-418
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-05-20 Released: 2021-04-28
Deposition Author(s): Senda, M., Senda, T.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.263
R-Value Work: 0.207
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Characterization of a novel type of carbonic anhydrase that acts without metal cofactors.

Hirakawa, Y., Senda, M., Fukuda, K., Yu, H.Y., Ishida, M., Taira, M., Kinbara, K., Senda, T.

(2021) BMC Biol 19: 105-105

PubMed: 34006275 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s12915-021-01039-8
Primary Citation of Related Structures:
7C5V, 7C5W, 7C5X, 7C5Y

PubMed Abstract:
Carbonic anhydrases (CAs) are universal metalloenzymes that catalyze the reversible conversion of carbon dioxide (CO ₂) and bicarbonate (HCO ₃ ^-). They are involved in various biological processes, including pH control, respiration, and photosynthesis. To date, eight evolutionarily unrelated classes of CA families (α, β, γ, δ, ζ, η, θ, and ι) have been identified. All are characterized by an active site accommodating the binding of a metal cofactor, which is assumed to play a central role in catalysis. This feature is thought to be the result of convergent evolution.

Organizational Affiliation

Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan. hirakawa.yoshi.fp@u.tsukuba.ac.jp.

Macromolecule Content

Total Structure Weight: 38.74 kDa
Atom Count: 2,414
Modelled Residue Count: 327
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
iota-carbonic anhydrase	A, B	178	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0 Gene Names: all2909
UniProt
Find proteins for Q8YT18 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q8YT18 Go to UniProtKB: Q8YT18
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8YT18
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCT (Subject of Investigation/LOI) Query on BCT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]