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Choline trimethylamine-lyase (Choline TMA-lyase) (EC 4.3.99.4) (Choline utilization protein C) (Glycyl radical enzyme CutC) (GRE CutC)

 CUTC_DESAG              Reviewed;         846 AA.
Q30W70;
16-MAR-2016, integrated into UniProtKB/Swiss-Prot.
06-DEC-2005, sequence version 1.
07-JUN-2017, entry version 74.
RecName: Full=Choline trimethylamine-lyase {ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000303|PubMed:23151509};
Short=Choline TMA-lyase {ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000303|PubMed:23151509};
EC=4.3.99.4 {ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000269|PubMed:23151509};
AltName: Full=Choline utilization protein C {ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000303|PubMed:23151509};
AltName: Full=Glycyl radical enzyme CutC {ECO:0000303|PubMed:23151509};
Short=GRE CutC {ECO:0000303|PubMed:24854437};
Name=cutC {ECO:0000255|HAMAP-Rule:MF_02058,
ECO:0000303|PubMed:23151509};
OrderedLocusNames=Dde_3282 {ECO:0000312|EMBL:ABB40076.1};
Desulfovibrio alaskensis (strain G20) (Desulfovibrio desulfuricans
(strain G20)).
Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
Desulfovibrionaceae; Desulfovibrio.
NCBI_TaxID=207559;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=G20;
PubMed=21685289; DOI=10.1128/JB.05400-11;
Hauser L.J., Land M.L., Brown S.D., Larimer F., Keller K.L.,
Rapp-Giles B.J., Price M.N., Lin M., Bruce D.C., Detter J.C.,
Tapia R., Han C.S., Goodwin L.A., Cheng J.F., Pitluck S., Copeland A.,
Lucas S., Nolan M., Lapidus A.L., Palumbo A.V., Wall J.D.;
"Complete genome sequence and updated annotation of Desulfovibrio
alaskensis G20.";
J. Bacteriol. 193:4268-4269(2011).
[2]
IDENTIFICATION, FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE,
GLYCYL RADICAL AT GLY-821, PATHWAY, AND MUTAGENESIS OF CYS-489 AND
GLY-821.
STRAIN=G20;
PubMed=23151509; DOI=10.1073/pnas.1215689109;
Craciun S., Balskus E.P.;
"Microbial conversion of choline to trimethylamine requires a glycyl
radical enzyme.";
Proc. Natl. Acad. Sci. U.S.A. 109:21307-21312(2012).
[3]
FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
SPECIFICITY, SUBUNIT, MUTAGENESIS OF ASP-216; THR-334; PHE-395;
CYS-489; GLU-491; THR-502 AND GLY-821, REACTION MECHANISM, AND
3D-STRUCTURE MODELING.
STRAIN=G20;
PubMed=24854437; DOI=10.1021/cb500113p;
Craciun S., Marks J.A., Balskus E.P.;
"Characterization of choline trimethylamine-lyase expands the
chemistry of glycyl radical enzymes.";
ACS Chem. Biol. 9:1408-1413(2014).
-!- FUNCTION: Glycine radical enzyme that catalyzes the cleavage of a
C-N bond in choline, producing trimethylamine (TMA) and
acetaldehyde (PubMed:23151509, PubMed:24854437). Is involved in
the anaerobic choline utilization pathway that allows D.alaskensis
to grow on choline as a source of carbon and energy
(PubMed:23151509). Is strictly specific for choline as substrate
(PubMed:24854437). {ECO:0000269|PubMed:23151509,
ECO:0000269|PubMed:24854437}.
-!- CATALYTIC ACTIVITY: Choline = trimethylamine + acetaldehyde.
{ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000269|PubMed:23151509}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=302.5 uM for choline {ECO:0000269|PubMed:24854437};
Vmax=22.7 umol/min/mg enzyme {ECO:0000269|PubMed:24854437};
Note=kcat is 747 sec(-1). Kinetic parameters measured with a
CutC -52 AA truncated variant. {ECO:0000269|PubMed:24854437};
-!- PATHWAY: Amine and polyamine metabolism; choline degradation.
{ECO:0000255|HAMAP-Rule:MF_02058, ECO:0000269|PubMed:23151509}.
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:24854437}.
-!- PTM: Requires the activating protein CutD to generate the key
active site glycyl radical on Gly-821 that is involved in
catalysis. {ECO:0000255|HAMAP-Rule:MF_02058,
ECO:0000269|PubMed:23151509}.
-!- DISRUPTION PHENOTYPE: Cells lacking this gene are unable to grow
on choline, in contrast to wild-type, and do not produce TMA.
{ECO:0000269|PubMed:23151509}.
-----------------------------------------------------------------------
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EMBL; CP000112; ABB40076.1; -; Genomic_DNA.
RefSeq; WP_011369019.1; NC_007519.1.
PDB; 5FAU; X-ray; 1.90 A; A/B/C/D=19-846.
PDB; 5FAV; X-ray; 1.60 A; A/B=53-846.
PDB; 5FAW; X-ray; 1.85 A; A/B=53-846.
PDB; 5FAY; X-ray; 1.90 A; A/B=53-846.
PDB; 5KDP; X-ray; 1.90 A; A/C=53-846.
PDBsum; 5FAU; -.
PDBsum; 5FAV; -.
PDBsum; 5FAW; -.
PDBsum; 5FAY; -.
PDBsum; 5KDP; -.
SMR; Q30W70; -.
STRING; 207559.Dde_3282; -.
EnsemblBacteria; ABB40076; ABB40076; Dde_3282.
KEGG; dde:Dde_3282; -.
eggNOG; ENOG4105C6N; Bacteria.
eggNOG; COG1882; LUCA.
HOGENOM; HOG000274401; -.
KO; K20038; -.
OMA; YCCETAP; -.
OrthoDB; POG091H0HBJ; -.
BioCyc; DALA207559:GH1L-2916-MONOMER; -.
BioCyc; MetaCyc:MONOMER-17848; -.
BRENDA; 4.3.99.4; 1902.
UniPathway; UPA01069; -.
Proteomes; UP000002710; Chromosome.
GO; GO:0016840; F:carbon-nitrogen lyase activity; IDA:UniProtKB.
GO; GO:0033265; F:choline binding; IDA:UniProtKB.
GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
GO; GO:0042426; P:choline catabolic process; IDA:UniProtKB.
HAMAP; MF_02058; Choline_CutC; 1.
InterPro; IPR030897; Choline_CutC.
InterPro; IPR019777; Form_AcTrfase_GR_CS.
InterPro; IPR001150; Gly_radical.
InterPro; IPR004184; PFL_dom.
Pfam; PF01228; Gly_radical; 1.
Pfam; PF02901; PFL-like; 1.
TIGRFAMs; TIGR04394; choline_CutC; 1.
PROSITE; PS00850; GLY_RADICAL_1; 1.
PROSITE; PS51149; GLY_RADICAL_2; 1.
PROSITE; PS51554; PFL; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Lyase; Organic radical;
Reference proteome.
CHAIN 1 846 Choline trimethylamine-lyase.
/FTId=PRO_0000435665.
DOMAIN 60 718 PFL. {ECO:0000255|PROSITE-
ProRule:PRU00887}.
DOMAIN 725 846 Glycine radical. {ECO:0000255|PROSITE-
ProRule:PRU00493}.
ACT_SITE 489 489 Cysteine radical intermediate.
{ECO:0000255|HAMAP-Rule:MF_02058,
ECO:0000305|PubMed:23151509,
ECO:0000305|PubMed:24854437}.
ACT_SITE 491 491 Proton acceptor. {ECO:0000255|HAMAP-
Rule:MF_02058,
ECO:0000305|PubMed:24854437}.
MOD_RES 821 821 Glycine radical. {ECO:0000255|HAMAP-
Rule:MF_02058,
ECO:0000305|PubMed:23151509,
ECO:0000305|PubMed:24854437}.
MUTAGEN 216 216 D->N: Loss of catalytic activity.
{ECO:0000269|PubMed:24854437}.
MUTAGEN 334 334 T->S: About 2-fold decrease in catalytic
activity. {ECO:0000269|PubMed:24854437}.
MUTAGEN 395 395 F->L: Loss of catalytic activity.
{ECO:0000269|PubMed:24854437}.
MUTAGEN 489 489 C->A: Loss of catalytic activity. Still
activated by CutD but the remaining
alpha-proton of the glycyl radical is no
longer exchangeable.
{ECO:0000269|PubMed:23151509,
ECO:0000269|PubMed:24854437}.
MUTAGEN 491 491 E->Q: Loss of catalytic activity.
{ECO:0000269|PubMed:24854437}.
MUTAGEN 502 502 T->S: About 3-fold decrease in catalytic
activity. {ECO:0000269|PubMed:24854437}.
MUTAGEN 821 821 G->A: Loss of catalytic activity.
{ECO:0000269|PubMed:23151509,
ECO:0000269|PubMed:24854437}.
HELIX 60 70 {ECO:0000244|PDB:5FAV}.
STRAND 75 77 {ECO:0000244|PDB:5FAV}.
HELIX 79 90 {ECO:0000244|PDB:5FAV}.
HELIX 96 110 {ECO:0000244|PDB:5FAV}.
STRAND 131 133 {ECO:0000244|PDB:5FAV}.
TURN 136 138 {ECO:0000244|PDB:5FAV}.
HELIX 141 146 {ECO:0000244|PDB:5FAV}.
TURN 147 152 {ECO:0000244|PDB:5FAV}.
STRAND 154 156 {ECO:0000244|PDB:5FAV}.
HELIX 162 170 {ECO:0000244|PDB:5FAV}.
HELIX 172 176 {ECO:0000244|PDB:5FAV}.
TURN 177 179 {ECO:0000244|PDB:5FAV}.
HELIX 181 191 {ECO:0000244|PDB:5FAV}.
HELIX 195 198 {ECO:0000244|PDB:5FAV}.
STRAND 203 205 {ECO:0000244|PDB:5FAV}.
HELIX 208 211 {ECO:0000244|PDB:5FAV}.
HELIX 221 225 {ECO:0000244|PDB:5FAV}.
HELIX 230 242 {ECO:0000244|PDB:5FAV}.
HELIX 249 251 {ECO:0000244|PDB:5FAV}.
HELIX 252 285 {ECO:0000244|PDB:5FAV}.
HELIX 289 304 {ECO:0000244|PDB:5FAV}.
TURN 305 307 {ECO:0000244|PDB:5FAV}.
HELIX 313 330 {ECO:0000244|PDB:5FAV}.
HELIX 341 344 {ECO:0000244|PDB:5FAV}.
HELIX 346 355 {ECO:0000244|PDB:5FAV}.
STRAND 356 358 {ECO:0000244|PDB:5FAV}.
HELIX 360 375 {ECO:0000244|PDB:5FAV}.
HELIX 383 386 {ECO:0000244|PDB:5FAV}.
HELIX 387 389 {ECO:0000244|PDB:5FAV}.
TURN 390 392 {ECO:0000244|PDB:5FAV}.
STRAND 397 403 {ECO:0000244|PDB:5FAV}.
STRAND 407 409 {ECO:0000244|PDB:5FAV}.
HELIX 413 425 {ECO:0000244|PDB:5FAV}.
STRAND 430 436 {ECO:0000244|PDB:5FAV}.
HELIX 442 453 {ECO:0000244|PDB:5FAV}.
STRAND 460 463 {ECO:0000244|PDB:5FAV}.
HELIX 464 473 {ECO:0000244|PDB:5FAV}.
HELIX 478 482 {ECO:0000244|PDB:5FAV}.
STRAND 485 487 {ECO:0000244|PDB:5FAV}.
TURN 488 490 {ECO:0000244|PDB:5FAV}.
STRAND 491 493 {ECO:0000244|PDB:5FAV}.
TURN 495 497 {ECO:0000244|PDB:5FAV}.
STRAND 503 509 {ECO:0000244|PDB:5FAV}.
HELIX 510 517 {ECO:0000244|PDB:5FAV}.
TURN 518 520 {ECO:0000244|PDB:5FAV}.
TURN 523 525 {ECO:0000244|PDB:5FAV}.
HELIX 536 538 {ECO:0000244|PDB:5FAV}.
HELIX 542 574 {ECO:0000244|PDB:5FAV}.
HELIX 578 582 {ECO:0000244|PDB:5FAV}.
HELIX 587 590 {ECO:0000244|PDB:5FAV}.
HELIX 594 596 {ECO:0000244|PDB:5FAV}.
STRAND 599 602 {ECO:0000244|PDB:5FAV}.
STRAND 606 610 {ECO:0000244|PDB:5FAV}.
HELIX 612 626 {ECO:0000244|PDB:5FAV}.
HELIX 634 642 {ECO:0000244|PDB:5FAV}.
TURN 643 647 {ECO:0000244|PDB:5FAV}.
HELIX 649 657 {ECO:0000244|PDB:5FAV}.
HELIX 666 683 {ECO:0000244|PDB:5FAV}.
STRAND 689 692 {ECO:0000244|PDB:5FAV}.
STRAND 694 697 {ECO:0000244|PDB:5FAV}.
TURN 700 702 {ECO:0000244|PDB:5FAV}.
HELIX 703 708 {ECO:0000244|PDB:5FAV}.
TURN 731 733 {ECO:0000244|PDB:5FAV}.
HELIX 738 746 {ECO:0000244|PDB:5FAV}.
HELIX 750 752 {ECO:0000244|PDB:5FAV}.
STRAND 760 764 {ECO:0000244|PDB:5FAV}.
HELIX 767 769 {ECO:0000244|PDB:5FAV}.
HELIX 771 787 {ECO:0000244|PDB:5FAV}.
STRAND 791 797 {ECO:0000244|PDB:5FAV}.
HELIX 799 807 {ECO:0000244|PDB:5FAV}.
HELIX 809 811 {ECO:0000244|PDB:5FAV}.
STRAND 816 818 {ECO:0000244|PDB:5FAV}.
STRAND 820 825 {ECO:0000244|PDB:5FAV}.
HELIX 826 828 {ECO:0000244|PDB:5FAV}.
HELIX 831 839 {ECO:0000244|PDB:5FAV}.
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


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