DMDD_RUEPO
ID DMDD_RUEPO Reviewed; 267 AA.
AC Q5LLW6;
DT 16-SEP-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=Methylthioacryloyl-CoA hydratase {ECO:0000303|PubMed:21562561};
DE EC=4.2.1.155 {ECO:0000269|PubMed:21562561, ECO:0000269|PubMed:23704947};
GN Name=dmdD {ECO:0000303|PubMed:21562561};
GN OrderedLocusNames=SPO3805 {ECO:0000312|EMBL:AAV97019.1};
OS Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (Silicibacter
OS pomeroyi).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Roseobacteraceae; Ruegeria.
OX NCBI_TaxID=246200;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700808 / DSM 15171 / DSS-3;
RX PubMed=15602564; DOI=10.1038/nature03170;
RA Moran M.A., Buchan A., Gonzalez J.M., Heidelberg J.F., Whitman W.B.,
RA Kiene R.P., Henriksen J.R., King G.M., Belas R., Fuqua C., Brinkac L.M.,
RA Lewis M., Johri S., Weaver B., Pai G., Eisen J.A., Rahe E., Sheldon W.M.,
RA Ye W., Miller T.R., Carlton J., Rasko D.A., Paulsen I.T., Ren Q.,
RA Daugherty S.C., DeBoy R.T., Dodson R.J., Durkin A.S., Madupu R.,
RA Nelson W.C., Sullivan S.A., Rosovitz M.J., Haft D.H., Selengut J., Ward N.;
RT "Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine
RT environment.";
RL Nature 432:910-913(2004).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 700808 / DSM 15171 / DSS-3;
RX PubMed=25780504; DOI=10.1186/1944-3277-9-11;
RA Rivers A.R., Smith C.B., Moran M.A.;
RT "An updated genome annotation for the model marine bacterium Ruegeria
RT pomeroyi DSS-3.";
RL Stand. Genomic Sci. 9:11-11(2014).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, PATHWAY, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 700808 / DSM 15171 / DSS-3;
RX PubMed=21562561; DOI=10.1038/nature10078;
RA Reisch C.R., Stoudemayer M.J., Varaljay V.A., Amster I.J., Moran M.A.,
RA Whitman W.B.;
RT "Novel pathway for assimilation of dimethylsulphoniopropionate widespread
RT in marine bacteria.";
RL Nature 473:208-211(2011).
RN [4] {ECO:0007744|PDB:4IZB, ECO:0007744|PDB:4IZC, ECO:0007744|PDB:4IZD}
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH
RP 3-(METHYLTHIO)ACRYLOYL-COA OF MUTANT ALA-121, FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE, SUBUNIT, AND MUTAGENESIS OF
RP GLU-121 AND GLU-141.
RX PubMed=23704947; DOI=10.1371/journal.pone.0063870;
RA Tan D., Crabb W.M., Whitman W.B., Tong L.;
RT "Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes
RT the hydration and hydrolysis of methylthioacryloyl-CoA.";
RL PLoS ONE 8:E63870-E63870(2013).
CC -!- FUNCTION: Involved in the assimilation of dimethylsulphoniopropionate
CC (DMSP), an important compound in the fixation of carbon in marine
CC phytoplankton, by catalyzing both the hydration and the hydrolysis of
CC 3-(methylthio)acryloyl-CoA (MTA-CoA) to acetaldehyde, CO2, MeSH, and
CC CoA (PubMed:21562561, PubMed:23704947). {ECO:0000269|PubMed:21562561,
CC ECO:0000269|PubMed:23704947}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-(methylsulfanyl)acryloyl-CoA + 2 H2O = acetaldehyde + CO2 +
CC CoA + methanethiol; Xref=Rhea:RHEA:45144, ChEBI:CHEBI:15343,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:16007, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:57287, ChEBI:CHEBI:84994; EC=4.2.1.155;
CC Evidence={ECO:0000269|PubMed:21562561, ECO:0000269|PubMed:23704947};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=8.2 uM for 3-(methylthio)acryloyl-CoA (for CoA ester hydrolysis)
CC {ECO:0000269|PubMed:23704947};
CC KM=69 uM for 3-(methylthio)propanoyl-CoA (for CoA ester hydrolysis)
CC {ECO:0000269|PubMed:23704947};
CC KM=119 uM for 3-hydroxybutyryl-CoA (for CoA ester hydrolysis)
CC {ECO:0000269|PubMed:23704947};
CC KM=9.4 uM for 3-(methylthio)acryloyl-CoA (for MeSH release)
CC {ECO:0000269|PubMed:23704947};
CC KM=19 uM for crotonyl-CoA (for hydration)
CC {ECO:0000269|PubMed:23704947};
CC Note=kcat is 44 sec(-1) for 3-(methylthio)acryloyl-CoA (for CoA ester
CC hydrolysis). kcat is 0.9 sec(-1) for 3-(methylthio)propanoyl-CoA (for
CC CoA ester hydrolysis). kcat is 13.2 sec(-1) for 3-hydroxybutyryl-CoA
CC (for CoA ester hydrolysis). kcat is 47 sec(-1) for 3-
CC (methylthio)acryloyl-CoA (for MeSH release). kcat is 42 sec(-1) for
CC crotonyl-CoA (for hydration). {ECO:0000269|PubMed:23704947};
CC -!- SUBUNIT: Homohexamer; dimer of trimers. {ECO:0000269|PubMed:23704947}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene do not grow on
CC methylmercaptopropionate (MMPA) as the sole source of carbon. Growth is
CC severely inhibited on dimethylsulphoniopropionate (DMSP).
CC {ECO:0000269|PubMed:21562561}.
CC -!- SIMILARITY: Belongs to the enoyl-CoA hydratase/isomerase family.
CC {ECO:0000255|RuleBase:RU003707}.
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DR EMBL; CP000031; AAV97019.1; -; Genomic_DNA.
DR RefSeq; WP_011049477.1; NC_003911.12.
DR PDB; 4IZB; X-ray; 1.50 A; A/B=1-267.
DR PDB; 4IZC; X-ray; 1.80 A; A/B=1-267.
DR PDB; 4IZD; X-ray; 1.80 A; A/B=1-267.
DR PDBsum; 4IZB; -.
DR PDBsum; 4IZC; -.
DR PDBsum; 4IZD; -.
DR AlphaFoldDB; Q5LLW6; -.
DR SMR; Q5LLW6; -.
DR STRING; 246200.SPO3805; -.
DR EnsemblBacteria; AAV97019; AAV97019; SPO3805.
DR KEGG; sil:SPO3805; -.
DR eggNOG; COG1024; Bacteria.
DR HOGENOM; CLU_009834_7_6_5; -.
DR OMA; MHALPRI; -.
DR BioCyc; MetaCyc:MON-16785; -.
DR BRENDA; 4.2.1.155; 8123.
DR Proteomes; UP000001023; Chromosome.
DR GO; GO:0016836; F:hydro-lyase activity; IDA:UniProtKB.
DR GO; GO:0034214; P:protein hexamerization; IDA:UniProtKB.
DR Gene3D; 1.10.12.10; -; 1.
DR InterPro; IPR029045; ClpP/crotonase-like_dom_sf.
DR InterPro; IPR018376; Enoyl-CoA_hyd/isom_CS.
DR InterPro; IPR001753; Enoyl-CoA_hydra/iso.
DR InterPro; IPR014748; Enoyl-CoA_hydra_C.
DR Pfam; PF00378; ECH_1; 1.
DR SUPFAM; SSF52096; SSF52096; 1.
DR PROSITE; PS00166; ENOYL_COA_HYDRATASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Reference proteome.
FT CHAIN 1..267
FT /note="Methylthioacryloyl-CoA hydratase"
FT /id="PRO_0000433903"
FT ACT_SITE 121
FT /note="Nucleophile"
FT /evidence="ECO:0000269|PubMed:23704947"
FT ACT_SITE 141
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:23704947"
FT BINDING 31..32
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23704947,
FT ECO:0007744|PDB:4IZC"
FT BINDING 69..73
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23704947,
FT ECO:0007744|PDB:4IZC"
FT BINDING 118
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23704947,
FT ECO:0007744|PDB:4IZC"
FT BINDING 144
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23704947,
FT ECO:0007744|PDB:4IZC"
FT BINDING 149
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23704947,
FT ECO:0007744|PDB:4IZC"
FT BINDING 255..258
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23704947,
FT ECO:0007744|PDB:4IZC"
FT BINDING 262..264
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23704947,
FT ECO:0007744|PDB:4IZC"
FT MUTAGEN 121
FT /note="E->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:23704947"
FT MUTAGEN 141
FT /note="E->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:23704947"
FT TURN 4..6
FT /evidence="ECO:0007829|PDB:4IZC"
FT STRAND 10..16
FT /evidence="ECO:0007829|PDB:4IZB"
FT STRAND 20..26
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 29..31
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 37..49
FT /evidence="ECO:0007829|PDB:4IZB"
FT TURN 50..54
FT /evidence="ECO:0007829|PDB:4IZB"
FT STRAND 57..65
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 73..79
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 83..102
FT /evidence="ECO:0007829|PDB:4IZB"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:4IZB"
FT STRAND 107..110
FT /evidence="ECO:0007829|PDB:4IZB"
FT STRAND 113..116
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 118..124
FT /evidence="ECO:0007829|PDB:4IZB"
FT STRAND 126..131
FT /evidence="ECO:0007829|PDB:4IZB"
FT STRAND 136..138
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 140..144
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 152..160
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 162..171
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 177..183
FT /evidence="ECO:0007829|PDB:4IZB"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 194..206
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 210..216
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 219..223
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 228..243
FT /evidence="ECO:0007829|PDB:4IZB"
FT HELIX 246..252
FT /evidence="ECO:0007829|PDB:4IZC"
SQ SEQUENCE 267 AA; 28836 MW; A6941E7AEB292F19 CRC64;
MTQDVTSGYS NLDLDLRDNG VCVVTLNRPD KRNALDVATI EELVTFFSTA HRKGVRAVVL
TGAGDHFCAG LDLVEHWKAD RSADDFMHVC LRWHEAFNKM EYGGVPIIAA LRGAVVGGGL
ELASAAHLRV MDQSTYFALP EGQRGIFTGG GATIRVSDMI GKYRMIDMIL TGRVYQGQEA
ADLGLAQYIT EGSSFDKAME LADKIASNLP LTNFAICSAI SHMQNMSGLD AAYAEAFVGG
IVNTQPAARE RLEAFANKTA ARVRPNS
