ID A0A3S0PGP5_9GAMM Unreviewed; 572 AA.
AC A0A3S0PGP5;
DT 10-APR-2019, integrated into UniProtKB/TrEMBL.
DT 10-APR-2019, sequence version 1.
DT 24-JAN-2024, entry version 15.
DE RecName: Full=Pyruvate dehydrogenase [ubiquinone] {ECO:0000256|HAMAP-Rule:MF_00850};
DE EC=1.2.5.1 {ECO:0000256|HAMAP-Rule:MF_00850};
DE AltName: Full=Pyruvate oxidase {ECO:0000256|HAMAP-Rule:MF_00850};
DE Short=POX {ECO:0000256|HAMAP-Rule:MF_00850};
DE AltName: Full=Pyruvate:ubiquinone-8 oxidoreductase {ECO:0000256|HAMAP-Rule:MF_00850};
GN Name=poxB {ECO:0000256|HAMAP-Rule:MF_00850};
GN ORFNames=EKH80_17475 {ECO:0000313|EMBL:RUL72474.1};
OS Dyella choica.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Xanthomonadales;
OC Rhodanobacteraceae; Dyella.
OX NCBI_TaxID=1927959 {ECO:0000313|EMBL:RUL72474.1, ECO:0000313|Proteomes:UP000274358};
RN [1] {ECO:0000313|EMBL:RUL72474.1, ECO:0000313|Proteomes:UP000274358}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=4M-K27 {ECO:0000313|EMBL:RUL72474.1,
RC ECO:0000313|Proteomes:UP000274358};
RA Qiu L.-H., Gao Z.-H.;
RT "Dyella dinghuensis sp. nov. DHOA06 and Dyella choica sp. nov. 4M-K27,
RT isolated from forest soil.";
RL Submitted (DEC-2018) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: A peripheral cell membrane enzyme that catalyzes the
CC oxidative decarboxylation of pyruvate to form acetate and CO(2). It
CC channels electrons from the cytoplasm to the respiratory chain at the
CC cell membrane via ubiquinone. {ECO:0000256|HAMAP-Rule:MF_00850}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ubiquinone + H2O + pyruvate = a ubiquinol + acetate + CO2;
CC Xref=Rhea:RHEA:27405, Rhea:RHEA-COMP:9565, Rhea:RHEA-COMP:9566,
CC ChEBI:CHEBI:15361, ChEBI:CHEBI:15377, ChEBI:CHEBI:16389,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:17976, ChEBI:CHEBI:30089; EC=1.2.5.1;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00850};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00850};
CC Note=Binds 1 FAD per subunit. {ECO:0000256|HAMAP-Rule:MF_00850};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00850};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000256|HAMAP-Rule:MF_00850};
CC -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00850};
CC Note=Binds 1 thiamine pyrophosphate per subunit. {ECO:0000256|HAMAP-
CC Rule:MF_00850};
CC -!- ACTIVITY REGULATION: The C-terminus inhibits activity; it has to move
CC for the enzyme to be active. Activated by lipid-binding, which occurs
CC via the C-terminus. {ECO:0000256|HAMAP-Rule:MF_00850}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000256|HAMAP-Rule:MF_00850}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000256|HAMAP-Rule:MF_00850};
CC Peripheral membrane protein {ECO:0000256|HAMAP-Rule:MF_00850};
CC Cytoplasmic side {ECO:0000256|HAMAP-Rule:MF_00850}.
CC -!- DOMAIN: Has 4 domains; the Pyr domain which binds the pyrimidine moiety
CC of the thiamine pyrophosphate cofactor, the FAD-binding domain, the PP-
CC binding domain which binds the pyrophosphate portion of thiamine
CC pyrophosphate and the C-terminal membrane binding region. The C-
CC terminus is held closely against the rest of the protein and covers the
CC active site; during activation it unfolds from the rest of the protein
CC and forms an amphipathic helix upon membrane binding, exposing the
CC active site. {ECO:0000256|HAMAP-Rule:MF_00850}.
CC -!- SIMILARITY: Belongs to the TPP enzyme family.
CC {ECO:0000256|ARBA:ARBA00007812, ECO:0000256|HAMAP-Rule:MF_00850,
CC ECO:0000256|RuleBase:RU362132}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_00850}.
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:RUL72474.1}.
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DR EMBL; RYYV01000015; RUL72474.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A3S0PGP5; -.
DR OrthoDB; 9785953at2; -.
DR Proteomes; UP000274358; Unassembled WGS sequence.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008289; F:lipid binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0052737; F:pyruvate dehydrogenase (quinone) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0048039; F:ubiquinone binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042867; P:pyruvate catabolic process; IEA:UniProtKB-UniRule.
DR CDD; cd02014; TPP_POX; 1.
DR Gene3D; 3.40.50.970; -; 2.
DR Gene3D; 3.40.50.1220; TPP-binding domain; 1.
DR HAMAP; MF_00850; POX; 1.
DR InterPro; IPR029035; DHS-like_NAD/FAD-binding_dom.
DR InterPro; IPR047211; POXB-like.
DR InterPro; IPR044261; Pyruvate_dehydrogenase.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR012000; Thiamin_PyroP_enz_cen_dom.
DR InterPro; IPR012001; Thiamin_PyroP_enz_TPP-bd_dom.
DR InterPro; IPR000399; TPP-bd_CS.
DR InterPro; IPR011766; TPP_enzyme_TPP-bd.
DR InterPro; IPR047212; TPP_POXB-like.
DR PANTHER; PTHR42981; PYRUVATE DEHYDROGENASE [UBIQUINONE]; 1.
DR PANTHER; PTHR42981:SF2; PYRUVATE DEHYDROGENASE [UBIQUINONE]; 1.
DR Pfam; PF02775; TPP_enzyme_C; 1.
DR Pfam; PF00205; TPP_enzyme_M; 1.
DR Pfam; PF02776; TPP_enzyme_N; 1.
DR SUPFAM; SSF52467; DHS-like NAD/FAD-binding domain; 1.
DR SUPFAM; SSF52518; Thiamin diphosphate-binding fold (THDP-binding); 2.
DR PROSITE; PS00187; TPP_ENZYMES; 1.
PE 3: Inferred from homology;
KW Cell membrane {ECO:0000256|HAMAP-Rule:MF_00850};
KW FAD {ECO:0000256|HAMAP-Rule:MF_00850};
KW Flavoprotein {ECO:0000256|HAMAP-Rule:MF_00850};
KW Lipid-binding {ECO:0000256|HAMAP-Rule:MF_00850};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00850};
KW Membrane {ECO:0000256|HAMAP-Rule:MF_00850};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_00850};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00850};
KW Oxidoreductase {ECO:0000256|HAMAP-Rule:MF_00850};
KW Pyruvate {ECO:0000256|HAMAP-Rule:MF_00850, ECO:0000313|EMBL:RUL72474.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000274358};
KW Thiamine pyrophosphate {ECO:0000256|HAMAP-Rule:MF_00850,
KW ECO:0000256|RuleBase:RU362132};
KW Ubiquinone {ECO:0000256|HAMAP-Rule:MF_00850, ECO:0000313|EMBL:RUL72474.1}.
FT DOMAIN 6..113
FT /note="Thiamine pyrophosphate enzyme N-terminal TPP-
FT binding"
FT /evidence="ECO:0000259|Pfam:PF02776"
FT DOMAIN 190..315
FT /note="Thiamine pyrophosphate enzyme central"
FT /evidence="ECO:0000259|Pfam:PF00205"
FT DOMAIN 379..525
FT /note="Thiamine pyrophosphate enzyme TPP-binding"
FT /evidence="ECO:0000259|Pfam:PF02775"
FT REGION 181..332
FT /note="FAD-binding domain"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT REGION 531..572
FT /note="Membrane-binding domain"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 49
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 272..276
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 290
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 406..408
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 433..435
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 433
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 460..466
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 460
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT SITE 465
FT /note="Moves into active site upon enzyme activation, plays
FT a role in electron transfer"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
SQ SEQUENCE 572 AA; 61874 MW; 260E021E0541676D CRC64;
MALSSAEYVA KVLELAGVKH VYGVVGDSLN GLTDAFRRSS IEWLHMRHEE AAAFAAGADA
HLTGELAVCA GSCGPGNLHL INGLFDCHRS GVPVLAIASH IPSSEIGIDY FQATHPENLF
KECSHYVELV ANPSQLPHVL GRAMRAAVAR RGVAVVVIPG DVSLKEAVAE VPRWVTPNKP
ILHPSLKDLQ RLTHLLKDAT RVTIFCGAGC AGAHDEVVEL ARRLKAPIVH TLRGKEYLEY
NNPYDVGMTG LVGFSSGYAA MKDCDTLLLL GTDFPYRQFF PKHAKIAQID VRPEALGNRC
PLDLGLIGDV RETLQILLPS VAEKTDSSHL DAALAHYQKA REGLDELADP RRGSDLIHPQ
YVTKLVSELA AEDAIFTCDV GTPILWTARY LKVNGKRRIV GSFNHGSMAN AMLHAIGAQV
ACPDRQVISM SGDGGFAMMM GEFLSLTQLD LPVKIILLNN GTLGFVEMEM KANGFLDSGC
DLINPNFAQM ASAVGVKGIR VERPDALRPA LIEAFSHTGP VLVDVVSARQ ELAMPPKTSF
DEAYKFGLFM IKAVLDGRGN QLVDLAKVNL LR
//
