(data stored in ACNUC7421 zone)

SWISSPROT: 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   08-MAY-2019, entry version 68.
DE   RecName: Full=Dimethlysulfonioproprionate 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)
OS   (Silicibacter pomeroyi).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC   Rhodobacteraceae; 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.,
RA   Brinkac L.M., Lewis M., Johri S., Weaver B., Pai G., Eisen J.A.,
RA   Rahe E., Sheldon W.M., Ye W., Miller T.R., Carlton J., Rasko D.A.,
RA   Paulsen I.T., Ren Q., Daugherty S.C., DeBoy R.T., Dodson R.J.,
RA   Durkin A.S., Madupu R., Nelson W.C., Sullivan S.A., Rosovitz M.J.,
RA   Haft D.H., Selengut J., Ward N.;
RT   "Genome sequence of Silicibacter pomeroyi reveals adaptations to the
RT   marine 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,
RT   Ruegeria 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 dimethlysulfonioproprionate (DMSP),
CC       releasing dimethyl sulfide (DMS) and acrylate. DMS is the
CC       principal form by which sulfur is transported from oceans to the
CC       atmosphere. {ECO:0000269|PubMed:21677693,
CC       ECO:0000269|PubMed:25993446}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=S,S-dimethyl-beta-propiothetin = acrylate + dimethyl
CC         sulfide + H(+); Xref=Rhea:RHEA:19965, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:16457, ChEBI:CHEBI:17437, ChEBI:CHEBI:37080;
CC         EC=4.4.1.3; 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.
CC       {ECO:0000305|PubMed:25993446};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=8.68 uM for dimethlysulfonioproprionate (in the presence of
CC         Fe(2+)) {ECO:0000269|PubMed:25993446};
CC         KM=4.50 uM for dimethlysulfonioproprionate (in the presence of
CC         Mn(2+)) {ECO:0000269|PubMed:25993446};
CC         Note=Kcat is 18,25 sec(-1) with dimethlysulfonioproprionate (in
CC         the presence of Fe(2+)). Kcat is 17.33 sec(-1) with
CC         dimethlysulfonioproprionate (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       dimethlysulfonioproprionate (DMSP). {ECO:0000269|PubMed:21677693}.
CC   -!- DISRUPTION PHENOTYPE: Decreased production of dimethyl sulfide
CC       (DMS). {ECO:0000269|PubMed:21677693}.
CC   -!- SIMILARITY: Belongs to the non-heme iron-dependent dioxygenase
CC       family. {ECO:0000305}.
DR   EMBL; CP000031; AAV93771.1; -; Genomic_DNA.
DR   RefSeq; WP_011046214.1; NC_003911.12.
DR   SMR; Q5LW89; -.
DR   STRING; 246200.SPO0453; -.
DR   EnsemblBacteria; AAV93771; AAV93771; SPO0453.
DR   KEGG; sil:SPO0453; -.
DR   eggNOG; ENOG4106BM2; Bacteria.
DR   eggNOG; ENOG4111WK5; LUCA.
DR   HOGENOM; HOG000234873; -.
DR   OMA; GHLCAHR; -.
DR   OrthoDB; 1928636at2; -.
DR   BioCyc; RPOM246200:G1G48-460-MONOMER; -.
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;
DR   PRODOM; Q5LW89.
DR   SWISS-2DPAGE; Q5LW89.
KW   Complete proteome; Lyase; Metal-binding; Reference proteome.
FT   CHAIN         1    152       Dimethlysulfonioproprionate lyase DddW.
FT                                /FTId=PRO_0000433900.
FT   METAL        83     83       Iron; via tele nitrogen.
FT                                {ECO:0000269|PubMed:25993446}.
FT   METAL        87     87       Iron. {ECO:0000269|PubMed:25993446}.
FT   METAL        89     89       Iron. {ECO:0000250|UniProtKB:D0CY60}.
FT   METAL       121    121       Iron; via tele nitrogen.
FT                                {ECO:0000269|PubMed:25993446}.
FT   MUTAGEN      81     81       H->A: Decreased iron binding and enzyme
FT                                activity toward DMSP.
FT                                {ECO:0000269|PubMed:25993446}.
FT   MUTAGEN      83     83       H->A: Decreased iron binding and enzyme
FT                                activity toward DMSP.
FT                                {ECO:0000269|PubMed:25993446}.
FT   MUTAGEN      87     87       E->A: Decreased iron binding and enzyme
FT                                activity toward DMSP.
FT                                {ECO:0000269|PubMed:25993446}.
FT   MUTAGEN     121    121       H->A: Decreased iron binding and enzyme
FT                                activity toward DMSP.
FT                                {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
//

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