CUTC_OLEA2
ID CUTC_OLEA2 Reviewed; 846 AA.
AC Q30W70;
DT 16-MAR-2016, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 89.
DE RecName: Full=Choline trimethylamine-lyase {ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000303|PubMed:23151509};
DE Short=Choline TMA-lyase {ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000303|PubMed:23151509};
DE EC=4.3.99.4 {ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000269|PubMed:23151509};
DE AltName: Full=Choline utilization protein C {ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000303|PubMed:23151509};
DE AltName: Full=Glycyl radical enzyme CutC {ECO:0000303|PubMed:23151509};
DE Short=GRE CutC {ECO:0000303|PubMed:24854437};
GN Name=cutC {ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000303|PubMed:23151509};
GN OrderedLocusNames=Dde_3282 {ECO:0000312|EMBL:ABB40076.1};
OS Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20)
OS (Desulfovibrio alaskensis).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
OC Desulfovibrionaceae; Oleidesulfovibrio.
OX NCBI_TaxID=207559;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-1058 / DSM 17464 / G20;
RX PubMed=21685289; DOI=10.1128/jb.05400-11;
RA Hauser L.J., Land M.L., Brown S.D., Larimer F., Keller K.L.,
RA Rapp-Giles B.J., Price M.N., Lin M., Bruce D.C., Detter J.C., Tapia R.,
RA Han C.S., Goodwin L.A., Cheng J.F., Pitluck S., Copeland A., Lucas S.,
RA Nolan M., Lapidus A.L., Palumbo A.V., Wall J.D.;
RT "Complete genome sequence and updated annotation of Desulfovibrio
RT alaskensis G20.";
RL J. Bacteriol. 193:4268-4269(2011).
RN [2]
RP IDENTIFICATION, FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, GLYCYL
RP RADICAL AT GLY-821, PATHWAY, AND MUTAGENESIS OF CYS-489 AND GLY-821.
RC STRAIN=ATCC BAA-1058 / DSM 17464 / G20;
RX PubMed=23151509; DOI=10.1073/pnas.1215689109;
RA Craciun S., Balskus E.P.;
RT "Microbial conversion of choline to trimethylamine requires a glycyl
RT radical enzyme.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:21307-21312(2012).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP SPECIFICITY, SUBUNIT, MUTAGENESIS OF ASP-216; THR-334; PHE-395; CYS-489;
RP GLU-491; THR-502 AND GLY-821, REACTION MECHANISM, AND 3D-STRUCTURE
RP MODELING.
RC STRAIN=ATCC BAA-1058 / DSM 17464 / G20;
RX PubMed=24854437; DOI=10.1021/cb500113p;
RA Craciun S., Marks J.A., Balskus E.P.;
RT "Characterization of choline trimethylamine-lyase expands the chemistry of
RT glycyl radical enzymes.";
RL ACS Chem. Biol. 9:1408-1413(2014).
CC -!- FUNCTION: Glycine radical enzyme that catalyzes the cleavage of a C-N
CC bond in choline, producing trimethylamine (TMA) and acetaldehyde
CC (PubMed:23151509, PubMed:24854437). Is involved in the anaerobic
CC choline utilization pathway that allows D.alaskensis to grow on choline
CC as a source of carbon and energy (PubMed:23151509). Is strictly
CC specific for choline as substrate (PubMed:24854437).
CC {ECO:0000269|PubMed:23151509, ECO:0000269|PubMed:24854437}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=choline = acetaldehyde + trimethylamine; Xref=Rhea:RHEA:35095,
CC ChEBI:CHEBI:15343, ChEBI:CHEBI:15354, ChEBI:CHEBI:58389; EC=4.3.99.4;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02058,
CC ECO:0000269|PubMed:23151509};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=302.5 uM for choline {ECO:0000269|PubMed:24854437};
CC Vmax=22.7 umol/min/mg enzyme {ECO:0000269|PubMed:24854437};
CC Note=kcat is 747 sec(-1). Kinetic parameters measured with a CutC -52
CC AA truncated variant. {ECO:0000269|PubMed:24854437};
CC -!- PATHWAY: Amine and polyamine metabolism; choline degradation.
CC {ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000269|PubMed:23151509}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:24854437}.
CC -!- PTM: Requires the activating protein CutD to generate the key active
CC site glycyl radical on Gly-821 that is involved in catalysis.
CC {ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000269|PubMed:23151509}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene are unable to grow on
CC choline, in contrast to wild-type, and do not produce TMA.
CC {ECO:0000269|PubMed:23151509}.
CC -!- SIMILARITY: Belongs to the glycyl radical enzyme (GRE) family. CutC
CC subfamily. {ECO:0000305}.
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DR EMBL; CP000112; ABB40076.1; -; Genomic_DNA.
DR RefSeq; WP_011369019.1; NC_007519.1.
DR PDB; 5FAU; X-ray; 1.90 A; A/B/C/D=19-846.
DR PDB; 5FAV; X-ray; 1.60 A; A/B=53-846.
DR PDB; 5FAW; X-ray; 1.85 A; A/B=53-846.
DR PDB; 5FAY; X-ray; 1.90 A; A/B=53-846.
DR PDB; 5KDP; X-ray; 1.90 A; A/C=53-846.
DR PDB; 6ND3; X-ray; 2.36 A; A/B/C/D/E/F/G/H=19-846.
DR PDB; 6VUE; X-ray; 2.28 A; A/B=53-846.
DR PDBsum; 5FAU; -.
DR PDBsum; 5FAV; -.
DR PDBsum; 5FAW; -.
DR PDBsum; 5FAY; -.
DR PDBsum; 5KDP; -.
DR PDBsum; 6ND3; -.
DR PDBsum; 6VUE; -.
DR AlphaFoldDB; Q30W70; -.
DR SMR; Q30W70; -.
DR STRING; 207559.Dde_3282; -.
DR BindingDB; Q30W70; -.
DR ChEMBL; CHEMBL4739856; -.
DR PRIDE; Q30W70; -.
DR EnsemblBacteria; ABB40076; ABB40076; Dde_3282.
DR KEGG; dde:Dde_3282; -.
DR eggNOG; COG1882; Bacteria.
DR HOGENOM; CLU_009096_0_1_7; -.
DR OMA; YCCETAP; -.
DR OrthoDB; 116406at2; -.
DR BioCyc; MetaCyc:MON-17848; -.
DR BRENDA; 4.3.99.4; 1902.
DR UniPathway; UPA01069; -.
DR Proteomes; UP000002710; Chromosome.
DR GO; GO:0016840; F:carbon-nitrogen lyase activity; IDA:UniProtKB.
DR GO; GO:0033265; F:choline binding; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0042426; P:choline catabolic process; IDA:UniProtKB.
DR HAMAP; MF_02058; Choline_CutC; 1.
DR InterPro; IPR030897; Choline_CutC.
DR InterPro; IPR019777; Form_AcTrfase_GR_CS.
DR InterPro; IPR001150; Gly_radical.
DR InterPro; IPR004184; PFL_dom.
DR Pfam; PF01228; Gly_radical; 1.
DR Pfam; PF02901; PFL-like; 1.
DR TIGRFAMs; TIGR04394; choline_CutC; 1.
DR PROSITE; PS00850; GLY_RADICAL_1; 1.
DR PROSITE; PS51149; GLY_RADICAL_2; 1.
DR PROSITE; PS51554; PFL; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Organic radical; Reference proteome.
FT CHAIN 1..846
FT /note="Choline trimethylamine-lyase"
FT /id="PRO_0000435665"
FT DOMAIN 60..718
FT /note="PFL"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00887"
FT DOMAIN 725..846
FT /note="Glycine radical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00493"
FT ACT_SITE 489
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02058,
FT ECO:0000305|PubMed:23151509, ECO:0000305|PubMed:24854437"
FT ACT_SITE 491
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02058,
FT ECO:0000305|PubMed:24854437"
FT MOD_RES 821
FT /note="Glycine radical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02058,
FT ECO:0000305|PubMed:23151509, ECO:0000305|PubMed:24854437"
FT MUTAGEN 216
FT /note="D->N: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:24854437"
FT MUTAGEN 334
FT /note="T->S: About 2-fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:24854437"
FT MUTAGEN 395
FT /note="F->L: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:24854437"
FT MUTAGEN 489
FT /note="C->A: Loss of catalytic activity. Still activated by
FT CutD but the remaining alpha-proton of the glycyl radical
FT is no longer exchangeable."
FT /evidence="ECO:0000269|PubMed:23151509,
FT ECO:0000269|PubMed:24854437"
FT MUTAGEN 491
FT /note="E->Q: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:24854437"
FT MUTAGEN 502
FT /note="T->S: About 3-fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:24854437"
FT MUTAGEN 821
FT /note="G->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:23151509,
FT ECO:0000269|PubMed:24854437"
FT HELIX 60..70
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 79..90
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 96..110
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 131..133
FT /evidence="ECO:0007829|PDB:5FAV"
FT TURN 136..138
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 141..146
FT /evidence="ECO:0007829|PDB:5FAV"
FT TURN 147..152
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 154..156
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 162..170
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 172..176
FT /evidence="ECO:0007829|PDB:5FAV"
FT TURN 177..179
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 181..191
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 195..198
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 203..205
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 208..211
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 221..225
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 230..242
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 249..251
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 252..285
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 289..304
FT /evidence="ECO:0007829|PDB:5FAV"
FT TURN 305..307
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 313..330
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 341..344
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 346..355
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 356..358
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 360..375
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 383..386
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 387..389
FT /evidence="ECO:0007829|PDB:5FAV"
FT TURN 390..392
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 397..403
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 407..409
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 413..425
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 430..436
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 442..453
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 460..463
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 464..473
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 478..482
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 485..487
FT /evidence="ECO:0007829|PDB:5FAV"
FT TURN 488..490
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 491..493
FT /evidence="ECO:0007829|PDB:5FAV"
FT TURN 495..497
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 503..509
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 510..517
FT /evidence="ECO:0007829|PDB:5FAV"
FT TURN 518..520
FT /evidence="ECO:0007829|PDB:5FAV"
FT TURN 523..525
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 536..538
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 542..574
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 578..582
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 587..590
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 594..596
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 599..602
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 606..610
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 612..626
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 634..642
FT /evidence="ECO:0007829|PDB:5FAV"
FT TURN 643..647
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 649..657
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 666..683
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 689..692
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 694..697
FT /evidence="ECO:0007829|PDB:5FAV"
FT TURN 700..702
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 703..708
FT /evidence="ECO:0007829|PDB:5FAV"
FT TURN 731..733
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 738..746
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 750..752
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 760..764
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 767..769
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 771..787
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 791..797
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 799..807
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 809..811
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 816..818
FT /evidence="ECO:0007829|PDB:5FAV"
FT STRAND 820..825
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 826..828
FT /evidence="ECO:0007829|PDB:5FAV"
FT HELIX 831..839
FT /evidence="ECO:0007829|PDB:5FAV"
SQ SEQUENCE 846 AA; 94640 MW; 8CF56E2D011D7DDD CRC64;
MDLQDFSHKL AEATKNLTPA ERASLKKIFE GVSAEVFSQP APVSAVATGA ESGIPDGPTP
RHVKLKENFL KQVPSITVQR AVAITKIAKE NPGLPKPLLR AKTFRYCCET APLVIQDHEL
IVGSPNGAPR AGAFSPEVAW RWLQDELDTI GSRPQDPFYI SEEDKKVLRE EVFPFWQNKS
VDEFCEGQYR EADLWEMSGE SFVSDCSYHA VNGGGDSNPG YDVILMKKGM LDIQREAREK
LEQLDYANPE DIDKIYFYKS VIETAEGVMI YARRLSAYAA ELAARETDPR RKAELQKISE
VNARVPAHAP SNFWEAIQAV WTVESLLVVE ENQTGMSIGR VDQYMYPFYR ADIDSGRLTE
YEAFDLAGCM LVKMSEMMWI TSEGASKFFA GYQPFVNMCV GGVTREGHDA TNDLTYMLMD
AVRHVRIYQP TLATRVHNKS PQKYLKKIVD VIRSGMGFPA VHFDDAHIKM MLAKGVSIED
ARDYCLMGCV EPQKSGRLYQ WTSTGYTQWP ICIELVLNHG VPLWYGKKVT PDMGDLSQYD
TYEKFEAAVK EQIRWITKNT SVATVISQRA HRELAPKPLM SLMYEGCMES GRDVSAGGAM
YNFGPGVVWS GLATYVDSMA AIKKLVYDDR KYTLAQLNEA LKADFAGYDQ ILADCLAAPK
YGNDDDYADM IAADLVHFTE TEHRKYKTLY SVLSHGTLSI SNNTPFGQLL GASANGRRAW
MPLSDGISPT QGADYKGPTA IIKSVSKMAN DNMNIGMVHN FKLMSGLLDT PEGENGLITL
IRTACMLGNG EMQFNYLDNE LLLDAQKHPE KYRDLVVRVA GYSAFFVELC KDVQDEIISR
TMLHGF
