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UniProtKB - Q4FP21 (DMDA_PELUB)

Entry version 108 (23 Feb 2022)
Sequence version 1 (30 Aug 2005)
Previous versions | rss
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Protein

Dimethylsulfonioproprionate demethylase DmdA

Gene

dmdA

Organism
Pelagibacter ubique (strain HTCC1062)
Status
Reviewed-Annotation score:

Annotation score:4 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

Major contributor to the demethylation of dimethylsulfonioproprionate (DMSP). Demethylates DMSP to methyl-mercaptopropionate (MMPA).

1 Publication

Miscellaneous

DMSP is used as an intracellular osmolyte, predator deterrent and antioxidant.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Non-competitively inhibited by MMPA, weakly inhibited by substrate analogs dimethylsulfoniobutanoate and dimethylsulfoniopentanoate. It is used as an intracellular osmolyte.1 Publication

<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

Upon expression and purification from E.coli.
  1. KM=0.29 mM for tetrahydrafolate1 Publication
  2. KM=13.2 mM for dimethylsulfonioproprionate1 Publication
  1. Vmax=11.7 µmol/min/mg enzyme1 Publication

pH dependencei

Optimum pH is 7.0-8.0.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei122Tetrahydrofolate1 Publication1
Binding sitei204Tetrahydrofolate1 Publication1
Binding sitei206Tetrahydrofolate1 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

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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 functionMethyltransferase, Transferase

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		CPEL335992:G1G4O-248-MONOMER

BRENDA Comprehensive Enzyme Information System

More...BRENDAi		2.1.1.269, 10071

<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%5Fand%5Ftaxonomy%5Fsection">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:
Dimethylsulfonioproprionate demethylase DmdA (EC:2.1.1.269)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:dmdA
Ordered Locus Names:SAR11_0246
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiPelagibacter ubique (strain HTCC1062)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri335992 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiBacteria › Proteobacteria › Alphaproteobacteria › Pelagibacterales › Pelagibacteraceae › Candidatus Pelagibacter ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000002528 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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 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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004206161 – 369Dimethylsulfonioproprionate demethylase DmdAAdd BLAST369

<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%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

2 Publications

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		335992.SAR11_0246

<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

1369
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

More...SMRi		Q4FP21

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		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

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the GcvT family. DmdA subfamily.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG0404, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_007884_10_2_5

Identification of Orthologs from Complete Genome Data

More...OMAi		MLNDPVA

Database of Orthologous Groups

More...OrthoDBi		282830at2

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.30.1360.120, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR028896, GCST/YgfZ/DmdA
IPR013977, GCV_T_C
IPR006222, GCV_T_N
IPR029043, GcvT/YgfZ_C
IPR027266, TrmE/GcvT_dom1

The PANTHER Classification System

More...PANTHERi		PTHR43757, PTHR43757, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01571, GCV_T, 1 hit
PF08669, GCV_T_C, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF101790, SSF101790, 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%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

Q4FP21-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKNFSIAKSR RLRSTPYTSR IEKQGVTAYT IYNHMLLPAA FGSIEDSYKH 
        60         70         80         90        100
LKEHVQIWDV AAERQVEISG KDSAELVQLM TCRDLSKSKI GRCYYCPIID 
       110        120        130        140        150
ENGNLVNDPV VLKLDENKWW ISIADSDVIF FAKGLASGHK FDVKIVEPVV 
       160        170        180        190        200
DIMAIQGPKS FALMEKVFGK KITELKFFGF DYFDFEGTKH LIARSGWSKQ 
       210        220        230        240        250
GGYEVYVENT QSGQKLYDHL FEVGKEFNVG PGCPNLIERI ESALLSYGND 
       260        270        280        290        300
FDNNDNPFEC GFDQYVSLDS DINFLGKEKL KEIKLKGPQK KLRGVKIDIK 
       310        320        330        340        350
EISLTGSKNI YDENNNVIGE LRSACYSPHF QKVIGIAMIK KSHWEASQGF 
       360 
KIQINDNTIN GNVCDLPFI
Length:369
Mass (Da):41,832
Last modified:August 30, 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:iDF1612F05044393B
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
CP000084 Genomic DNA Translation: AAZ21068.1

NCBI Reference Sequences

More...RefSeqi		WP_011281570.1, NC_007205.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAZ21068; AAZ21068; SAR11_0246

Database of genes from NCBI RefSeq genomes

More...GeneIDi		66294744

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		pub:SAR11_0246

<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
CP000084 Genomic DNA Translation: AAZ21068.1
RefSeqiWP_011281570.1, NC_007205.1

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
3TFHX-ray2.10A/B1-369[»]
3TFIX-ray1.60A/B1-369[»]
3TFJX-ray1.60A/B1-369[»]
SMRiQ4FP21
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi335992.SAR11_0246

Genome annotation databases

EnsemblBacteriaiAAZ21068; AAZ21068; SAR11_0246
GeneIDi66294744
KEGGipub:SAR11_0246

Phylogenomic databases

eggNOGiCOG0404, Bacteria
HOGENOMiCLU_007884_10_2_5
OMAiMLNDPVA
OrthoDBi282830at2

Enzyme and pathway databases

BioCyciCPEL335992:G1G4O-248-MONOMER
BRENDAi2.1.1.269, 10071

Family and domain databases

Gene3Di3.30.1360.120, 1 hit
InterProiView protein in InterPro
IPR028896, GCST/YgfZ/DmdA
IPR013977, GCV_T_C
IPR006222, GCV_T_N
IPR029043, GcvT/YgfZ_C
IPR027266, TrmE/GcvT_dom1
PANTHERiPTHR43757, PTHR43757, 1 hit
PfamiView protein in Pfam
PF01571, GCV_T, 1 hit
PF08669, GCV_T_C, 1 hit
SUPFAMiSSF101790, SSF101790, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		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 nameiDMDA_PELUB
<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: Q4FP21
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 9, 2013
Last sequence update: August 30, 2005
Last modified: February 23, 2022
This is version 108 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, Reference proteome

Documents

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