SPT_SPHMU
ID SPT_SPHMU Reviewed; 399 AA.
AC A7BFV6; A0A653ZZB6;
DT 03-AUG-2022, integrated into UniProtKB/Swiss-Prot.
DT 11-SEP-2007, sequence version 1.
DT 03-AUG-2022, entry version 70.
DE RecName: Full=Serine palmitoyltransferase {ECO:0000303|PubMed:17557831};
DE Short=SPT {ECO:0000303|PubMed:17557831};
DE EC=2.3.1.50 {ECO:0000269|PubMed:17557831};
GN Name=spt {ECO:0000303|PubMed:17557831};
GN ORFNames=I6J33_20140 {ECO:0000312|EMBL:QRQ60415.1},
GN NCTC11343_02561 {ECO:0000312|EMBL:SPZ86886.1},
GN SPHINGO8BC_150128 {ECO:0000312|EMBL:VXC60648.1};
OS Sphingobacterium multivorum.
OC Bacteria; Bacteroidetes; Sphingobacteriia; Sphingobacteriales;
OC Sphingobacteriaceae; Sphingobacterium.
OX NCBI_TaxID=28454;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND SUBCELLULAR LOCATION.
RC STRAIN=GTC97;
RX PubMed=17557831; DOI=10.1128/jb.00194-07;
RA Ikushiro H., Islam M.M., Tojo H., Hayashi H.;
RT "Molecular characterization of membrane-associated soluble serine
RT palmitoyltransferases from Sphingobacterium multivorum and Bdellovibrio
RT stolpii.";
RL J. Bacteriol. 189:5749-5761(2007).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NCTC 11343;
RG Pathogen Informatics;
RA Doyle S.;
RL Submitted (JUN-2018) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Sphingobacterium sp. 8BC;
RA Karimi E.;
RL Submitted (OCT-2019) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33613 / DSM 11691 / FDAARGOS_1203;
RA Sproer C., Gronow S., Severitt S., Schroder I., Tallon L., Sadzewicz L.,
RA Zhao X., Boylan J., Ott S., Bowen H., Vavikolanu K., Mehta A.,
RA Aluvathingal J., Nadendla S., Lowell S., Myers T., Yan Y., Sichtig H.;
RT "FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
RT Supporting development and validation of Infectious Disease Dx tests.";
RL Submitted (FEB-2021) to the EMBL/GenBank/DDBJ databases.
RN [5] {ECO:0007744|PDB:3A2B}
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 2-399 IN COMPLEX WITH PLP-BOUND
RP SERINE, AND SUBUNIT.
RC STRAIN=GTC97;
RX PubMed=19564159; DOI=10.1093/jb/mvp100;
RA Ikushiro H., Islam M.M., Okamoto A., Hoseki J., Murakawa T., Fujii S.,
RA Miyahara I., Hayashi H.;
RT "Structural insights into the enzymatic mechanism of serine
RT palmitoyltransferase from Sphingobacterium multivorum.";
RL J. Biochem. 146:549-562(2009).
CC -!- FUNCTION: Catalyzes the condensation of L-serine with palmitoyl-CoA
CC (hexadecanoyl-CoA) to produce 3-oxosphinganine (PubMed:17557831).
CC Exhibits a broad substrate specificity concerning the chain length and
CC the degree of unsaturation of acyl-CoA (PubMed:17557831).
CC {ECO:0000269|PubMed:17557831}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + hexadecanoyl-CoA + L-serine = 3-oxosphinganine + CO2 +
CC CoA; Xref=Rhea:RHEA:14761, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:33384, ChEBI:CHEBI:57287, ChEBI:CHEBI:57379,
CC ChEBI:CHEBI:58299; EC=2.3.1.50;
CC Evidence={ECO:0000269|PubMed:17557831};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14762;
CC Evidence={ECO:0000269|PubMed:17557831};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:17557831};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.8 mM for L-serine {ECO:0000269|PubMed:17557831};
CC KM=0.10 mM for palmitoyl-CoA {ECO:0000269|PubMed:17557831};
CC Note=kcat is 0.12 sec(-1). {ECO:0000269|PubMed:17557831};
CC pH dependence:
CC Optimum pH is 7.4 to 8.0. {ECO:0000269|PubMed:17557831};
CC -!- PATHWAY: Lipid metabolism; sphingolipid metabolism.
CC {ECO:0000305|PubMed:17557831}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:17557831,
CC ECO:0000269|PubMed:19564159}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:17557831}. Cell
CC inner membrane {ECO:0000269|PubMed:17557831}; Peripheral membrane
CC protein {ECO:0000269|PubMed:17557831}. Note=Distributed mainly near the
CC inner membrane of the cell. {ECO:0000269|PubMed:17557831}.
CC -!- SIMILARITY: Belongs to the class-II pyridoxal-phosphate-dependent
CC aminotransferase family. {ECO:0000305}.
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DR EMBL; AB259214; BAF73751.1; -; Genomic_DNA.
DR EMBL; UAUU01000009; SPZ86886.1; -; Genomic_DNA.
DR EMBL; CABWMV010000007; VXC60648.1; -; Genomic_DNA.
DR EMBL; CP069793; QRQ60415.1; -; Genomic_DNA.
DR RefSeq; WP_046672730.1; NZ_UGYX01000002.1.
DR PDB; 3A2B; X-ray; 2.30 A; A=2-399.
DR PDBsum; 3A2B; -.
DR SMR; A7BFV6; -.
DR EnsemblBacteria; SPZ86886; SPZ86886; NCTC11343_02561.
DR EnsemblBacteria; SUJ02286; SUJ02286; NCTC11034_01090.
DR GeneID; 66689277; -.
DR BRENDA; 2.3.1.50; 2288.
DR UniPathway; UPA00222; -.
DR EvolutionaryTrace; A7BFV6; -.
DR PRO; PR:A7BFV6; -.
DR Proteomes; UP000251241; Unassembled WGS sequence.
DR GO; GO:0008710; F:8-amino-7-oxononanoate synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0004758; F:serine C-palmitoyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0008483; F:transaminase activity; IEA:UniProtKB-KW.
DR GO; GO:0009058; P:biosynthetic process; IEA:InterPro.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR001917; Aminotrans_II_pyridoxalP_BS.
DR InterPro; IPR004839; Aminotransferase_I/II.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR Pfam; PF00155; Aminotran_1_2; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR PROSITE; PS00599; AA_TRANSFER_CLASS_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acyltransferase; Cell inner membrane; Cell membrane;
KW Cytoplasm; Lipid metabolism; Membrane; Pyridoxal phosphate; Transferase.
FT CHAIN 1..399
FT /note="Serine palmitoyltransferase"
FT /id="PRO_0000456078"
FT BINDING 113..114
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000305|PubMed:19564159"
FT BINDING 213
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000305|PubMed:19564159"
FT BINDING 241
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:Q93UV0"
FT BINDING 243
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000305|PubMed:19564159"
FT MOD_RES 244
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250|UniProtKB:Q93UV0"
SQ SEQUENCE 399 AA; 43772 MW; E765F69D9663811E CRC64;
MSKGKLGEKI SQFKIVEELK AKGLYAYFRP IQSKQDTEVK IDGRRVLMFG SNSYLGLTTD
TRIIKAAQDA LEKYGTGCAG SRFLNGTLDI HVELEEKLSA YVGKEAAILF STGFQSNLGP
LSCLMGRNDY ILLDERDHAS IIDGSRLSFS KVIKYGHNNM EDLRAKLSRL PEDSAKLICT
DGIFSMEGDI VNLPELTSIA NEFDAAVMVD DAHSLGVIGH KGAGTASHFG LNDDVDLIMG
TFSKSLASLG GFVAGDADVI DFLKHNARSV MFSASMTPAS VASTLKALEI IQNEPEHIEK
LWKNTDYAKA QLLDHGFDLG ATESPILPIF IRSNEKTFWV TKMLQDDGVF VNPVVSPAVP
AEESLIRFSL MATHTYDQID EAIEKMVKVF KQAEVETLI
