7COJ | pdb_00007coj

Crystal structure of the b-carbonic anhydrase CafA of the fungal pathogen Aspergillus fumigatus

PDB DOI: https://doi.org/10.2210/pdb7COJ/pdb

Classification: LYASE
Organism(s): Aspergillus fumigatus Af293
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-08-04 Released: 2020-10-14
Deposition Author(s): Jin, M.S., Kim, S., Yeon, J., Sung, J.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.205 (Depositor), 0.213 (DCC)
R-Value Work:
0.161 (Depositor), 0.173 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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Literature

Crystal Structure of beta-Carbonic Anhydrase CafA from the Fungal Pathogen Aspergillus fumigatus .

Kim, S., Yeon, J., Sung, J., Jin, M.S.

(2020) Mol Cells 43: 831-840

PubMed: 32975213 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.14348/molcells.2020.0168
Primary Citation Related Structures:
7COI, 7COJ

PubMed Abstract:
The β-class of carbonic anhydrases (β-CAs) are zinc metalloenzymes widely distributed in the fungal kingdom that play essential roles in growth, survival, differentiation, and virulence by catalyzing the reversible interconversion of carbon dioxide (CO ₂) and bicarbonate (HCO ₃ ^-). Herein, we report the biochemical and crystallographic characterization of the β-CA CafA from the fungal pathogen Aspergillus fumigatus , the main causative agent of invasive aspergillosis. CafA exhibited apparent in vitro CO ₂ hydration activity in neutral to weak alkaline conditions, but little activity at acidic pH. The high-resolution crystal structure of CafA revealed a tetramer comprising a dimer of dimers, in which the catalytic zinc ion is tetrahedrally coordinated by three conserved residues (C119, H175, C178) and an acetate anion presumably acquired from the crystallization solution, indicating a freely accessible ″open″ conformation. Furthermore, knowledge of the structure of CafA in complex with the potent inhibitor acetazolamide, together with its functional intolerance of nitrate (NO ₃ ^-) ions, could be exploited to develop new antifungal agents for the treatment of invasive aspergillosis.

Organizational Affiliation

School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea.

Macromolecule Content

Total Structure Weight: 124.62 kDa
Atom Count: 7,014
Modeled Residue Count: 840
Deposited Residue Count: 1,148
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase	A, B, C, D	287	Aspergillus fumigatus Af293	Mutation(s): 0 Gene Names: AFUA_4G11250 EC: 4.2.1.1
UniProt
Find proteins for Q4WQ18 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WQ18 Go to UniProtKB: Q4WQ18
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4WQ18
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZM (Subject of Investigation/LOI) Query on AZM Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE C₄ H₆ N₄ O₃ S₂ BZKPWHYZMXOIDC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.205 (Depositor), 0.213 (DCC)
R-Value Work: 0.161 (Depositor), 0.173 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.921	α = 90
b = 87.953	β = 90
c = 144.717	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017M3A9F6029753
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2019M3E5D6063908