9RJD | pdb_00009rjd

X-ray structure of Leptospira interrogans Histone deacetylase 11 (HDAC11) in complex with cis-dodec-5-enoic acid

• PDB DOI: https://doi.org/10.2210/pdb9RJD/pdb

• Classification: HYDROLASE
• Organism(s): Leptospira interrogans
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-06-12 Released: 2026-06-24 
• Deposition Author(s): Novakova, Z., Schenkmayerova, A., Motlova, L., Barinka, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: in silico

Literature

Functional divergence and structural changes of Class IV histone deacetylases (HDACs) across the tree of life.

Novakova, Z., Bartosova-Sojkova, P., Kudlacova, J., Baselious, F., Kutilova, Z., Jaklova, P., Meleshin, M., Motlova, L., Schenkmayerova, A., Vrkoslav, V., Strnad, S., Horacek, N., Gruber, A., Zacek, P., Kroll, S., Havlinova, B., Ondrakova, M., Tuckova, R., Krunclova, T., Cvacka, J., Obornik, M., Schutkowski, M., Sippl, W., Barinka, C.

(2026) Mol Biol Evol 43

• PubMed: 42308148 
• DOI: https://doi.org/10.1093/molbev/msag150
• Primary Citation Related Structures: 
  9RJD, 9RJE


• PubMed Abstract: 
  

  Class IV histone deacetylases (HDACs) are the least understood branch of the classical zinc-dependent HDAC family with HDAC11 standing out as the sole member of Class IV HDACs. Using a broad phylogenetic dataset spanning bacteria, archaea, and eukaryotes, we identified two deeply conserved HDAC11 lineages, clades A and B, that differ in evolutionary origin, predicted subcellular localization, and enzymatic properties. Clade A is enriched in phototrophic eukaryotes and targeted to mitochondria or plastids, whereas clade B predominates in heterotrophs and localizes mainly to the cytoplasm or nucleus. High-resolution crystal structures of selected representatives from each clade revealed a conserved catalytic core but distinct structural features-including electrostatic surface profiles, loop architectures, and foot pocket geometries-that clearly separate the two lineages and act as sequential "selectivity filters" shaping substrate specificity. Biochemical assays show robust long-chain fatty acid deacylase activity in clade B enzymes, but no detectable activity for any of clade A representatives against peptide substrates, suggesting adaptation to alternative, nonpeptidic targets. Together, these findings define a revised evolutionary framework for HDAC11 and provide structural and functional insights into the diversification of this ancient enzyme family.

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Organizational Affiliation: 
• Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic.
Biology Centre of the Czech Academy of Sciences, Institute of Parasitology, Ceske Budejovice, Czech Republic.
Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany.
Charles Tanford Protein Center, Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany.
Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.
OMICS Mass Spectrometry Core Facility, Biology Department, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 71.09 kDa 
• Atom Count: 5,759 
• Modeled Residue Count: 601 
• Deposited Residue Count: 610 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase	A, B	305	Leptospira interrogans	Mutation(s): 0  Gene Names: acuC, LA_2923
UniProt
Find proteins for Q8F254 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)) Explore Q8F254  Go to UniProtKB:  Q8F254

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1KD0( Subject of Investigation/LOI)	D [auth A], K [auth B]	cis-dodec-5-enoic acid C12 H22 O2 IJBFSOLHRKELLR-FPLPWBNLSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	F [auth A], M [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	G [auth A], H [auth A], N [auth B], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	I [auth A], P [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.739	α = 88.49
b = 50.366	β = 89.97
c = 62.175	γ = 79.72

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
Auto-Rickshaw	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-24 
Deposition Author(s): Novakova, Z., Schenkmayerova, A., Motlova, L., Barinka, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-06-24
  Type: Initial release
  
• Version 2.0: 2026-07-15
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 3.0: 2026-07-22
  Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary