GLPDH_CALMK
ID GLPDH_CALMK Reviewed; 480 AA.
AC A0A0R3K2G2;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 20-JAN-2016, sequence version 1.
DT 03-AUG-2022, entry version 16.
DE RecName: Full=Glycerol 3-phosphate dehydrogenase {ECO:0000305|PubMed:34555022};
DE EC=1.1.99.- {ECO:0000269|PubMed:34555022};
GN Name=lhgO_1 {ECO:0000312|EMBL:KRQ87604.1};
GN ORFNames=ABG79_00405 {ECO:0000312|EMBL:KRQ87604.1};
OS Caloramator mitchellensis.
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Clostridiaceae;
OC Caloramator.
OX NCBI_TaxID=908809;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 25793 / JCM 15828 / KCTC 5735 / VF08;
RA Patel B.K.;
RT "Draft genome sequence of a Caloramator mitchellensis, a moderate
RT thermophile from the Great Artesian Basin of Australia.";
RL Submitted (SEP-2015) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=34555022; DOI=10.1371/journal.pcbi.1009446;
RA Rembeza E., Engqvist M.K.M.;
RT "Experimental and computational investigation of enzyme functional
RT annotations uncovers misannotation in the EC 1.1.3.15 enzyme class.";
RL PLoS Comput. Biol. 17:e1009446-e1009446(2021).
CC -!- FUNCTION: Catalyzes the dehydrogenation of glycerol 3-phosphate to
CC dihydroxyacetone phosphate (PubMed:34555022). Is probably involved in
CC anaerobic glycerol metabolism (Probable). Active in vitro with the
CC artificial electron acceptor 2,6-dichlorophenolindophenol (DCPIP), but
CC not with NAD or NADP. Also displays a very low oxidase activity in
CC vitro on glycerol 3-phosphate with O2 as the electron acceptor, but
CC this activity is most likely not physiological (PubMed:34555022).
CC {ECO:0000269|PubMed:34555022, ECO:0000305}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=A + sn-glycerol 3-phosphate = AH2 + dihydroxyacetone
CC phosphate; Xref=Rhea:RHEA:68972, ChEBI:CHEBI:13193,
CC ChEBI:CHEBI:17499, ChEBI:CHEBI:57597, ChEBI:CHEBI:57642;
CC Evidence={ECO:0000269|PubMed:34555022};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:68973;
CC Evidence={ECO:0000305};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000250|UniProtKB:P05340};
CC Note=Binds 1 [2Fe-2S] cluster. {ECO:0000250|UniProtKB:P05340};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.97 mM for glycerol-3-phosphate (at pH 7.4 and 25 degrees
CC Celsius) {ECO:0000269|PubMed:34555022};
CC Note=kcat is 0.24 sec(-1) with DCPIP as electron acceptor (at pH 7.4
CC and 25 degrees Celsius). Since this protein comes from the
CC thermophilic bacterium C.mitchellensis, whose optimal growth
CC temperature is 55 degrees Celsius, it can be speculated that its
CC catalytic efficiency would be higher at higher experimental
CC temperatures. {ECO:0000269|PubMed:34555022};
CC -!- PATHWAY: Polyol metabolism; glycerol degradation via glycerol kinase
CC pathway; glycerone phosphate from sn-glycerol 3-phosphate (aerobic
CC route): step 1/1. {ECO:0000305}.
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DR EMBL; LKHP01000002; KRQ87604.1; -; Genomic_DNA.
DR RefSeq; WP_057976602.1; NZ_LKHP01000002.1.
DR STRING; 908809.ABG79_00405; -.
DR EnsemblBacteria; KRQ87604; KRQ87604; ABG79_00405.
DR PATRIC; fig|908809.3.peg.410; -.
DR OrthoDB; 1371190at2; -.
DR UniPathway; UPA00618; UER00674.
DR Proteomes; UP000052015; Unassembled WGS sequence.
DR GO; GO:0003973; F:(S)-2-hydroxy-acid oxidase activity; IEA:UniProtKB-EC.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019563; P:glycerol catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 1.10.10.1100; -; 1.
DR Gene3D; 3.50.50.60; -; 1.
DR InterPro; IPR007419; BFD-like_2Fe2S-bd_dom.
DR InterPro; IPR041854; BFD-like_2Fe2S-bd_dom_sf.
DR InterPro; IPR006076; FAD-dep_OxRdtase.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR Pfam; PF01266; DAO; 1.
DR Pfam; PF04324; Fer2_BFD; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; FAD; Flavoprotein; Iron; Iron-sulfur; Metal-binding;
KW Oxidoreductase; Reference proteome.
FT CHAIN 1..480
FT /note="Glycerol 3-phosphate dehydrogenase"
FT /id="PRO_0000454854"
FT ACT_SITE 49
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 12
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 31
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 40..41
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 45..47
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 45
FT /ligand="sn-glycerol 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:57597"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 49
FT /ligand="sn-glycerol 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:57597"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 172
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 249
FT /ligand="sn-glycerol 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:57597"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 310
FT /ligand="sn-glycerol 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:57597"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 335..336
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 337
FT /ligand="sn-glycerol 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:57597"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 341
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P75063"
FT BINDING 400
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000250|UniProtKB:P05340"
FT BINDING 402
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000250|UniProtKB:P05340"
FT BINDING 437
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000250|UniProtKB:P05340"
FT BINDING 442
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000250|UniProtKB:P05340"
SQ SEQUENCE 480 AA; 52962 MW; C43BD9099F7D507C CRC64;
MFDVAIIGAG VIGCSIAREL SKYNLNVALI EKENDVGNVT TKANSAIIHA GYDAKPGTLK
GKLNAKGNLM FDELCRELEV PFKRVGSLVL AFDDDEMKTL GKLYEQGIQN GVPELYILSK
EKVLEMDPNI SDNIKGALYA KTGGIIGPWE FTIALAENAV ENGVNIFLSN EVVDIEKKDF
GYRIITNKDT YDTKYVVNCA GLYADKINNM VSNNKMEIIP RRGQYYLLDK TVGNLVKYVI
FQCPSKLGKG VLVTPTVHGN LLIGPDAEDL IDKTALNTTS EGLNFIVEVA RRSVKTLPLN
MAITNFAGLR ARTERDDFII EEAVDAKGFI NVAGIESPGL SSAPAISLYV IDILKNIAKK
IEKKENFNPY RRAIPKFIEL SEDEKNELVK KDKRFGKIIC RCESITEGEI VSAIHRNVGA
RTVDAVKRRV RAGMGRCQGG FCSPRVIEIL ARELGVEMTE IEKDHEGSYI LTGPTKSEVQ
