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Database: UniProt
Entry: A0A5C6YBJ1_9FLAO
LinkDB: A0A5C6YBJ1_9FLAO
Original site: A0A5C6YBJ1_9FLAO 
ID   A0A5C6YBJ1_9FLAO        Unreviewed;       576 AA.
AC   A0A5C6YBJ1;
DT   13-NOV-2019, integrated into UniProtKB/TrEMBL.
DT   13-NOV-2019, sequence version 1.
DT   02-APR-2025, entry version 15.
DE   RecName: Full=2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase {ECO:0000256|HAMAP-Rule:MF_01659};
DE            Short=SEPHCHC synthase {ECO:0000256|HAMAP-Rule:MF_01659};
DE            EC=2.2.1.9 {ECO:0000256|HAMAP-Rule:MF_01659};
DE   AltName: Full=Menaquinone biosynthesis protein MenD {ECO:0000256|HAMAP-Rule:MF_01659};
GN   Name=menD {ECO:0000256|HAMAP-Rule:MF_01659,
GN   ECO:0000313|EMBL:TXD60920.1};
GN   ORFNames=ES044_06115 {ECO:0000313|EMBL:TXD60920.1};
OS   Polaribacter sp. IC066.
OC   Bacteria; Pseudomonadati; Bacteroidota; Flavobacteriia; Flavobacteriales;
OC   Flavobacteriaceae.
OX   NCBI_TaxID=57032 {ECO:0000313|EMBL:TXD60920.1, ECO:0000313|Proteomes:UP000321094};
RN   [1] {ECO:0000313|EMBL:TXD60920.1, ECO:0000313|Proteomes:UP000321094}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=IC066 {ECO:0000313|EMBL:TXD60920.1,
RC   ECO:0000313|Proteomes:UP000321094};
RA   Bowman J.P.;
RT   "Genomes of sea-ice associated Polaribacter species.";
RL   Submitted (AUG-2019) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Catalyzes the thiamine diphosphate-dependent decarboxylation
CC       of 2-oxoglutarate and the subsequent addition of the resulting succinic
CC       semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-
CC       succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC).
CC       {ECO:0000256|HAMAP-Rule:MF_01659}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=isochorismate + 2-oxoglutarate + H(+) = 5-enolpyruvoyl-6-
CC         hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2;
CC         Xref=Rhea:RHEA:25593, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC         ChEBI:CHEBI:16810, ChEBI:CHEBI:29780, ChEBI:CHEBI:58818; EC=2.2.1.9;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01659};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01659};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01659};
CC   -!- COFACTOR:
CC       Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01659};
CC       Note=Binds 1 thiamine pyrophosphate per subunit. {ECO:0000256|HAMAP-
CC       Rule:MF_01659};
CC   -!- PATHWAY: Quinol/quinone metabolism; 1,4-dihydroxy-2-naphthoate
CC       biosynthesis; 1,4-dihydroxy-2-naphthoate from chorismate: step 2/7.
CC       {ECO:0000256|HAMAP-Rule:MF_01659}.
CC   -!- PATHWAY: Quinol/quinone metabolism; menaquinone biosynthesis.
CC       {ECO:0000256|HAMAP-Rule:MF_01659}.
CC   -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_01659}.
CC   -!- SIMILARITY: Belongs to the TPP enzyme family. MenD subfamily.
CC       {ECO:0000256|HAMAP-Rule:MF_01659}.
CC   -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC       whole genome shotgun (WGS) entry which is preliminary data.
CC       {ECO:0000313|EMBL:TXD60920.1}.
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DR   EMBL; VORR01000013; TXD60920.1; -; Genomic_DNA.
DR   RefSeq; WP_147118484.1; NZ_VORR01000013.1.
DR   AlphaFoldDB; A0A5C6YBJ1; -.
DR   UniPathway; UPA00079; -.
DR   UniPathway; UPA01057; UER00164.
DR   Proteomes; UP000321094; Unassembled WGS sequence.
DR   GO; GO:0070204; F:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0030976; F:thiamine pyrophosphate binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0009234; P:menaquinone biosynthetic process; IEA:UniProtKB-UniRule.
DR   CDD; cd07037; TPP_PYR_MenD; 1.
DR   CDD; cd02009; TPP_SHCHC_synthase; 1.
DR   Gene3D; 3.40.50.970; -; 2.
DR   Gene3D; 3.40.50.1220; TPP-binding domain; 1.
DR   HAMAP; MF_01659; MenD; 1.
DR   InterPro; IPR004433; MenaQ_synth_MenD.
DR   InterPro; IPR032264; MenD_middle.
DR   InterPro; IPR029061; THDP-binding.
DR   InterPro; IPR012001; Thiamin_PyroP_enz_TPP-bd_dom.
DR   NCBIfam; TIGR00173; menD; 1.
DR   PANTHER; PTHR42916; 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE-1-CARBOXYLATE SYNTHASE; 1.
DR   PANTHER; PTHR42916:SF1; PROTEIN PHYLLO, CHLOROPLASTIC; 1.
DR   Pfam; PF16582; TPP_enzyme_M_2; 1.
DR   Pfam; PF02776; TPP_enzyme_N; 1.
DR   PIRSF; PIRSF004983; MenD; 1.
DR   SUPFAM; SSF52518; Thiamin diphosphate-binding fold (THDP-binding); 2.
PE   3: Inferred from homology;
KW   Magnesium {ECO:0000256|HAMAP-Rule:MF_01659};
KW   Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|HAMAP-Rule:MF_01659};
KW   Menaquinone biosynthesis {ECO:0000256|HAMAP-Rule:MF_01659};
KW   Metal-binding {ECO:0000256|HAMAP-Rule:MF_01659};
KW   Reference proteome {ECO:0000313|Proteomes:UP000321094};
KW   Thiamine pyrophosphate {ECO:0000256|ARBA:ARBA00023052, ECO:0000256|HAMAP-
KW   Rule:MF_01659};
KW   Transferase {ECO:0000256|HAMAP-Rule:MF_01659, ECO:0000313|EMBL:TXD60920.1}.
FT   DOMAIN          30..139
FT                   /note="Thiamine pyrophosphate enzyme N-terminal TPP-
FT                   binding"
FT                   /evidence="ECO:0000259|Pfam:PF02776"
FT   DOMAIN          232..332
FT                   /note="Menaquinone biosynthesis protein MenD middle"
FT                   /evidence="ECO:0000259|Pfam:PF16582"
SQ   SEQUENCE   576 AA;  65309 MW;  93A251D8DADD1487 CRC64;
     MIKKDKQTLS NKSFSPSGKL KGAFFYPKKE LAQIVISACC QFNIETVVVS PGSRSAPLTI
     GFFNHPEIET LSIVDERCAA FFALGIAQQT RKPVAVLCTS GSALLNYYPA IAEAFYSNIP
     LVVISADRPK HLIDIGDGQT IRQENVFENH ILFSANLIEN EKYKTRNSQL IGEALQISVS
     QQGPVHINVP FDEPLYETVT EMKTFNFPHI SLSSLDNSHI NYDELAEIWN ASKKKMILVG
     VNYPNAELHK LIDLYAEDES VLLFTETTSN LRHSKAIDSI DQLVFSLDHA EFNELKPDVL
     ITFGGMIISK RIKKFLREYQ PKHHWNIDSR KATNTFFCLS EFIQTSPVDF FSHFNQFITP
     LKSNYQPKWL AFRDEMRKKH AAYFQDLQHS DFKVFEQVLE SIPAICQLQV SNSSIIRYAQ
     LFSIKEAVHI FCNRGTSGID GSTSTAIGAA FASEKRTVFI TGDLSFFYDS NALWNKHIPA
     DFRIVLINNS GGGIFKIIPG PGTTNALEYF DTPHCLTAEH LCKMYEFEYQ QASSTKTVKT
     ELENFYKVSD KPKILEIFTP SLVNDSVLKE YFKYIK
//
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