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Histone deacetylase-like amidohydrolase (HDAH) (EC 3.5.1.-) (Acetylated lysine deacetylase) (Histone deacetylase homolog PA3774)

 HDAH_PSEAE              Reviewed;         380 AA.
Q9HXM1;
12-APR-2017, integrated into UniProtKB/Swiss-Prot.
01-MAR-2001, sequence version 1.
12-SEP-2018, entry version 84.
RecName: Full=Histone deacetylase-like amidohydrolase {ECO:0000303|PubMed:27756124};
Short=HDAH {ECO:0000303|PubMed:27756124};
EC=3.5.1.- {ECO:0000269|PubMed:26956223};
AltName: Full=Acetylated lysine deacetylase {ECO:0000305};
AltName: Full=Histone deacetylase homolog PA3774 {ECO:0000303|PubMed:27951649};
OrderedLocusNames=PA3774 {ECO:0000312|EMBL:AAG07161.1};
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 /
JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
Pseudomonadaceae; Pseudomonas.
NCBI_TaxID=208964;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 /
1C / PRS 101 / PAO1;
PubMed=10984043; DOI=10.1038/35023079;
Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T.,
Reizer J., Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
"Complete genome sequence of Pseudomonas aeruginosa PAO1, an
opportunistic pathogen.";
Nature 406:959-964(2000).
[2]
FUNCTION, DEACETYLASE ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
DISRUPTION PHENOTYPE.
STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 /
1C / PRS 101 / PAO1, and PA14;
PubMed=26956223; DOI=10.1186/s12858-016-0063-z;
Kraemer A., Herzer J., Overhage J., Meyer-Almes F.J.;
"Substrate specificity and function of acetylpolyamine amidohydrolases
from Pseudomonas aeruginosa.";
BMC Biochem. 17:4-4(2016).
[3]
X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH ZINC AND A
PHOTOSWITCHABLE LIGAND INHIBITOR, BIOTECHNOLOGY, AND ACTIVITY
REGULATION.
STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 /
1C / PRS 101 / PAO1;
PubMed=27756124; DOI=10.1021/acsinfecdis.6b00148;
Weston C.E., Kramer A., Colin F., Yildiz O., Baud M.G.,
Meyer-Almes F.J., Fuchter M.J.;
"Toward photopharmacological antimicrobial chemotherapy using
photoswitchable amidohydrolase inhibitors.";
ACS Infect. Dis. 3:152-161(2017).
[4]
X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 2-380 OF WILD-TYPE AND
MUTANTS ALA-143 AND PHE-313 IN COMPLEXES WITH ZINC; A
TRIFLUOROMETHYLKETONE INHIBITOR; ACETATE AND A HYDROXAMATE INHIBITOR,
MUTAGENESIS OF HIS-143; HIS-144 AND TYR-313, COFACTOR, AND SUBUNIT.
STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 /
1C / PRS 101 / PAO1;
PubMed=27951649; DOI=10.1021/acs.biochem.6b00613;
Kraemer A., Wagner T., Yildiz O., Meyer-Almes F.J.;
"Crystal structure of a histone deacetylase homologue from Pseudomonas
aeruginosa.";
Biochemistry 55:6858-6868(2016).
-!- FUNCTION: Probable protein deacetylase that catalyzes
deacetylation of acetylated lysine residues. In vitro, exhibits
high activity against artificial HDAC (histone deacetylase)
substrates containing acetylated and trifluoroacetylated lysine
residues. Is not able to deacetylate acetylated polyamines.
{ECO:0000269|PubMed:26956223}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000305|PubMed:27951649};
Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:27951649};
-!- ACTIVITY REGULATION: Is inhibited by azobenzenes, stilbenes and
arylazopyrazoles. {ECO:0000269|PubMed:27756124}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=95 uM for Boc-Lys(Ac)-AMC {ECO:0000269|PubMed:26956223};
KM=21 uM for Boc-Lys(TFA)-AMC {ECO:0000269|PubMed:26956223};
Vmax=3.4 nmol/sec/mg enzyme with Boc-Lys(Ac)-AMC as substrate
{ECO:0000269|PubMed:26956223};
Vmax=8.6 nmol/sec/mg enzyme with Boc-Lys(TFA)-AMC as substrate
{ECO:0000269|PubMed:26956223};
-!- SUBUNIT: Homotetramer; dimer of head-to-head dimers.
{ECO:0000269|PubMed:27951649}.
-!- DISRUPTION PHENOTYPE: Growth of a mutant strain lacking this gene
in the presence of both acetylcadaverine and acetylputrescine is
comparable to growth of the wild-type. The deletion mutant strain
shows a 25% increase in biofilm biomass after 24 hours of
incubation compared to wild-type cells.
{ECO:0000269|PubMed:26956223}.
-!- BIOTECHNOLOGY: Could be a suitable photopharmacological target for
photopharmacological antimicrobial chemotherapy using
photoswitchable inhibitors. {ECO:0000305|PubMed:27756124}.
-!- SIMILARITY: Belongs to the histone deacetylase family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AE004091; AAG07161.1; -; Genomic_DNA.
PIR; D83174; D83174.
RefSeq; NP_252463.1; NC_002516.2.
RefSeq; WP_003113816.1; NC_002516.2.
PDB; 5G0X; X-ray; 1.70 A; A/C=2-380.
PDB; 5G0Y; X-ray; 2.29 A; A/B=2-380.
PDB; 5G10; X-ray; 1.71 A; A/B=2-380.
PDB; 5G11; X-ray; 2.48 A; A/B=2-380.
PDB; 5G12; X-ray; 2.02 A; A/B=2-380.
PDB; 5G13; X-ray; 1.99 A; A/B=2-380.
PDB; 5LI3; X-ray; 2.40 A; A/B=1-380.
PDBsum; 5G0X; -.
PDBsum; 5G0Y; -.
PDBsum; 5G10; -.
PDBsum; 5G11; -.
PDBsum; 5G12; -.
PDBsum; 5G13; -.
PDBsum; 5LI3; -.
ProteinModelPortal; Q9HXM1; -.
SMR; Q9HXM1; -.
STRING; 208964.PA3774; -.
PaxDb; Q9HXM1; -.
EnsemblBacteria; AAG07161; AAG07161; PA3774.
GeneID; 880599; -.
KEGG; pae:PA3774; -.
PATRIC; fig|208964.12.peg.3951; -.
PseudoCAP; PA3774; -.
eggNOG; ENOG4105DGU; Bacteria.
eggNOG; COG0123; LUCA.
HOGENOM; HOG000225183; -.
InParanoid; Q9HXM1; -.
OMA; FCLFSNA; -.
PhylomeDB; Q9HXM1; -.
BioCyc; PAER208964:G1FZ6-3845-MONOMER; -.
Proteomes; UP000002438; Chromosome.
GO; GO:0016787; F:hydrolase activity; IDA:PseudoCAP.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
Gene3D; 3.40.800.20; -; 1.
InterPro; IPR000286; His_deacetylse.
InterPro; IPR023801; His_deacetylse_dom.
InterPro; IPR037138; His_deacetylse_dom_sf.
InterPro; IPR023696; Ureohydrolase_dom_sf.
PANTHER; PTHR10625; PTHR10625; 1.
Pfam; PF00850; Hist_deacetyl; 1.
PRINTS; PR01270; HDASUPER.
SUPFAM; SSF52768; SSF52768; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Hydrolase; Metal-binding;
Reference proteome; Zinc.
CHAIN 1 380 Histone deacetylase-like amidohydrolase.
/FTId=PRO_0000439409.
ACT_SITE 144 144 Proton donor/acceptor.
{ECO:0000250|UniProtKB:Q48935}.
METAL 181 181 Zinc. {ECO:0000244|PDB:5G0X,
ECO:0000269|PubMed:27756124,
ECO:0000269|PubMed:27951649,
ECO:0000312|PDB:5LI3}.
METAL 183 183 Zinc; via pros nitrogen.
{ECO:0000244|PDB:5G0X,
ECO:0000269|PubMed:27756124,
ECO:0000269|PubMed:27951649,
ECO:0000312|PDB:5LI3}.
METAL 269 269 Zinc. {ECO:0000244|PDB:5G0X,
ECO:0000269|PubMed:27756124,
ECO:0000269|PubMed:27951649,
ECO:0000312|PDB:5LI3}.
SITE 313 313 Polarizes the scissile carbonyl of the
substrate.
{ECO:0000250|UniProtKB:Q48935}.
MUTAGEN 143 143 H->A: Loss of enzymatic activity against
both acetylated and trifluoroacetylated
lysine substrates.
{ECO:0000269|PubMed:27951649}.
MUTAGEN 144 144 H->A: Loss of enzymatic activity against
both acetylated and trifluoroacetylated
lysine substrates.
{ECO:0000269|PubMed:27951649}.
MUTAGEN 313 313 Y->F: Loss of enzymatic activity against
acetylated lysine substrate but no effect
on activity with trifluoroacetylated
lysine substrate.
{ECO:0000269|PubMed:27951649}.
MUTAGEN 313 313 Y->H: Loss of enzymatic activity against
acetylated lysine substrate but only 15%
decrease in activity against
trifluoroacetylated lysine substrate.
{ECO:0000269|PubMed:27951649}.
STRAND 5 8 {ECO:0000244|PDB:5G0X}.
HELIX 11 15 {ECO:0000244|PDB:5G0X}.
STRAND 21 23 {ECO:0000244|PDB:5G0X}.
STRAND 25 28 {ECO:0000244|PDB:5G0X}.
STRAND 39 41 {ECO:0000244|PDB:5G0X}.
HELIX 44 55 {ECO:0000244|PDB:5G0X}.
HELIX 58 61 {ECO:0000244|PDB:5G0X}.
STRAND 62 65 {ECO:0000244|PDB:5G0X}.
HELIX 72 76 {ECO:0000244|PDB:5G0X}.
HELIX 81 92 {ECO:0000244|PDB:5G0X}.
STRAND 96 99 {ECO:0000244|PDB:5G0X}.
STRAND 102 104 {ECO:0000244|PDB:5G0X}.
HELIX 108 127 {ECO:0000244|PDB:5G0X}.
STRAND 132 136 {ECO:0000244|PDB:5G0X}.
STRAND 154 156 {ECO:0000244|PDB:5G0X}.
HELIX 158 170 {ECO:0000244|PDB:5G0X}.
STRAND 175 179 {ECO:0000244|PDB:5G0X}.
STRAND 181 183 {ECO:0000244|PDB:5G0X}.
HELIX 186 191 {ECO:0000244|PDB:5G0X}.
TURN 192 194 {ECO:0000244|PDB:5G0X}.
STRAND 196 205 {ECO:0000244|PDB:5G0X}.
TURN 206 212 {ECO:0000244|PDB:5G0X}.
HELIX 222 224 {ECO:0000244|PDB:5G0X}.
STRAND 227 233 {ECO:0000244|PDB:5G0X}.
HELIX 239 248 {ECO:0000244|PDB:5G0X}.
HELIX 250 257 {ECO:0000244|PDB:5G0X}.
STRAND 260 266 {ECO:0000244|PDB:5G0X}.
HELIX 283 300 {ECO:0000244|PDB:5G0X}.
STRAND 305 309 {ECO:0000244|PDB:5G0X}.
TURN 315 317 {ECO:0000244|PDB:5G0X}.
HELIX 318 330 {ECO:0000244|PDB:5G0X}.
HELIX 341 346 {ECO:0000244|PDB:5G0X}.
HELIX 351 367 {ECO:0000244|PDB:5G0X}.
SEQUENCE 380 AA; 41049 MW; 07042D0FADED1936 CRC64;
MTRRTAFFFD ELCLWHAAGP HALTLPVGGW VQPPAAAGHA ESPETKRRLK SLLDVSGLTA
RLQLRSAPPA SDEDLLRVHP AHYLERFKAL SDAGGGSLGQ DAPIGPGSYE IARLSAGLAI
AALDAVLAGE ADNAYSLSRP PGHHCLPDQA MGFCFFANIA VAIEAAKARH GVERVAVLDW
DVHHGNGTQA IYYRRDDVLS ISLHQDGCFP PGYSGAEDIG EDRGRGFNLN VPLLPGGGHD
AYMQAMQRIV LPALERFRPQ LIVVASGFDA NAVDPLARMQ LHSDSFRAMT AMVRDAAERH
AGGRLVVVHE GGYSEAYVPF CGLAVIEELS GVRSAVRDPL RDFIELQQPN AAFRDFQRQR
LEELAAQFGL CPAQPLQAAR


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