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 of 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 2 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 2 monomers, coordinates the zinc ion with 3 histidine residues (H65, H82, and H87) and a water molecule in a tetrahedral configuration. The 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 noncatalytic zinc and sulfate ions trapped at the trimer core and trimer-trimer noncrystallographic interfaces. These may contribute to stabilizing enzyme assembly and promoting crystal packing.

Organizational Affiliation

School of Life Sciences, GIST, 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

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 M [auth B] SDF format, chain R [auth D] MOL2 format, chain M [auth B] MOL2 format, chain R [auth D] mmCIF format, chain M [auth B] mmCIF format, chain R [auth D]	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 G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain T [auth F] SDF format, chain Q [auth D] SDF format, chain N [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C]	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

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