FRD_KLEP3
ID FRD_KLEP3 Reviewed; 925 AA.
AC B5XRB0;
DT 07-APR-2021, integrated into UniProtKB/Swiss-Prot.
DT 25-NOV-2008, sequence version 1.
DT 03-AUG-2022, entry version 79.
DE RecName: Full=NADH:fumarate oxidoreductase {ECO:0000303|PubMed:33107907};
DE EC=1.3.1.6 {ECO:0000269|PubMed:33107907};
DE AltName: Full=Fumarate reductase {ECO:0000303|PubMed:24361839, ECO:0000303|PubMed:33107907};
DE Short=FRD {ECO:0000303|PubMed:33107907};
GN OrderedLocusNames=KPK_2907 {ECO:0000312|EMBL:ACI10570.1};
OS Klebsiella pneumoniae (strain 342).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
OX NCBI_TaxID=507522;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=342;
RX PubMed=18654632; DOI=10.1371/journal.pgen.1000141;
RA Fouts D.E., Tyler H.L., DeBoy R.T., Daugherty S., Ren Q., Badger J.H.,
RA Durkin A.S., Huot H., Shrivastava S., Kothari S., Dodson R.J., Mohamoud Y.,
RA Khouri H., Roesch L.F.W., Krogfelt K.A., Struve C., Triplett E.W.,
RA Methe B.A.;
RT "Complete genome sequence of the N2-fixing broad host range endophyte
RT Klebsiella pneumoniae 342 and virulence predictions verified in mice.";
RL PLoS Genet. 4:E1000141-E1000141(2008).
RN [2]
RP FUNCTION, COFACTOR, DISRUPTION PHENOTYPE, FLAVINYLATION, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=204;
RX PubMed=24361839; DOI=10.1016/j.bbabio.2013.12.006;
RA Bertsova Y.V., Kostyrko V.A., Baykov A.A., Bogachev A.V.;
RT "Localization-controlled specificity of FAD:threonine flavin transferases
RT in Klebsiella pneumoniae and its implications for the mechanism of Na(+)-
RT translocating NADH:quinone oxidoreductase.";
RL Biochim. Biophys. Acta 1837:1122-1129(2014).
RN [3]
RP FLAVINYLATION AT THR-447 (FMN PROSTHETIC GROUP AT THR-447), AND MUTAGENESIS
RP OF GLY-445; ALA-446 AND THR-447.
RX PubMed=31834358; DOI=10.1093/femsle/fnz252;
RA Bertsova Y.V., Serebryakova M.V., Anashkin V.A., Baykov A.A.,
RA Bogachev A.V.;
RT "Mutational analysis of the flavinylation and binding motifs in two protein
RT targets of the flavin transferase ApbE.";
RL FEMS Microbiol. Lett. 366:0-0(2019).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
RP INDUCTION, AND MUTAGENESIS OF THR-447.
RC STRAIN=204;
RX PubMed=33107907; DOI=10.1093/femsle/fnaa175;
RA Bertsova Y.V., Oleynikov I.P., Bogachev A.V.;
RT "A new water-soluble bacterial NADH: fumarate oxidoreductase.";
RL FEMS Microbiol. Lett. 367:0-0(2020).
CC -!- FUNCTION: Catalyzes the anaerobic reduction of fumarate to succinate
CC (PubMed:24361839, PubMed:33107907). Uses NADH as the inherent electron
CC donor in this process (PubMed:33107907). Is involved in anaerobic
CC fumarate respiration in K.pneumoniae (PubMed:33107907).
CC {ECO:0000269|PubMed:24361839, ECO:0000269|PubMed:33107907}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=NAD(+) + succinate = fumarate + H(+) + NADH;
CC Xref=Rhea:RHEA:18281, ChEBI:CHEBI:15378, ChEBI:CHEBI:29806,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.3.1.6;
CC Evidence={ECO:0000269|PubMed:33107907};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:18283;
CC Evidence={ECO:0000305|PubMed:33107907};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:24361839};
CC Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:24361839};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:24361839};
CC Note=Binds 2 FMN prosthetic groups per subunit. 1 FMN is bound
CC covalently, while the other is non-covalent.
CC {ECO:0000269|PubMed:24361839};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=75 uM for NADH {ECO:0000269|PubMed:33107907};
CC Note=kcat is about 10 sec(-1). {ECO:0000269|PubMed:33107907};
CC pH dependence:
CC Optimum pH is 6.0-6.5. {ECO:0000269|PubMed:33107907};
CC -!- SUBUNIT: Monomer. {ECO:0000305|PubMed:33107907}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:24361839}.
CC -!- INDUCTION: Induced under anaerobic conditions in the presence of
CC fumarate or malate, but not tartrate. Is repressed under aerobic
CC conditions. {ECO:0000269|PubMed:33107907}.
CC -!- DOMAIN: Consists of three domains. The first domain of FRD (OYE-like,
CC PF00724) is homologous to Old Yellow Enzyme (OYE). It carries a non-
CC covalently bound FMN and is used for NADH oxidation. The second,
CC FMN_bind domain (PF04205) contains a covalently bound FMN, that acts as
CC an electron carrier between the two other domains of FRD. The C-
CC terminal FAD_binding_2 domain contains a non-covalently bound FAD and
CC forms a site for fumarate reduction. {ECO:0000305|PubMed:33107907}.
CC -!- PTM: Is flavinylated on Thr-447 by ApbE2, encoded in a neighboring gene
CC (PubMed:24361839). Flavinylation is essential for catalytic activity
CC (PubMed:31834358). {ECO:0000269|PubMed:24361839,
CC ECO:0000269|PubMed:31834358}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene lack cytoplasmic fumarate
CC reductase activity, while retaining this activity in the membrane
CC fraction. {ECO:0000269|PubMed:24361839}.
CC -!- SIMILARITY: Belongs to the FAD-dependent oxidoreductase 2 family.
CC FRD/SDH subfamily. {ECO:0000305}.
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DR EMBL; CP000964; ACI10570.1; -; Genomic_DNA.
DR AlphaFoldDB; B5XRB0; -.
DR SMR; B5XRB0; -.
DR EnsemblBacteria; ACI10570; ACI10570; KPK_2907.
DR KEGG; kpe:KPK_2907; -.
DR HOGENOM; CLU_011398_1_2_6; -.
DR OMA; YAYILFD; -.
DR OrthoDB; 153138at2; -.
DR BioCyc; KPNE507522:GI0B-2895-MON; -.
DR Proteomes; UP000001734; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016020; C:membrane; IEA:InterPro.
DR GO; GO:0010181; F:FMN binding; IEA:InterPro.
DR GO; GO:0016156; F:fumarate reductase (NADH) activity; IEA:UniProtKB-EC.
DR GO; GO:0008152; P:metabolic process; IEA:UniProt.
DR Gene3D; 3.20.20.70; -; 1.
DR Gene3D; 3.50.50.60; -; 1.
DR Gene3D; 3.90.700.10; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR003953; FAD-binding_2.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR010960; Flavocytochrome_c.
DR InterPro; IPR007329; FMN-bd.
DR InterPro; IPR001155; OxRdtase_FMN_N.
DR InterPro; IPR027477; Succ_DH/fumarate_Rdtase_cat_sf.
DR Pfam; PF00890; FAD_binding_2; 1.
DR Pfam; PF04205; FMN_bind; 1.
DR Pfam; PF00724; Oxidored_FMN; 1.
DR SMART; SM00900; FMN_bind; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
DR SUPFAM; SSF56425; SSF56425; 1.
DR TIGRFAMs; TIGR01813; flavo_cyto_c; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; FAD; Flavoprotein; FMN; Oxidoreductase; Phosphoprotein.
FT CHAIN 1..925
FT /note="NADH:fumarate oxidoreductase"
FT /id="PRO_0000452180"
FT ACT_SITE 756
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P0C278"
FT BINDING 492
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT BINDING 511..512
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT BINDING 519..526
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT BINDING 633
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT BINDING 731..732
FT /ligand="fumarate"
FT /ligand_id="ChEBI:CHEBI:29806"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT BINDING 859
FT /ligand="fumarate"
FT /ligand_id="ChEBI:CHEBI:29806"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT BINDING 889
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT BINDING 899
FT /ligand="fumarate"
FT /ligand_id="ChEBI:CHEBI:29806"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT BINDING 904..905
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT MOD_RES 447
FT /note="FMN phosphoryl threonine"
FT /evidence="ECO:0000269|PubMed:24361839,
FT ECO:0000269|PubMed:31834358"
FT MUTAGEN 445
FT /note="G->A: 50% decrease in covalent flavinylation."
FT /evidence="ECO:0000269|PubMed:31834358"
FT MUTAGEN 446
FT /note="A->V: 50% decrease in covalent flavinylation."
FT /evidence="ECO:0000269|PubMed:31834358"
FT MUTAGEN 447
FT /note="T->A: Abolishes covalent flavinylation and anaerobic
FT NADH:fumarate oxidoreductase activity."
FT /evidence="ECO:0000269|PubMed:31834358,
FT ECO:0000269|PubMed:33107907"
FT MUTAGEN 447
FT /note="T->S: 50% decrease in covalent flavinylation. Shows
FT 40% of wild-type FRD activity."
FT /evidence="ECO:0000269|PubMed:31834358"
SQ SEQUENCE 925 AA; 99523 MW; 2F1ADB78AD1C4F9F CRC64;
MTSNERILQP FTLPNGTELK NRLLMAPMTT CTGYFDGTVT SELVEYYRAR AGSIGTIIVE
CCFIDDYGLA FPGAIGIDND EKIAGLAKIA EAIKAQGSKA ILQIYHGGRM VDPQLIGGRQ
PVAPSAIAAP REGAAMPRAL SGEEVEGMIA KFGDGVRRAI LAGFDGVEIH GANTYLIQQF
YSPNSNQRDD EWGGSRDNRA RFPLAVLDIT HKMARQYADD AFIIGYRFSP EEMEVPGIRF
DDTMYLLEKL AARGVDYLHF SVGATLRPSI VDTSDPTPLI EKYCAMRSET LAQVPVMGVG
GVVNVADAEL GLDHGYDLIA VGRACIAYPD WAARIAAGEE LELFIDSTQR EALHIPEPLW
RFSLVEAMIR DMSMGDAKFK PGMFVETVQD DANELVINVS LENDHIADIE LAASPVQTVE
FTTSFEEIRE RILTANTPHV DAISGATSQS EAVKKAVAKA MLKSSKALAA EEGGNDAAPK
SYDVVVVGSG GAGLAAAIQA HDEGASVLIV EKMPTIGGNT IKASAGMNAA ETRFQRVKGI
QDSKELFYQE TLKGGHNKNN PQLLRRFVEN APQAIEWLAD RGIMLNDITT TGGMSIDRTH
RPRDGSAVGG YLISGLVRNI TKRGIDVLLD TSVEEILMSG DEVSGVRLVN DEKEVIEVQT
KSIVVATGGF SANSAMVVKY RPDLDGFVTT NHKGATGSGI ALLERIGAGT VDMGEIQIHP
TVEQQTSYLI SESIRGGGAI LVNQQGNRFF NEMETRDKVS AAIIALPEHY AYIVFDEHVR
AKNKAADEYI AKGFVTSASS PRELAEKLGM DYHAFLATLE CYNGAVEKQH DEQFGRTTAL
RAPINEGPFH AIRIAPGVHH TMGGVTINTD GEVLNVDQQP IRGAYAAGEV VGGIHGGNRI
GGNAVADIII FGTLAGHQAA KRARG
