ID A0A0X8CEZ0_9BRAD Unreviewed; 578 AA.
AC A0A0X8CEZ0;
DT 06-JUL-2016, integrated into UniProtKB/TrEMBL.
DT 06-JUL-2016, sequence version 1.
DT 24-JAN-2024, entry version 31.
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=BCCGELA001_07260 {ECO:0000313|EMBL:AMA56073.1};
OS Bradyrhizobium sp. CCGE-LA001.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC Nitrobacteraceae; Bradyrhizobium.
OX NCBI_TaxID=1223566 {ECO:0000313|EMBL:AMA56073.1, ECO:0000313|Proteomes:UP000019052};
RN [1] {ECO:0000313|EMBL:AMA56073.1, ECO:0000313|Proteomes:UP000019052}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CCGE-LA001 {ECO:0000313|EMBL:AMA56073.1,
RC ECO:0000313|Proteomes:UP000019052};
RX PubMed=24952318; DOI=10.1016/j.ympev.2014.06.006;
RA Servin-Garciduenas L.E., Zayas-Del Moral A., Ormeno-Orrillo E., Rogel M.A.,
RA Delgado-Salinas A., Sanchez F., Martinez-Romero E.;
RT "Symbiont shift towards Rhizobium nodulation in a group of phylogenetically
RT related Phaseolus species.";
RL Mol. Phylogenet. Evol. 79:1-11(2014).
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}.
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DR EMBL; CP013949; AMA56073.1; -; Genomic_DNA.
DR RefSeq; WP_008563388.1; NZ_CP013949.1.
DR AlphaFoldDB; A0A0X8CEZ0; -.
DR STRING; 1223566.BCCGELA001_07260; -.
DR KEGG; brc:BCCGELA001_07260; -.
DR Proteomes; UP000019052; Chromosome.
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 CDD; cd07039; TPP_PYR_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 InterPro; IPR047210; TPP_PYR_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:AMA56073.1};
KW Thiamine pyrophosphate {ECO:0000256|HAMAP-Rule:MF_00850,
KW ECO:0000256|RuleBase:RU362132};
KW Ubiquinone {ECO:0000256|HAMAP-Rule:MF_00850}.
FT DOMAIN 5..116
FT /note="Thiamine pyrophosphate enzyme N-terminal TPP-
FT binding"
FT /evidence="ECO:0000259|Pfam:PF02776"
FT DOMAIN 195..322
FT /note="Thiamine pyrophosphate enzyme central"
FT /evidence="ECO:0000259|Pfam:PF00205"
FT DOMAIN 384..530
FT /note="Thiamine pyrophosphate enzyme TPP-binding"
FT /evidence="ECO:0000259|Pfam:PF02775"
FT REGION 186..337
FT /note="FAD-binding domain"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT REGION 536..577
FT /note="Membrane-binding domain"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 51
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 277..281
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 295
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 411..413
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 438..440
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 438
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 465..471
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT BINDING 465
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00850"
FT SITE 470
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 578 AA; 61589 MW; B4425D369918D4C2 CRC64;
MAINNVADLF VATLEQAGVK RIYGIVGDSL NGLTEALRRR GTIDWIHVRH EEVAAFAAAG
EAEMTGSLAV CAGSCGPGNL HLINGLFDAH RSRAPVLAIA AQIPSAEIGG GYFQETHPQN
LFRECSHYCE LISDPSQLPF VLENAIRAAV GLRGVAVVAM PGDVAFRSPP KRALSTTRGL
ALAPPKIVPQ ADELKALADL LNGTERITLF CGRGCAGAHA PLMQLAEALK SPIVHALGGK
EHVEYDNPYD VGMTGFIGFS SGYAAMHACD TLVMLGTDFP YKQFFPTDAK VAQIDIRPEN
LGRRCKIDLG LVGDVKLTIE ALLPLLKSKT QRKHLDDAVA HYKKAREGLD SLAKGTPGSK
PIHPQYLAKV ISDHASDDAV FTADVGTPTV WAARYLDMNG GRRLIGSFVH GSMANAMPQA
IGAQAAQPGR QVISLSGDGG FTMLMGDLIT LTQEKLPVKV VVFNNGVLGF VALEMKAAGF
VDTNVDLENP DFAAMARAMG IFAKRVEDPG ELPGAVKEML AHDGPALLDV VTAKQELSMP
PTITAEQVKG FSLWVLRAVM NGRGDEVLDL AKTNLLPR
//
