NCASE_PSEAE
ID NCASE_PSEAE Reviewed; 670 AA.
AC Q9I596; Q7AY51; Q9RHQ0;
DT 25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Neutral ceramidase;
DE Short=N-CDase;
DE Short=NCDase;
DE EC=3.5.1.23;
DE AltName: Full=Acylsphingosine deacylase;
DE AltName: Full=N-acylsphingosine amidohydrolase;
DE Flags: Precursor;
GN OrderedLocusNames=PA0845;
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 25-48; 546-574;
RP 583-591 AND 653-668, AND ENZYME ACTIVITY.
RX PubMed=10593963; DOI=10.1074/jbc.274.51.36616;
RA Okino N., Ichinose S., Omori A., Imayama S., Nakamura T., Ito M.;
RT "Molecular cloning, sequencing, and expression of the gene encoding
RT alkaline ceramidase from Pseudomonas aeruginosa. Cloning of a ceramidase
RT homologue from Mycobacterium tuberculosis.";
RL J. Biol. Chem. 274:36616-36622(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT pathogen.";
RL Nature 406:959-964(2000).
RN [3]
RP PROTEIN SEQUENCE OF 26-58, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND SUBCELLULAR LOCATION.
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=12821326; DOI=10.1016/s1046-5928(03)00099-8;
RA Nieuwenhuizen W.F., van Leeuwen S., Jack R.W., Egmond M.R., Goetz F.;
RT "Molecular cloning and characterization of the alkaline ceramidase from
RT Pseudomonas aeruginosa PA01.";
RL Protein Expr. Purif. 30:94-104(2003).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=9603946; DOI=10.1074/jbc.273.23.14368;
RA Okino N., Tani M., Imayama S., Ito M.;
RT "Purification and characterization of a novel ceramidase from Pseudomonas
RT aeruginosa.";
RL J. Biol. Chem. 273:14368-14373(1998).
RN [5]
RP ACTIVITY REGULATION.
RX PubMed=11879188; DOI=10.1042/0264-6021:3620619;
RA Kita K., Sueyoshi N., Okino N., Inagaki M., Ishida H., Kiso M., Imayama S.,
RA Nakamura T., Ito M.;
RT "Activation of bacterial ceramidase by anionic glycerophospholipids:
RT possible involvement in ceramide hydrolysis on atopic skin by Pseudomonas
RT ceramidase.";
RL Biochem. J. 362:619-626(2002).
RN [6]
RP MUTAGENESIS OF VAL-665.
RX PubMed=15123644; DOI=10.1074/jbc.m404012200;
RA Tani M., Okino N., Sueyoshi N., Ito M.;
RT "Conserved amino acid residues in the COOH-terminal tail are indispensable
RT for the correct folding and localization and enzyme activity of neutral
RT ceramidase.";
RL J. Biol. Chem. 279:29351-29358(2004).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 25-670 COMPLEX WITH SUBSTRATE
RP ANALOGS AND DIVALENT CATIONS, FUNCTION, MUTAGENESIS OF HIS-121; HIS-123;
RP ARG-184; GLU-435; TYR-472 AND TYR-484, REACTION MECHANISM, COFACTOR, AND
RP SUBUNIT.
RX PubMed=19088069; DOI=10.1074/jbc.m808232200;
RA Inoue T., Okino N., Kakuta Y., Hijikata A., Okano H., Goda H.M., Tani M.,
RA Sueyoshi N., Kambayashi K., Matsumura H., Kai Y., Ito M.;
RT "Mechanistic insights into the hydrolysis and synthesis of ceramide by
RT neutral ceramidase.";
RL J. Biol. Chem. 284:9566-9577(2009).
CC -!- FUNCTION: Catalyzes the cleavage of the N-acyl linkage of the ceramides
CC (Cers) to yield sphingosine (Sph) and free fatty acid at an optimal pH
CC of 8-9. Also catalyzes the synthesis of Cers from Sph and fatty acid.
CC {ECO:0000269|PubMed:19088069, ECO:0000269|PubMed:9603946}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an N-acylsphing-4-enine + H2O = a fatty acid + sphing-4-enine;
CC Xref=Rhea:RHEA:20856, ChEBI:CHEBI:15377, ChEBI:CHEBI:28868,
CC ChEBI:CHEBI:52639, ChEBI:CHEBI:57756; EC=3.5.1.23;
CC Evidence={ECO:0000269|PubMed:10593963, ECO:0000269|PubMed:12821326,
CC ECO:0000269|PubMed:9603946};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:19088069};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:19088069};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:19088069};
CC -!- ACTIVITY REGULATION: Inhibited by EDTA, EGTA and D/L-sphinganine D-
CC erythro-sphingosine. L-erythro-sphingosine is a less powerful
CC inhibitor. Stimulated by glycerophospholipids: cardiolipin is the most
CC effective, followed by phosphatidic acid, phosphatidylethanolamine and
CC phosphatidylglycerol, whereas phosphatidylcholine, lysophosphatidic
CC acid and diacylglycerol are less effective.
CC {ECO:0000269|PubMed:11879188}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=139 uM for N-palmitoylsphingosine {ECO:0000269|PubMed:12821326,
CC ECO:0000269|PubMed:9603946};
CC Vmax=5.3 umol/min/mg enzyme with N-palmitoylsphingosine as substrate
CC {ECO:0000269|PubMed:12821326, ECO:0000269|PubMed:9603946};
CC pH dependence:
CC Optimum pH is 7.5-9.5. {ECO:0000269|PubMed:12821326,
CC ECO:0000269|PubMed:9603946};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:19088069}.
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000305}.
CC -!- MISCELLANEOUS: Alternate N-termini have been proposed by different
CC authors. It either starts from Asp-25 (PubMed:10593963) or from Leu-27
CC (PubMed:12821326). {ECO:0000305|PubMed:10593963,
CC ECO:0000305|PubMed:12821326}.
CC -!- SIMILARITY: Belongs to the neutral ceramidase family. {ECO:0000305}.
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DR EMBL; AB028646; BAA88409.1; -; Genomic_DNA.
DR EMBL; AJ315932; CAC67511.1; -; Genomic_DNA.
DR EMBL; AE004091; AAG04234.1; -; Genomic_DNA.
DR PIR; C83540; C83540.
DR RefSeq; NP_249536.1; NC_002516.2.
DR RefSeq; WP_003114226.1; NZ_QZGE01000007.1.
DR PDB; 2ZWS; X-ray; 1.40 A; A=25-670.
DR PDB; 2ZXC; X-ray; 2.20 A; A/B=25-670.
DR PDBsum; 2ZWS; -.
DR PDBsum; 2ZXC; -.
DR AlphaFoldDB; Q9I596; -.
DR SMR; Q9I596; -.
DR STRING; 287.DR97_1099; -.
DR DrugBank; DB06960; N-[(1R,2R,3E)-2-hydroxy-1-(hydroxymethyl)heptadec-3-en-1-yl]acetamide.
DR PaxDb; Q9I596; -.
DR EnsemblBacteria; AAG04234; AAG04234; PA0845.
DR GeneID; 880698; -.
DR KEGG; pae:PA0845; -.
DR PATRIC; fig|208964.12.peg.877; -.
DR PseudoCAP; PA0845; -.
DR HOGENOM; CLU_011300_2_0_6; -.
DR InParanoid; Q9I596; -.
DR OMA; VWHRTNT; -.
DR BioCyc; PAER208964:G1FZ6-860-MON; -.
DR BRENDA; 3.5.1.23; 5087.
DR EvolutionaryTrace; Q9I596; -.
DR Proteomes; UP000002438; Chromosome.
DR GO; GO:0005576; C:extracellular region; IBA:GO_Central.
DR GO; GO:0102121; F:ceramidase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0017040; F:N-acylsphingosine amidohydrolase activity; IDA:UniProtKB.
DR GO; GO:0046514; P:ceramide catabolic process; IBA:GO_Central.
DR GO; GO:0042759; P:long-chain fatty acid biosynthetic process; IDA:UniProtKB.
DR GO; GO:0046512; P:sphingosine biosynthetic process; IDA:UniProtKB.
DR GO; GO:0051872; P:sphingosine catabolic process; IDA:PseudoCAP.
DR Gene3D; 2.60.40.2300; -; 1.
DR InterPro; IPR006823; Ceramidase_alk.
DR InterPro; IPR038445; NCDase_C_sf.
DR InterPro; IPR031331; NEUT/ALK_ceramidase_C.
DR InterPro; IPR031329; NEUT/ALK_ceramidase_N.
DR PANTHER; PTHR12670; PTHR12670; 1.
DR Pfam; PF04734; Ceramidase_alk; 1.
DR Pfam; PF17048; Ceramidse_alk_C; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Disulfide bond; Hydrolase;
KW Lipid metabolism; Magnesium; Metal-binding; Reference proteome; Secreted;
KW Signal; Zinc.
FT SIGNAL 1..24
FT /evidence="ECO:0000269|PubMed:10593963"
FT CHAIN 25..670
FT /note="Neutral ceramidase"
FT /id="PRO_0000247111"
FT REGION 644..670
FT /note="Required for correct folding and localization"
FT ACT_SITE 274
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 61
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:19088069,
FT ECO:0007744|PDB:2ZWS, ECO:0007744|PDB:2ZXC"
FT BINDING 84
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:19088069"
FT BINDING 92
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:19088069"
FT BINDING 111
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:19088069"
FT BINDING 121
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:19088069,
FT ECO:0007744|PDB:2ZWS, ECO:0007744|PDB:2ZXC"
FT BINDING 130
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:19088069"
FT BINDING 228
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:19088069,
FT ECO:0007744|PDB:2ZWS, ECO:0007744|PDB:2ZXC"
FT BINDING 435
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:19088069,
FT ECO:0007744|PDB:2ZWS, ECO:0007744|PDB:2ZXC"
FT BINDING 469
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:19088069"
FT BINDING 472
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:19088069,
FT ECO:0007744|PDB:2ZWS, ECO:0007744|PDB:2ZXC"
FT BINDING 603
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:19088069,
FT ECO:0007744|PDB:2ZWS, ECO:0007744|PDB:2ZXC"
FT BINDING 605
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:19088069,
FT ECO:0007744|PDB:2ZWS, ECO:0007744|PDB:2ZXC"
FT BINDING 608
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:19088069,
FT ECO:0007744|PDB:2ZWS, ECO:0007744|PDB:2ZXC"
FT DISULFID 346..394
FT /evidence="ECO:0000305|PubMed:19088069"
FT MUTAGEN 121
FT /note="H->A: No ceramidase activity; when associated with
FT A-123."
FT /evidence="ECO:0000269|PubMed:19088069"
FT MUTAGEN 123
FT /note="H->A: No ceramidase activity; when associated with
FT A-121."
FT /evidence="ECO:0000269|PubMed:19088069"
FT MUTAGEN 184
FT /note="R->A: No ceramidase activity; when associated."
FT /evidence="ECO:0000269|PubMed:19088069"
FT MUTAGEN 435
FT /note="E->A: Slight ceramidase activity."
FT /evidence="ECO:0000269|PubMed:19088069"
FT MUTAGEN 472
FT /note="Y->A: No ceramidase activity; when associated."
FT /evidence="ECO:0000269|PubMed:19088069"
FT MUTAGEN 484
FT /note="Y->A: Slight ceramidase activity."
FT /evidence="ECO:0000269|PubMed:19088069"
FT MUTAGEN 665
FT /note="V->D: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:15123644"
FT CONFLICT 90
FT /note="I -> T (in Ref. 1; BAA88409)"
FT /evidence="ECO:0000305"
FT CONFLICT 181
FT /note="N -> S (in Ref. 1; BAA88409)"
FT /evidence="ECO:0000305"
FT CONFLICT 196
FT /note="V -> A (in Ref. 1; BAA88409)"
FT /evidence="ECO:0000305"
FT CONFLICT 598
FT /note="E -> V (in Ref. 1; BAA88409)"
FT /evidence="ECO:0000305"
FT STRAND 28..37
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 43..50
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 56..62
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 65..76
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 79..88
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 92..105
FT /evidence="ECO:0007829|PDB:2ZWS"
FT TURN 107..109
FT /evidence="ECO:0007829|PDB:2ZWS"
FT TURN 112..114
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 115..119
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 122..126
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 133..136
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 137..139
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 144..162
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 166..176
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 179..184
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 186..189
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 205..213
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 218..224
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 238..240
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 242..253
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 258..260
FT /evidence="ECO:0007829|PDB:2ZXC"
FT STRAND 262..266
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 277..281
FT /evidence="ECO:0007829|PDB:2ZXC"
FT STRAND 283..285
FT /evidence="ECO:0007829|PDB:2ZXC"
FT HELIX 289..310
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 313..315
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 319..327
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 335..337
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 338..341
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 359..363
FT /evidence="ECO:0007829|PDB:2ZXC"
FT HELIX 374..378
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 389..394
FT /evidence="ECO:0007829|PDB:2ZWS"
FT TURN 395..397
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 400..402
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 408..410
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 415..424
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 427..431
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 433..436
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 438..452
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 453..455
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 459..463
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 465..468
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 476..481
FT /evidence="ECO:0007829|PDB:2ZWS"
FT TURN 484..487
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 495..512
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 526..528
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 550..552
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 556..559
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 563..569
FT /evidence="ECO:0007829|PDB:2ZWS"
FT HELIX 573..575
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 583..593
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 598..602
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 608..615
FT /evidence="ECO:0007829|PDB:2ZWS"
FT TURN 616..618
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 619..627
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 634..646
FT /evidence="ECO:0007829|PDB:2ZWS"
FT TURN 648..650
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 653..659
FT /evidence="ECO:0007829|PDB:2ZWS"
FT STRAND 663..666
FT /evidence="ECO:0007829|PDB:2ZWS"
SQ SEQUENCE 670 AA; 73373 MW; F12C73EAC9CED287 CRC64;
MSRSAFTALL LSCVLLALSM PARADDLPYR FGLGKADITG EAAEVGMMGY SSLEQKTAGI
HMRQWARAFV IEEAASGRRL VYVNTDLGMI FQAVHLKVLA RLKAKYPGVY DENNVMLAAT
HTHSGPGGFS HYAMYNLSVL GFQEKTFNAI VDGIVRSIER AQARLQPGRL FYGSGELRNA
NRNRSLLSHL KNPDIVGYED GIDPQMSVLS FVDANGELAG AISWFPVHST SMTNANHLIS
PDNKGYASYH WEHDVSRKSG FVAAFAQTNA GNLSPNLNLK PGSGPFDNEF DNTREIGLRQ
FAKAYEIAGQ AQEEVLGELD SRFRFVDFTR LPIRPEFTDG QPRQLCTAAI GTSLAAGSTE
DGPGPLGLEE GNNPFLSALG GLLTGVPPQE LVQCQAEKTI LADTGNKKPY PWTPTVLPIQ
MFRIGQLELL GAPAEFTVMA GVRIRRAVQA ASEAAGIRHV VFNGYANAYA SYVTTREEYA
AQEYEGGSTL YGPWTQAAYQ QLFVDMAVAL RERLPVETSA IAPDLSCCQM NFQTGVVADD
PYIGKSFGDV LQQPRESYRI GDKVTVAFVT GHPKNDLRTE KTFLEVVNIG KDGKQTPETV
ATDNDWDTQY RWERVGISAS KATISWSIPP GTEPGHYYIR HYGNAKNFWT QKISEIGGST
RSFEVLGTTP
