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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

Manual assertion based on experiment ini

  • Ref.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.

  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)DescriptionActionsGraphical viewLength
    Binding sitei118Substrate; via amide nitrogenCombined sources1 Publication1
    Active sitei121Nucleophile1 Publication1
    Active sitei141Proton acceptor1 Publication1
    Binding sitei144SubstrateCombined sources1 Publication1
    Binding sitei149Substrate; via amide nitrogenCombined sources1 Publication1

    GO - Molecular functioni

    • hydro-lyase activity Source: UniProtKB

    GO - Biological processi

    • metabolic process Source: InterPro
    • 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)DescriptionActionsGraphical viewLength
    Mutagenesisi121E → A: Abolishes catalytic activity. 1 Publication1
    Mutagenesisi141E → A: Abolishes catalytic activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004339031 – 267Methylthioacryloyl-CoA hydrataseAdd BLAST267

    Interactioni

    Subunit structurei

    Homohexamer; dimer of trimers.1 Publication

    Protein-protein interaction databases

    STRINGi246200.SPO3805.

    Structurei

    Secondary structure

    1267
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Turni4 – 6Combined sources3
    Beta strandi10 – 16Combined sources7
    Beta strandi20 – 26Combined sources7
    Helixi29 – 31Combined sources3
    Helixi37 – 49Combined sources13
    Turni50 – 54Combined sources5
    Beta strandi57 – 65Combined sources9
    Helixi73 – 79Combined sources7
    Helixi83 – 102Combined sources20
    Beta strandi103 – 105Combined sources3
    Beta strandi107 – 110Combined sources4
    Beta strandi113 – 116Combined sources4
    Helixi118 – 124Combined sources7
    Beta strandi126 – 131Combined sources6
    Beta strandi136 – 138Combined sources3
    Helixi140 – 144Combined sources5
    Helixi152 – 160Combined sources9
    Helixi162 – 171Combined sources10
    Helixi177 – 183Combined sources7
    Beta strandi187 – 189Combined sources3
    Helixi194 – 206Combined sources13
    Helixi210 – 216Combined sources7
    Helixi219 – 223Combined sources5
    Helixi228 – 243Combined sources16
    Helixi246 – 252Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4IZBX-ray1.50A/B1-267[»]
    4IZCX-ray1.80A/B1-267[»]
    4IZDX-ray1.80A/B1-267[»]
    ProteinModelPortaliQ5LLW6.
    SMRiQ5LLW6.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni31 – 32Substrate bindingCombined sources1 Publication2
    Regioni69 – 73Substrate bindingCombined sources1 Publication5
    Regioni255 – 258Substrate bindingCombined sources1 Publication4
    Regioni262 – 264Substrate bindingCombined sources1 Publication3

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiENOG4105E9F. Bacteria.
    COG1024. LUCA.
    HOGENOMiHOG000027939.
    KOiK20036.
    OMAiWHRAFDK.
    OrthoDBiPOG091H01K6.

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4IZBX-ray1.50A/B1-267[»]
    4IZCX-ray1.80A/B1-267[»]
    4IZDX-ray1.80A/B1-267[»]
    ProteinModelPortaliQ5LLW6.
    SMRiQ5LLW6.
    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.
    OrthoDBiPOG091H01K6.

    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...

    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: November 2, 2016
    This is version 73 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.