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Entry version 78 (10 Apr 2019)
Sequence version 1 (06 Dec 2005)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

kcat is 747 sec(-1). Kinetic parameters measured with a CutC -52 AA truncated variant.1 Publication
  1. KM=302.5 µM for choline1 Publication
  1. Vmax=22.7 µmol/min/mg enzyme1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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
<p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei489Cysteine radical intermediateUniRule annotation2 Publications1
Active sitei491Proton acceptorUniRule annotation1 Publication1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionLyase

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
DALA207559:G1G52-3076-MONOMER
MetaCyc:MONOMER-17848

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
4.3.99.4 1902

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA01069

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:cutC1 PublicationUniRule annotation
Ordered Locus Names:Dde_3282Imported
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiDesulfovibrio alaskensis (strain G20) (Desulfovibrio desulfuricans (strain G20))
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri207559 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002710 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>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

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004356651 – 846Choline trimethylamine-lyaseAdd BLAST846

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei821Glycine radicalUniRule annotation2 Publications1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>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

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.1 Publication

GO - Molecular functioni

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
207559.Dde_3282

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1846
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
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[»]
6ND3X-ray2.36A/B/C/D/E/F/G/H19-846[»]

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
Q30W70

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini60 – 718PFLPROSITE-ProRule annotationAdd BLAST659
Domaini725 – 846Glycine radicalPROSITE-ProRule annotationAdd BLAST122

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105C6N Bacteria
COG1882 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000274401

KEGG Orthology (KO)

More...
KOi
K20038

Identification of Orthologs from Complete Genome Data

More...
OMAi
YCCETAP

Database of Orthologous Groups

More...
OrthoDBi
116406at2

Family and domain databases

HAMAP database of protein families

More...
HAMAPi
MF_02058 Choline_CutC, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR030897 Choline_CutC
IPR019777 Form_AcTrfase_GR_CS
IPR001150 Gly_radical
IPR004184 PFL_dom

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01228 Gly_radical, 1 hit
PF02901 PFL-like, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR04394 choline_CutC, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00850 GLY_RADICAL_1, 1 hit
PS51149 GLY_RADICAL_2, 1 hit
PS51554 PFL, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i8CF56E2D011D7DDD
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
CP000112 Genomic DNA Translation: ABB40076.1

NCBI Reference Sequences

More...
RefSeqi
WP_011369019.1, NC_007519.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ABB40076; ABB40076; Dde_3282

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
dde:Dde_3282

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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[»]
6ND3X-ray2.36A/B/C/D/E/F/G/H19-846[»]
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

Phylogenomic databases

eggNOGiENOG4105C6N Bacteria
COG1882 LUCA
HOGENOMiHOG000274401
KOiK20038
OMAiYCCETAP
OrthoDBi116406at2

Enzyme and pathway databases

UniPathwayi
UPA01069

BioCyciDALA207559:G1G52-3076-MONOMER
MetaCyc:MONOMER-17848
BRENDAi4.3.99.4 1902

Family and domain databases

HAMAPiMF_02058 Choline_CutC, 1 hit
InterProiView protein in InterPro
IPR030897 Choline_CutC
IPR019777 Form_AcTrfase_GR_CS
IPR001150 Gly_radical
IPR004184 PFL_dom
PfamiView protein in Pfam
PF01228 Gly_radical, 1 hit
PF02901 PFL-like, 1 hit
TIGRFAMsiTIGR04394 choline_CutC, 1 hit
PROSITEiView protein in PROSITE
PS00850 GLY_RADICAL_1, 1 hit
PS51149 GLY_RADICAL_2, 1 hit
PS51554 PFL, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiCUTC_DESAG
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q30W70
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 16, 2016
Last sequence update: December 6, 2005
Last modified: April 10, 2019
This is version 78 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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