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Protein

Choline trimethylamine-lyase

Gene

cutC

Organism
Desulfovibrio alaskensis (strain G20) (Desulfovibrio desulfuricans (strain G20))
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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).2 Publications

Catalytic activityi

Choline = trimethylamine + acetaldehyde.UniRule annotation1 Publication

Kineticsi

kcat is 747 sec(-1). Kinetic parameters measured with a CutC -52 AA truncated variant.1 Publication

Manual assertion based on experiment ini

  1. KM=302.5 µM for choline1 Publication
  1. Vmax=22.7 µmol/min/mg enzyme1 Publication

Pathwayi: choline degradation

This protein is involved in the pathway choline degradation, which is part of Amine and polyamine metabolism.UniRule annotation1 Publication
View all proteins of this organism that are known to be involved in the pathway choline degradation and in Amine and polyamine metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei489Cysteine radical intermediateUniRule annotation2 Publications1
Active sitei491Proton acceptorUniRule annotation1 Publication1

GO - Molecular functioni

  • carbon-nitrogen lyase activity Source: UniProtKB
  • choline binding Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB

GO - Biological processi

  • choline catabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Enzyme and pathway databases

BioCyciDALA207559:GH1L-2916-MONOMER.
MetaCyc:MONOMER-17848.
BRENDAi4.3.99.4. 1902.
UniPathwayiUPA01069.

Names & Taxonomyi

Protein namesi
Recommended name:
Choline trimethylamine-lyase1 PublicationUniRule annotation (EC:4.3.99.4UniRule annotation1 Publication)
Short name:
Choline TMA-lyase1 PublicationUniRule annotation
Alternative name(s):
Choline utilization protein C1 PublicationUniRule annotation
Glycyl radical enzyme CutC1 Publication
Short name:
GRE CutC1 Publication
Gene namesi
Name:cutC1 PublicationUniRule annotation
Ordered Locus Names:Dde_3282Imported
OrganismiDesulfovibrio alaskensis (strain G20) (Desulfovibrio desulfuricans (strain G20))
Taxonomic identifieri207559 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
Proteomesi
  • UP000002710 Componenti: Chromosome

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene are unable to grow on choline, in contrast to wild-type, and do not produce TMA.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi216D → N: Loss of catalytic activity. 1 Publication1
Mutagenesisi334T → S: About 2-fold decrease in catalytic activity. 1 Publication1
Mutagenesisi395F → L: Loss of catalytic activity. 1 Publication1
Mutagenesisi489C → A: Loss of catalytic activity. Still activated by CutD but the remaining alpha-proton of the glycyl radical is no longer exchangeable. 2 Publications1
Mutagenesisi491E → Q: Loss of catalytic activity. 1 Publication1
Mutagenesisi502T → S: About 3-fold decrease in catalytic activity. 1 Publication1
Mutagenesisi821G → A: Loss of catalytic activity. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004356651 – 846Choline trimethylamine-lyaseAdd BLAST846

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei821Glycine radicalUniRule annotation2 Publications1

Post-translational modificationi

Requires the activating protein CutD to generate the key active site glycyl radical on Gly-821 that is involved in catalysis.UniRule annotation1 Publication

Keywords - PTMi

Organic radical

Interactioni

Subunit structurei

Homodimer.1 Publication

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

STRINGi207559.Dde_3282.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5FAUX-ray1.90A/B/C/D19-846[»]
5FAVX-ray1.60A/B53-846[»]
5FAWX-ray1.85A/B53-846[»]
5FAYX-ray1.90A/B53-846[»]
5KDPX-ray1.90A/C53-846[»]
SMRiQ30W70.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini60 – 718PFLPROSITE-ProRule annotationAdd BLAST659
Domaini725 – 846Glycine radicalPROSITE-ProRule annotationAdd BLAST122

Sequence similaritiesi

Contains 1 glycine radical domain.PROSITE-ProRule annotation
Contains 1 PFL domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105C6N. Bacteria.
COG1882. LUCA.
HOGENOMiHOG000274401.
KOiK20038.
OMAiMQFNYLD.
OrthoDBiPOG091H0HBJ.

Family and domain databases

HAMAPiMF_02058. Choline_CutC. 1 hit.
InterProiIPR030897. Choline_CutC.
IPR019777. Form_AcTrfase_GR_CS.
IPR001150. Gly_radical.
IPR004184. PFL_dom.
[Graphical view]
PfamiPF01228. Gly_radical. 1 hit.
PF02901. PFL-like. 1 hit.
[Graphical view]
TIGRFAMsiTIGR04394. choline_CutC. 1 hit.
PROSITEiPS00850. GLY_RADICAL_1. 1 hit.
PS51149. GLY_RADICAL_2. 1 hit.
PS51554. PFL. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q30W70-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDLQDFSHKL AEATKNLTPA ERASLKKIFE GVSAEVFSQP APVSAVATGA
60 70 80 90 100
ESGIPDGPTP RHVKLKENFL KQVPSITVQR AVAITKIAKE NPGLPKPLLR
110 120 130 140 150
AKTFRYCCET APLVIQDHEL IVGSPNGAPR AGAFSPEVAW RWLQDELDTI
160 170 180 190 200
GSRPQDPFYI SEEDKKVLRE EVFPFWQNKS VDEFCEGQYR EADLWEMSGE
210 220 230 240 250
SFVSDCSYHA VNGGGDSNPG YDVILMKKGM LDIQREAREK LEQLDYANPE
260 270 280 290 300
DIDKIYFYKS VIETAEGVMI YARRLSAYAA ELAARETDPR RKAELQKISE
310 320 330 340 350
VNARVPAHAP SNFWEAIQAV WTVESLLVVE ENQTGMSIGR VDQYMYPFYR
360 370 380 390 400
ADIDSGRLTE YEAFDLAGCM LVKMSEMMWI TSEGASKFFA GYQPFVNMCV
410 420 430 440 450
GGVTREGHDA TNDLTYMLMD AVRHVRIYQP TLATRVHNKS PQKYLKKIVD
460 470 480 490 500
VIRSGMGFPA VHFDDAHIKM MLAKGVSIED ARDYCLMGCV EPQKSGRLYQ
510 520 530 540 550
WTSTGYTQWP ICIELVLNHG VPLWYGKKVT PDMGDLSQYD TYEKFEAAVK
560 570 580 590 600
EQIRWITKNT SVATVISQRA HRELAPKPLM SLMYEGCMES GRDVSAGGAM
610 620 630 640 650
YNFGPGVVWS GLATYVDSMA AIKKLVYDDR KYTLAQLNEA LKADFAGYDQ
660 670 680 690 700
ILADCLAAPK YGNDDDYADM IAADLVHFTE TEHRKYKTLY SVLSHGTLSI
710 720 730 740 750
SNNTPFGQLL GASANGRRAW MPLSDGISPT QGADYKGPTA IIKSVSKMAN
760 770 780 790 800
DNMNIGMVHN FKLMSGLLDT PEGENGLITL IRTACMLGNG EMQFNYLDNE
810 820 830 840
LLLDAQKHPE KYRDLVVRVA GYSAFFVELC KDVQDEIISR TMLHGF
Length:846
Mass (Da):94,640
Last modified:December 6, 2005 - v1
Checksum:i8CF56E2D011D7DDD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000112 Genomic DNA. Translation: ABB40076.1.
RefSeqiWP_011369019.1. NC_007519.1.

Genome annotation databases

EnsemblBacteriaiABB40076; ABB40076; Dde_3282.
KEGGidde:Dde_3282.
PATRICi21745457. VBIDesDes50040_3211.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000112 Genomic DNA. Translation: ABB40076.1.
RefSeqiWP_011369019.1. NC_007519.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5FAUX-ray1.90A/B/C/D19-846[»]
5FAVX-ray1.60A/B53-846[»]
5FAWX-ray1.85A/B53-846[»]
5FAYX-ray1.90A/B53-846[»]
5KDPX-ray1.90A/C53-846[»]
SMRiQ30W70.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi207559.Dde_3282.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABB40076; ABB40076; Dde_3282.
KEGGidde:Dde_3282.
PATRICi21745457. VBIDesDes50040_3211.

Phylogenomic databases

eggNOGiENOG4105C6N. Bacteria.
COG1882. LUCA.
HOGENOMiHOG000274401.
KOiK20038.
OMAiMQFNYLD.
OrthoDBiPOG091H0HBJ.

Enzyme and pathway databases

UniPathwayiUPA01069.
BioCyciDALA207559:GH1L-2916-MONOMER.
MetaCyc:MONOMER-17848.
BRENDAi4.3.99.4. 1902.

Family and domain databases

HAMAPiMF_02058. Choline_CutC. 1 hit.
InterProiIPR030897. Choline_CutC.
IPR019777. Form_AcTrfase_GR_CS.
IPR001150. Gly_radical.
IPR004184. PFL_dom.
[Graphical view]
PfamiPF01228. Gly_radical. 1 hit.
PF02901. PFL-like. 1 hit.
[Graphical view]
TIGRFAMsiTIGR04394. choline_CutC. 1 hit.
PROSITEiPS00850. GLY_RADICAL_1. 1 hit.
PS51149. GLY_RADICAL_2. 1 hit.
PS51554. PFL. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCUTC_DESAG
AccessioniPrimary (citable) accession number: Q30W70
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 16, 2016
Last sequence update: December 6, 2005
Last modified: November 30, 2016
This is version 70 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.