6GUR | pdb_00006gur

Siderophore hydrolase EstB from Aspergillus fumigatus in complex with TAFC

PDB DOI: https://doi.org/10.2210/pdb6GUR/pdb

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

Deposited: 2018-06-19 Released: 2018-08-15
Deposition Author(s): Ecker, F., Haas, H., Groll, M., Huber, E.M.
Funding Organization(s): German Research Foundation, Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.238 (Depositor), 0.246 (DCC)
R-Value Work:
0.198 (Depositor), 0.207 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Iron Scavenging in Aspergillus Species: Structural and Biochemical Insights into Fungal Siderophore Esterases.

Ecker, F., Haas, H., Groll, M., Huber, E.M.

(2018) Angew Chem Int Ed Engl 57: 14624-14629

PubMed: 30070018 Search on PubMed
DOI: https://doi.org/10.1002/anie.201807093
Primary Citation Related Structures:
6GUD, 6GUG, 6GUI, 6GUL, 6GUN, 6GUO, 6GUP, 6GUR

PubMed Abstract:
Fungi utilize high-affinity chelators termed siderophores with chemically diverse structures to scavenge the essential nutrient iron from their surroundings. Since they are among the strongest known Fe ³⁺ binding agents, intracellular release of the heavy metal atom is facilitated by the activity of specific hydrolases. In this work, we report the characterization and X-ray crystal structures of four siderophore esterases: AfEstB and AfSidJ from Aspergillus fumigatus, as well as AnEstB and AnEstA from Aspergillus nidulans. Even though they all display the conserved α/β-hydrolase fold, we found significant structural and enzymatic discrepancies in their adaption to both related and chemically diverse substrates. A structure of AfEstB in complex with its substrate triacetylfusarinine C gives insight into the active enzyme and shows tetrahedral coordination between the catalytic serine and the scissile ester bond.

Organizational Affiliation

Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.

Macromolecule Content

Total Structure Weight: 66.91 kDa
Atom Count: 4,725
Modeled Residue Count: 561
Deposited Residue Count: 584
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Siderophore triacetylfusarinine C esterase	A, B	292	Aspergillus fumigatus Af293	Mutation(s): 0 Gene Names: estB, AFUA_3G03660 EC: 3.1
UniProt
Find proteins for Q4WF29 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WF29 Go to UniProtKB: Q4WF29
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4WF29
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FN8 Query on FN8 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	(~{Z})-5-[(1~{S},2~{S})-2-acetamido-1-oxidanyl-5-[oxidanyl(propanoyl)amino]pentoxy]-~{N},3-dimethyl-~{N}-oxidanyl-pent-2-enamide C₁₇ H₃₁ N₃ O₇ RTBUQAUWUAENOT-KGZSOMBESA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] J [auth B] K [auth B] E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
CO3 Query on CO3 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	M [auth B], N [auth B]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain M [auth B] Focus chain N [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.238 (Depositor), 0.246 (DCC)
R-Value Work: 0.198 (Depositor), 0.207 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.74	α = 90
b = 89.99	β = 90
c = 129.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-08-15

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation	Germany	GR 1861/8-1
Austrian Science Fund	Austria	FWF I 1346-B21

Revision History (Full details and data files)

Version 1.0: 2018-08-15
Type: Initial release
Version 1.1: 2018-10-31
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary