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Protein

Methylthioacryloyl-CoA hydratase

Gene

dmdD

Organism
Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (Silicibacter pomeroyi)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the assimilation of dimethylsulphoniopropionate (DMSP), an important compound in the fixation of carbon in marine phytoplankton, by catalyzing both the hydration and the hydrolysis of 3-(methylthio)acryloyl-CoA (MTA-CoA) to acetaldehyde, CO2, MeSH, and CoA (PubMed:21562561, PubMed:23704947).2 Publications

Catalytic activityi

3-(methylthio)acryloyl-CoA + 2 H2O = acetaldehyde + methanethiol + CoA + CO2.2 Publications

Kineticsi

Kcat is 44 sec(-1) for 3-(methylthio)acryloyl-CoA (for CoA ester hydrolysis). Kcat is 0.9 sec(-1) for 3-(methylthio)propanoyl-CoA (for CoA ester hydrolysis). Kcat is 13.2 sec(-1) for 3-hydroxybutyryl-CoA (for CoA ester hydrolysis). Kcat is 47 sec(-1) for 3-(methylthio)acryloyl-CoA (for MeSH release). Kcat is 42 sec(-1) for crotonyl-CoA (for hydration).1 Publication

  1. KM=8.2 µM for 3-(methylthio)acryloyl-CoA (for CoA ester hydrolysis)1 Publication
  2. KM=69 µM for 3-(methylthio)propanoyl-CoA (for CoA ester hydrolysis)1 Publication
  3. KM=119 µM for 3-hydroxybutyryl-CoA (for CoA ester hydrolysis)1 Publication
  4. KM=9.4 µM for 3-(methylthio)acryloyl-CoA (for MeSH release)1 Publication
  5. KM=19 µM for crotonyl-CoA (for hydration)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei118 – 1181Substrate; via amide nitrogenCombined sources1 Publication
    Active sitei121 – 1211Nucleophile1 Publication
    Active sitei141 – 1411Proton acceptor1 Publication
    Binding sitei144 – 1441SubstrateCombined sources1 Publication
    Binding sitei149 – 1491Substrate; via amide nitrogenCombined sources1 Publication

    GO - Molecular functioni

    • hydro-lyase activity Source: UniProtKB

    GO - Biological processi

    • protein hexamerization Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16785.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Methylthioacryloyl-CoA hydratase1 Publication (EC:4.2.1.1552 Publications)
    Gene namesi
    Name:dmdD1 Publication
    Ordered Locus Names:SPO3805Imported
    OrganismiRuegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (Silicibacter pomeroyi)
    Taxonomic identifieri246200 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRuegeria
    Proteomesi
    • UP000001023 Componenti: Chromosome

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene do not grow on methylmercaptopropionate (MMPA) as the sole source of carbon. Growth is severely inhibited on dimethylsulphoniopropionate (DMSP).1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi121 – 1211E → A: Abolishes catalytic activity. 1 Publication
    Mutagenesisi141 – 1411E → A: Abolishes catalytic activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 267267Methylthioacryloyl-CoA hydratasePRO_0000433903Add
    BLAST

    Interactioni

    Subunit structurei

    Homohexamer; dimer of trimers.1 Publication

    Protein-protein interaction databases

    STRINGi246200.SPO3805.

    Structurei

    Secondary structure

    1
    267
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni4 – 63Combined sources
    Beta strandi10 – 167Combined sources
    Beta strandi20 – 267Combined sources
    Helixi29 – 313Combined sources
    Helixi37 – 4913Combined sources
    Turni50 – 545Combined sources
    Beta strandi57 – 659Combined sources
    Helixi73 – 797Combined sources
    Helixi83 – 10220Combined sources
    Beta strandi103 – 1053Combined sources
    Beta strandi107 – 1104Combined sources
    Beta strandi113 – 1164Combined sources
    Helixi118 – 1247Combined sources
    Beta strandi126 – 1316Combined sources
    Beta strandi136 – 1383Combined sources
    Helixi140 – 1445Combined sources
    Helixi152 – 1609Combined sources
    Helixi162 – 17110Combined sources
    Helixi177 – 1837Combined sources
    Beta strandi187 – 1893Combined sources
    Helixi194 – 20613Combined sources
    Helixi210 – 2167Combined sources
    Helixi219 – 2235Combined sources
    Helixi228 – 24316Combined sources
    Helixi246 – 2527Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IZBX-ray1.50A/B1-267[»]
    4IZCX-ray1.80A/B1-267[»]
    4IZDX-ray1.80A/B1-267[»]
    ProteinModelPortaliQ5LLW6.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni31 – 322Substrate bindingCombined sources1 Publication
    Regioni69 – 735Substrate bindingCombined sources1 Publication
    Regioni255 – 2584Substrate bindingCombined sources1 Publication
    Regioni262 – 2643Substrate bindingCombined sources1 Publication

    Sequence similaritiesi

    Belongs to the enoyl-CoA hydratase/isomerase family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105E9F. Bacteria.
    COG1024. LUCA.
    HOGENOMiHOG000027939.
    KOiK20036.
    OMAiWHRAFDK.
    OrthoDBiEOG6M9F0M.

    Family and domain databases

    Gene3Di3.90.226.10. 1 hit.
    InterProiIPR029045. ClpP/crotonase-like_dom.
    IPR001753. Crotonase_core_superfam.
    IPR018376. Enoyl-CoA_hyd/isom_CS.
    [Graphical view]
    PfamiPF00378. ECH_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF52096. SSF52096. 1 hit.
    PROSITEiPS00166. ENOYL_COA_HYDRATASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q5LLW6-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTQDVTSGYS NLDLDLRDNG VCVVTLNRPD KRNALDVATI EELVTFFSTA
    60 70 80 90 100
    HRKGVRAVVL TGAGDHFCAG LDLVEHWKAD RSADDFMHVC LRWHEAFNKM
    110 120 130 140 150
    EYGGVPIIAA LRGAVVGGGL ELASAAHLRV MDQSTYFALP EGQRGIFTGG
    160 170 180 190 200
    GATIRVSDMI GKYRMIDMIL TGRVYQGQEA ADLGLAQYIT EGSSFDKAME
    210 220 230 240 250
    LADKIASNLP LTNFAICSAI SHMQNMSGLD AAYAEAFVGG IVNTQPAARE
    260
    RLEAFANKTA ARVRPNS
    Length:267
    Mass (Da):28,836
    Last modified:February 1, 2005 - v1
    Checksum:iA6941E7AEB292F19
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP000031 Genomic DNA. Translation: AAV97019.1.
    RefSeqiWP_011049477.1. NC_003911.12.

    Genome annotation databases

    EnsemblBacteriaiAAV97019; AAV97019; SPO3805.
    KEGGisil:SPO3805.
    PATRICi23381109. VBIRuePom114501_3880.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP000031 Genomic DNA. Translation: AAV97019.1.
    RefSeqiWP_011049477.1. NC_003911.12.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IZBX-ray1.50A/B1-267[»]
    4IZCX-ray1.80A/B1-267[»]
    4IZDX-ray1.80A/B1-267[»]
    ProteinModelPortaliQ5LLW6.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi246200.SPO3805.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAV97019; AAV97019; SPO3805.
    KEGGisil:SPO3805.
    PATRICi23381109. VBIRuePom114501_3880.

    Phylogenomic databases

    eggNOGiENOG4105E9F. Bacteria.
    COG1024. LUCA.
    HOGENOMiHOG000027939.
    KOiK20036.
    OMAiWHRAFDK.
    OrthoDBiEOG6M9F0M.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16785.

    Family and domain databases

    Gene3Di3.90.226.10. 1 hit.
    InterProiIPR029045. ClpP/crotonase-like_dom.
    IPR001753. Crotonase_core_superfam.
    IPR018376. Enoyl-CoA_hyd/isom_CS.
    [Graphical view]
    PfamiPF00378. ECH_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF52096. SSF52096. 1 hit.
    PROSITEiPS00166. ENOYL_COA_HYDRATASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700808 / DSM 15171 / DSS-3.
    2. "An updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3."
      Rivers A.R., Smith C.B., Moran M.A.
      Stand. Genomic Sci. 9:11-11(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENOME REANNOTATION.
      Strain: ATCC 700808 / DSM 15171 / DSS-3.
    3. "Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria."
      Reisch C.R., Stoudemayer M.J., Varaljay V.A., Amster I.J., Moran M.A., Whitman W.B.
      Nature 473:208-211(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, PATHWAY, DISRUPTION PHENOTYPE.
      Strain: ATCC 700808 / DSM 15171 / DSS-3.
    4. "Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoA."
      Tan D., Crabb W.M., Whitman W.B., Tong L.
      PLoS ONE 8:E63870-E63870(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH 3-(METHYLTHIO)ACRYLOYL-COA OF MUTANT ALA-121, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE, SUBUNIT, MUTAGENESIS OF GLU-121 AND GLU-141.

    Entry informationi

    Entry nameiDMDD_RUEPO
    AccessioniPrimary (citable) accession number: Q5LLW6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 16, 2015
    Last sequence update: February 1, 2005
    Last modified: June 8, 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. 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.