DDDW_RUEPO
ID DDDW_RUEPO Reviewed; 152 AA.
AC Q5LW89;
DT 16-SEP-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 77.
DE RecName: Full=Dimethylsulfonioproprionate lyase DddW {ECO:0000305};
DE Short=DMSP lyase;
DE EC=4.4.1.3 {ECO:0000269|PubMed:25993446};
GN Name=dddW {ECO:0000312|EMBL:AAV93771.1};
GN OrderedLocusNames=SPO0453 {ECO:0000312|EMBL:AAV93771.1};
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, DISRUPTION PHENOTYPE, AND INDUCTION.
RC STRAIN=ATCC 700808 / DSM 15171 / DSS-3;
RX PubMed=21677693; DOI=10.1038/ismej.2011.79;
RA Todd J.D., Kirkwood M., Newton-Payne S., Johnston A.W.;
RT "DddW, a third DMSP lyase in a model Roseobacter marine bacterium, Ruegeria
RT pomeroyi DSS-3.";
RL ISME J. 6:223-226(2012).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
RP COFACTOR, AND MUTAGENESIS OF HIS-81; HIS-83; GLU-87 AND HIS-121.
RC STRAIN=ATCC 700808 / DSM 15171 / DSS-3;
RX PubMed=25993446; DOI=10.1371/journal.pone.0127288;
RA Brummett A.E., Schnicker N.J., Crider A., Todd J.D., Dey M.;
RT "Biochemical, kinetic, and spectroscopic characterization of Ruegeria
RT pomeroyi DddW-A mononuclear iron-dependent DMSP lyase.";
RL PLoS ONE 10:E0127288-E0127288(2015).
CC -!- FUNCTION: Able to cleave dimethylsulfonioproprionate (DMSP), releasing
CC dimethyl sulfide (DMS) and acrylate. DMS is the principal form by which
CC sulfur is transported from oceans to the atmosphere.
CC {ECO:0000269|PubMed:21677693, ECO:0000269|PubMed:25993446}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S,S-dimethyl-beta-propiothetin = acrylate + dimethyl sulfide +
CC H(+); Xref=Rhea:RHEA:19965, ChEBI:CHEBI:15378, ChEBI:CHEBI:16457,
CC ChEBI:CHEBI:17437, ChEBI:CHEBI:37080; EC=4.4.1.3;
CC Evidence={ECO:0000269|PubMed:25993446};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:25993446};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000305|PubMed:25993446};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=8.68 uM for dimethylsulfonioproprionate (in the presence of
CC Fe(2+)) {ECO:0000269|PubMed:25993446};
CC KM=4.50 uM for dimethylsulfonioproprionate (in the presence of
CC Mn(2+)) {ECO:0000269|PubMed:25993446};
CC Note=kcat is 18,25 sec(-1) with dimethylsulfonioproprionate (in the
CC presence of Fe(2+)). kcat is 17.33 sec(-1) with
CC dimethylsulfonioproprionate (in the presence of Mn(2+)).
CC {ECO:0000269|PubMed:25993446};
CC pH dependence:
CC Optimum pH is 8.0. {ECO:0000269|PubMed:25993446};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:25993446}.
CC -!- INDUCTION: Up-regulated by pre-growth of cells with
CC dimethylsulfonioproprionate (DMSP). {ECO:0000269|PubMed:21677693}.
CC -!- DISRUPTION PHENOTYPE: Decreased production of dimethyl sulfide (DMS).
CC {ECO:0000269|PubMed:21677693}.
CC -!- SIMILARITY: Belongs to the non-heme iron-dependent dioxygenase family.
CC {ECO:0000305}.
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DR EMBL; CP000031; AAV93771.1; -; Genomic_DNA.
DR RefSeq; WP_011046214.1; NC_003911.12.
DR AlphaFoldDB; Q5LW89; -.
DR SMR; Q5LW89; -.
DR STRING; 246200.SPO0453; -.
DR EnsemblBacteria; AAV93771; AAV93771; SPO0453.
DR KEGG; sil:SPO0453; -.
DR eggNOG; COG0662; Bacteria.
DR HOGENOM; CLU_122927_1_0_5; -.
DR OMA; GHLCAHR; -.
DR OrthoDB; 1928636at2; -.
DR BRENDA; 4.4.1.3; 8123.
DR Proteomes; UP000001023; Chromosome.
DR GO; GO:0047869; F:dimethylpropiothetin dethiomethylase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 2.60.120.10; -; 1.
DR InterPro; IPR013096; Cupin_2.
DR InterPro; IPR014710; RmlC-like_jellyroll.
DR InterPro; IPR011051; RmlC_Cupin_sf.
DR Pfam; PF07883; Cupin_2; 1.
DR SUPFAM; SSF51182; SSF51182; 1.
PE 1: Evidence at protein level;
KW Iron; Lyase; Metal-binding; Reference proteome.
FT CHAIN 1..152
FT /note="Dimethylsulfonioproprionate lyase DddW"
FT /id="PRO_0000433900"
FT BINDING 83
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:25993446"
FT BINDING 87
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:25993446"
FT BINDING 89
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:D0CY60"
FT BINDING 121
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:25993446"
FT MUTAGEN 81
FT /note="H->A: Decreased iron binding and enzyme activity
FT toward DMSP."
FT /evidence="ECO:0000269|PubMed:25993446"
FT MUTAGEN 83
FT /note="H->A: Decreased iron binding and enzyme activity
FT toward DMSP."
FT /evidence="ECO:0000269|PubMed:25993446"
FT MUTAGEN 87
FT /note="E->A: Decreased iron binding and enzyme activity
FT toward DMSP."
FT /evidence="ECO:0000269|PubMed:25993446"
FT MUTAGEN 121
FT /note="H->A: Decreased iron binding and enzyme activity
FT toward DMSP."
FT /evidence="ECO:0000269|PubMed:25993446"
SQ SEQUENCE 152 AA; 16132 MW; 90EF8584AEFCA325 CRC64;
MTAMLDSFAT DLTAATSLHQ PGNLPHPPHA IDAENVPLSG GTDPTYGEVR WRTLINGTEA
APRDMVLGIA EFGPGHQLRP HRHTPPEFYL GLEGSGIVTI DGVPHEIRAG VALYIPGDAE
HGTVAGPEGL RFAYGFASAS FEAIEYRFTA SA
