9JYW | pdb_00009jyw

Crystal structure of the gamma-carbonic anhydrase from the polyextremophilic bacterium Aeribacillus pallidus

PDB DOI: https://doi.org/10.2210/pdb9JYW/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Aeribacillus pallidus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-13 Released: 2024-12-11
Deposition Author(s): Choi, S.H., Jin, M.S.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.245 (Depositor), 0.225 (DCC)
R-Value Work:
0.213 (Depositor), 0.205 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of gamma-carbonic anhydrase from the polyextremophilic bacterium Aeribacillus pallidus.

Choi, S.H., Jin, M.S.

(2024) Mol Cells 48: 100165-100165

PubMed: 39637945 Search on PubMed
DOI: https://doi.org/10.1016/j.mocell.2024.100165
Primary Citation Related Structures:
9JYW

PubMed Abstract:
The polyextremophilic bacterium Aeribacillus pallidus produces a thermo- and alkali-stable γ-carbonic anhydrase (γ-apCA), a homotrimeric metalloenzyme containing a zinc ion in its active site that catalyzes the reversible hydration of carbon dioxide (CO ₂). Here, we present the first crystal structure of γ-apCA at 1.7 Å resolution, revealing two trimers in the asymmetric unit. The overall structure is consistent with other γ-CAs, where each monomer adopts a prism-like structure consisting of an N-terminal left-handed β-helix and a C-terminal α-helix. The active site, located at the interface between two monomers, coordinates the zinc ion with three histidine residues (H65, H82, and H87) and a water molecule in a tetrahedral configuration. Structural comparison indicates that the amino acid composition at the active site of γ-apCA differs significantly from the prototypic γ-CA from Methanosarcina thermophila. This variation likely accounts for the lack of measurable CO ₂ hydration activity in γ-apCA. Additionally, the structure reveals non-catalytic zinc and sulfate ions trapped at the trimer core and trimer-trimer non-crystallographic interfaces. These may contribute to stabilizing enzyme assembly and promoting crystal packing.

Organizational Affiliation

School of Life Sciences, GIST, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.

Macromolecule Content

Total Structure Weight: 117.14 kDa
Atom Count: 8,550
Modeled Residue Count: 1,026
Deposited Residue Count: 1,050
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma carbonic anhydrase family protein	A, B, C, D, E A, B, C, D, E, F	175	Aeribacillus pallidus	Mutation(s): 0 Gene Names: AP3564_09575
UniProt
Find proteins for A0A223E5F5 (Aeribacillus pallidus) Explore A0A223E5F5 Go to UniProtKB: A0A223E5F5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A223E5F5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain M [auth B] MOL2 format, chain R [auth D] MOL2 format, chain M [auth B] mmCIF format, chain R [auth D] mmCIF format, chain M [auth B]	M [auth B], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth B] Focus chain R [auth D] Interactions & Density Focus chain M [auth B] Focus chain R [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth D] SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain P [auth D] SDF format, chain L [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain P [auth D] MOL2 format, chain L [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain P [auth D] mmCIF format, chain L [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth B] G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], N [auth C], O [auth D], P [auth D], Q [auth D], S [auth E], T [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.245 (Depositor), 0.225 (DCC)
R-Value Work: 0.213 (Depositor), 0.205 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.911	α = 90
b = 110.672	β = 118.8
c = 98.578	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-11

Deposition Author(s):

Choi, S.H.

Jin, M.S.

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2022R1A2C1091278
National Research Foundation (NRF, Korea)	Korea, Republic Of	RS-2024-00344154