1UKC | pdb_00001ukc

Crystal Structure of Aspergillus niger EstA

PDB DOI: https://doi.org/10.2210/pdb1UKC/pdb

Classification: HYDROLASE
Organism(s): Aspergillus niger
Expression System: Aspergillus niger
Mutation(s): No

Deposited: 2003-08-19 Released: 2004-07-27
Deposition Author(s): Bourne, Y., Hasper, A.A., Chahinian, H., Juin, M., De Graaff, L.H., Marchot, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.184 (Depositor), 0.190 (DCC)
R-Value Work:
0.158 (Depositor), 0.170 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Aspergillus niger protein EstA defines a new class of fungal esterases within the alpha/beta hydrolase fold superfamily of proteins

Bourne, Y., Hasper, A.A., Chahinian, H., Juin, M., De Graaff, L.H., Marchot, P.

(2004) Structure 12: 677-687

PubMed: 15062090 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2004.03.005
Primary Citation of Related Structures:
1UKC

PubMed Abstract:
From the fungus Aspergillus niger, we identified a new gene encoding protein EstA, a member of the alpha/beta-hydrolase fold superfamily but of unknown substrate specificity. EstA was overexpressed and its crystal structure was solved by molecular replacement using a lipase-acetylcholinesterase chimera template. The 2.1 A resolution structure of EstA reveals a canonical Ser/Glu/His catalytic triad located in a small pocket at the bottom of a large solvent-accessible, bowl-shaped cavity. Potential substrates selected by manual docking procedures were assayed for EstA activity. Consistent with the pocket geometry, preference for hydrolysis of short acyl/propyl chain substrates was found. Identification of close homologs from the genome of other fungi, of which some are broad host-range pathogens, defines EstA as the first member of a novel class of fungal esterases within the superfamily. Hence the structure of EstA constitutes a lead template in the design of new antifungal agents directed toward its pathogenic homologs.

Organizational Affiliation

Architecture et Fonction des Macromolécules Biologiques, CNRS UMR-6098, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France. yves@afmb.cnrs-mrs.fr

Macromolecule Content

Total Structure Weight: 118.46 kDa
Atom Count: 9,377
Modelled Residue Count: 1,030
Deposited Residue Count: 1,044
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EstA	A, B	522	Aspergillus niger	Mutation(s): 0 Gene Names: EstA EC: 3.1.1
UniProt
Find proteins for Q6ED33 (Aspergillus niger) Explore Q6ED33 Go to UniProtKB: Q6ED33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6ED33
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	E [auth A] F [auth A] I [auth A] J [auth A] K [auth A] E [auth A], F [auth A], I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], V [auth B], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	G [auth A], H [auth A], S [auth B], T [auth B], U [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Y [auth B] MOL2 format, chain L [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain L [auth A] mmCIF format, chain Y [auth B]	L [auth A], Y [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain Y [auth B] Interactions & Density Focus chain L [auth A] Focus chain Y [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Z [auth B] MOL2 format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Z [auth B]	N [auth A], O [auth A], P [auth A], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Z [auth B] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Z [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.184 (Depositor), 0.190 (DCC)
R-Value Work: 0.158 (Depositor), 0.170 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.489	α = 90
b = 167.489	β = 90
c = 112.827	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-07-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-07-27
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-23
Changes: Structure summary

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Crystal Structure of Aspergillus niger EstA

Aspergillus niger protein EstA defines a new class of fungal esterases within the alpha/beta hydrolase fold superfamily of proteins

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3