9GV8 | pdb_00009gv8

N-Acyl-D-amino-acid deacylase (D-acylase) from Klebsiella pneumoniae in the absence of glycerol

PDB DOI: https://doi.org/10.2210/pdb9GV8/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae Kp13
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-23 Released: 2025-06-18
Deposition Author(s): Gavira, J.A., Martinez-Rodriguez, S.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.269 (Depositor), 0.266 (DCC)
R-Value Work:
0.226 (Depositor), 0.224 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Revisiting D-Acylases for D-Amino Acid Production.

Martinez-Rodriguez, S., Gavira, J.A.

(2025) Microb Biotechnol 18: e70179-e70179

PubMed: 40491232 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1111/1751-7915.70179
Primary Citation Related Structures:
9G5M, 9GV8

PubMed Abstract:
N-Acyl-D-amino acid deacylases (EC 3.5.1.81, also known as D-acylases) have been studied for decades for their utility in the kinetic resolution of N-acetyl-D,L-amino acids (NAAs) due to a marked stereospecificity. In conjunction with an N-succinyl-amino acid racemase (NSAR), they impulse the dynamic kinetic resolution (DKR) of different NAAs until the corresponding enantiomerically pure D-amino acids. Besides the clear interest in this enzyme cascade, the application of D-acylase/NSAR tandems has been only briefly described outside the industrial field. In this work, we revisit D-acylases for the DKR of NAAs, reporting the characterisation of two new recombinant D-acylases belonging to Bordetella petrii and Klebsiella pneumoniae. The enzymes were successfully coupled with the recombinant NSAR from Geobacillus stearothermophilus for the biosynthesis of D-methionine or D-aminobutyric acid. We also carried out the structural characterisation of the D-acylase from Klebsiella pneumoniae (KleDacyl), providing the second experimental 3-D structure of a member of this family of enzymes. The structural model shows a highly dynamic character of this amidohydrolase superfamily member, supplying a snapshot of an open conformation of the enzyme most likely preceding substrate entrance into the catalytic cleft. Our results confirm for the first time the importance of an α/β mobile domain in the substrate specificity of D-acylases (region 282-341 in KleDacyl), opening up new strategies for structural-based protein engineering strategies.

Organizational Affiliation

Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain.

Macromolecule Content

Total Structure Weight: 54.32 kDa
Atom Count: 3,966
Modeled Residue Count: 478
Deposited Residue Count: 485
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase family protein	A	485	Klebsiella pneumoniae subsp. pneumoniae Kp13	Mutation(s): 0 Gene Names: dan, B5L96_17380, B6I68_16395, BANRA_04485, BL124_00028775, DW281_07100, EAO17_17410, FXN67_23300, G4V31_23420, GJJ08_023370... dan, B5L96_17380, B6I68_16395, BANRA_04485, BL124_00028775, DW281_07100, EAO17_17410, FXN67_23300, G4V31_23420, GJJ08_023370, GJJ13_021835, GJJ18_03715, GNF00_21165, NCTC11679_04932, NCTC13443_01470, NCTC5052_02702, NCTC9601_05682, NCTC9661_05441, QIG75_04865, SAMEA3499874_02915, SAMEA3499901_00964, SAMEA3512100_03687, SAMEA3515122_03158, SAMEA3538658_01149, SAMEA3538828_01003, SAMEA3673026_03520, SAMEA3720909_04521, SAMEA4364603_03367, SAMEA4873597_03320, SAMEA4873632_03948, VKR_04363 EC: 3.5.1 (PDB Primary Data), 3.5.1.81 (PDB Primary Data)
UniProt
Find proteins for W8VI54 (Klebsiella pneumoniae 30684/NJST258_2) Explore W8VI54 Go to UniProtKB: W8VI54
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8VI54
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
NI (Subject of Investigation/LOI) Query on NI Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]