ID Q24ME8_DESHY Unreviewed; 327 AA.
AC Q24ME8;
DT 18-APR-2006, integrated into UniProtKB/TrEMBL.
DT 18-APR-2006, sequence version 1.
DT 27-MAR-2024, entry version 106.
DE RecName: Full=Choline trimethylamine-lyase activating enzyme {ECO:0000256|HAMAP-Rule:MF_02059};
DE EC=1.97.1.- {ECO:0000256|HAMAP-Rule:MF_02059};
DE AltName: Full=Choline utilization protein D {ECO:0000256|HAMAP-Rule:MF_02059};
DE AltName: Full=GRE activase CutD {ECO:0000256|HAMAP-Rule:MF_02059};
DE AltName: Full=Glycyl-radical enzyme activating enzyme CutD {ECO:0000256|HAMAP-Rule:MF_02059};
DE Short=GRE activating enzyme CutD {ECO:0000256|HAMAP-Rule:MF_02059};
GN Name=cutD {ECO:0000256|HAMAP-Rule:MF_02059};
GN OrderedLocusNames=DSY5005 {ECO:0000313|EMBL:BAE86794.1};
OS Desulfitobacterium hafniense (strain Y51).
OC Bacteria; Bacillota; Clostridia; Eubacteriales; Desulfitobacteriaceae;
OC Desulfitobacterium.
OX NCBI_TaxID=138119 {ECO:0000313|EMBL:BAE86794.1, ECO:0000313|Proteomes:UP000001946};
RN [1] {ECO:0000313|EMBL:BAE86794.1, ECO:0000313|Proteomes:UP000001946}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Y51 {ECO:0000313|EMBL:BAE86794.1,
RC ECO:0000313|Proteomes:UP000001946};
RX PubMed=16513756; DOI=10.1128/JB.188.6.2262-2274.2006;
RA Nonaka H., Keresztes G., Shinoda Y., Ikenaga Y., Abe M., Naito K.,
RA Inatomi K., Furukawa K., Inui M., Yukawa H.;
RT "Complete genome sequence of the dehalorespiring bacterium
RT Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides
RT ethenogenes 195.";
RL J. Bacteriol. 188:2262-2274(2006).
CC -!- FUNCTION: Catalyzes activation of the choline trimethylamine-lyase CutC
CC under anaerobic conditions by generation of an organic free radical on
CC a glycine residue, via an homolytic cleavage of S-adenosyl-L-methionine
CC (SAM). {ECO:0000256|HAMAP-Rule:MF_02059}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=glycyl-[protein] + reduced [flavodoxin] + S-adenosyl-L-
CC methionine = 5'-deoxyadenosine + glycin-2-yl radical-[protein] + H(+)
CC + L-methionine + semiquinone [flavodoxin]; Xref=Rhea:RHEA:61976,
CC Rhea:RHEA-COMP:10622, Rhea:RHEA-COMP:14480, Rhea:RHEA-COMP:15993,
CC Rhea:RHEA-COMP:15994, ChEBI:CHEBI:15378, ChEBI:CHEBI:17319,
CC ChEBI:CHEBI:29947, ChEBI:CHEBI:32722, ChEBI:CHEBI:57618,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:59789, ChEBI:CHEBI:140311;
CC Evidence={ECO:0000256|ARBA:ARBA00000544, ECO:0000256|HAMAP-
CC Rule:MF_02059};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_02059};
CC Note=Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000256|HAMAP-Rule:MF_02059};
CC -!- PATHWAY: Amine and polyamine metabolism; choline degradation.
CC {ECO:0000256|HAMAP-Rule:MF_02059}.
CC -!- SIMILARITY: Belongs to the organic radical-activating enzymes family.
CC {ECO:0000256|ARBA:ARBA00009777, ECO:0000256|HAMAP-Rule:MF_02059}.
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DR EMBL; AP008230; BAE86794.1; -; Genomic_DNA.
DR RefSeq; WP_011462301.1; NC_007907.1.
DR AlphaFoldDB; Q24ME8; -.
DR STRING; 138119.DSY5005; -.
DR KEGG; dsy:DSY5005; -.
DR eggNOG; COG1180; Bacteria.
DR HOGENOM; CLU_058969_0_0_9; -.
DR UniPathway; UPA01069; -.
DR Proteomes; UP000001946; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0042426; P:choline catabolic process; IEA:UniProtKB-UniRule.
DR Gene3D; 3.30.70.20; -; 1.
DR Gene3D; 3.80.30.10; pyruvate-formate lyase- activating enzyme; 1.
DR HAMAP; MF_02059; Activ_enz_CutD; 1.
DR InterPro; IPR017896; 4Fe4S_Fe-S-bd.
DR InterPro; IPR017900; 4Fe4S_Fe_S_CS.
DR InterPro; IPR040074; BssD/PflA/YjjW.
DR InterPro; IPR030905; CutC_activ_rSAM.
DR InterPro; IPR034457; Organic_radical-activating.
DR InterPro; IPR012839; Organic_radical_activase.
DR InterPro; IPR001989; Radical_activat_CS.
DR InterPro; IPR007197; rSAM.
DR NCBIfam; TIGR04395; cutC_activ_rSAM; 1.
DR NCBIfam; TIGR02494; PFLE_PFLC; 1.
DR PANTHER; PTHR30352:SF4; PYRUVATE FORMATE-LYASE 2-ACTIVATING ENZYME; 1.
DR PANTHER; PTHR30352; PYRUVATE FORMATE-LYASE-ACTIVATING ENZYME; 1.
DR Pfam; PF13353; Fer4_12; 1.
DR Pfam; PF12838; Fer4_7; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR PIRSF; PIRSF000371; PFL_act_enz; 1.
DR SFLD; SFLDG01118; activating_enzymes__group_2; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SUPFAM; SSF54862; 4Fe-4S ferredoxins; 1.
DR SUPFAM; SSF102114; Radical SAM enzymes; 1.
DR PROSITE; PS00198; 4FE4S_FER_1; 2.
DR PROSITE; PS51379; 4FE4S_FER_2; 2.
DR PROSITE; PS01087; RADICAL_ACTIVATING; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 3: Inferred from homology;
KW 4Fe-4S {ECO:0000256|ARBA:ARBA00022485, ECO:0000256|HAMAP-Rule:MF_02059};
KW Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|HAMAP-Rule:MF_02059};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014, ECO:0000256|HAMAP-
KW Rule:MF_02059}; Lyase {ECO:0000313|EMBL:BAE86794.1};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_02059};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002, ECO:0000256|HAMAP-
KW Rule:MF_02059}; Pyruvate {ECO:0000313|EMBL:BAE86794.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000001946};
KW Repeat {ECO:0000256|HAMAP-Rule:MF_02059};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691, ECO:0000256|HAMAP-
KW Rule:MF_02059}.
FT DOMAIN 24..319
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT DOMAIN 55..84
FT /note="4Fe-4S ferredoxin-type"
FT /evidence="ECO:0000259|PROSITE:PS51379"
FT DOMAIN 96..126
FT /note="4Fe-4S ferredoxin-type"
FT /evidence="ECO:0000259|PROSITE:PS51379"
FT BINDING 38
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02059"
FT BINDING 42
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02059"
FT BINDING 44..46
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02059"
FT BINDING 45
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02059"
FT BINDING 64
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02059"
FT BINDING 67
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02059"
FT BINDING 70
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02059"
FT BINDING 116
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02059"
FT BINDING 156
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02059"
FT BINDING 205..207
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02059"
FT BINDING 281
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02059"
SQ SEQUENCE 327 AA; 37395 MW; 2FA08FEF39560AE6 CRC64;
MNTEICSILE RQARIFNVQK YSLYDGPGIR TLIFFKGCPL RCKWCSNPEG LERKYQVMYM
EDSCIHCGNC IPVCPVNIHS FANRDGETVP THYEPPKHTI NRNIDCVGCR KCETICPKKA
LSIAGTDLKI SEVLEIIQQD TLFYLSSDGG VTLGGGEVTA QPEFATNLLM ECQRMGINTA
IETCGYAKLD TLLMIAQFTD LFLYDLKHID PERHYELTGV RNERILDNLT ELIHRGFNIK
IRMPLIRGMN DSQDTIRRTM EFLQPFSSCK NFQGIDLLPY HKLGINKYKQ LDMNYTITED
LSFKAEELDE IARIIGGYDL RAAVIRH
//
