DDDP_ROSNI
ID DDDP_ROSNI Reviewed; 446 AA.
AC A3SK19;
DT 16-SEP-2015, integrated into UniProtKB/Swiss-Prot.
DT 03-APR-2007, sequence version 1.
DT 03-AUG-2022, entry version 59.
DE RecName: Full=Dimethylsulfonioproprionate lyase DddP {ECO:0000305};
DE Short=DMSP lyase;
DE EC=4.4.1.3 {ECO:0000269|PubMed:20378650};
GN Name=dddP {ECO:0000303|PubMed:19220400};
GN ORFNames=ISM_05385 {ECO:0000312|EMBL:EAP77700.1};
OS Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Roseobacteraceae; Roseovarius.
OX NCBI_TaxID=89187;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-591 / DSM 15170 / ISM;
RA Moran M.A., Ferriera S., Johnson J., Kravitz S., Halpern A., Remington K.,
RA Beeson K., Tran B., Rogers Y.-H., Friedman R., Venter J.C.;
RL Submitted (DEC-2005) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP FUNCTION.
RX PubMed=19220400; DOI=10.1111/j.1462-2920.2009.01864.x;
RA Todd J.D., Curson A.R., Dupont C.L., Nicholson P., Johnston A.W.;
RT "The dddP gene, encoding a novel enzyme that converts
RT dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean
RT metagenomes and marine bacteria and also occurs in some Ascomycete fungi.";
RL Environ. Microbiol. 11:1376-1385(2009).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF ASP-295; ASP-297; ASP-307; HIS-371; GLU-406 AND GLU-421.
RX PubMed=20378650; DOI=10.1099/mic.0.038927-0;
RA Kirkwood M., Le Brun N.E., Todd J.D., Johnston A.W.;
RT "The dddP gene of Roseovarius nubinhibens encodes a novel lyase that
RT cleaves dimethylsulfoniopropionate into acrylate plus dimethyl sulfide.";
RL Microbiology 156:1900-1906(2010).
RN [4]
RP DISCUSSION ON FUNCTION.
RX PubMed=25140443; DOI=10.1021/bi500853s;
RA Alcolombri U., Laurino P., Lara-Astiaso P., Vardi A., Tawfik D.S.;
RT "DddD is a CoA-transferase/lyase producing dimethyl sulfide in the marine
RT environment.";
RL Biochemistry 53:5473-5475(2014).
CC -!- FUNCTION: Able to cleave dimethylsulfonioproprionate (DMSP), releasing
CC dimethyl sulfide (DMS). DMS is the principal form by which sulfur is
CC transported from oceans to the atmosphere (PubMed:19220400,
CC PubMed:20378650). The real activity of the protein is however subject
CC to debate and it is unclear whether it constitutes a real
CC dimethylsulfonioproprionate lyase in vivo: the low activity with DMSP
CC as substrate suggests that DMSP is not its native substrate
CC (PubMed:25140443). {ECO:0000269|PubMed:19220400,
CC ECO:0000269|PubMed:20378650, ECO:0000303|PubMed:25140443}.
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:20378650};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250|UniProtKB:Q166H0};
CC Note=According to a report, does not bind any metal ion as cofactor
CC (PubMed:20378650). A crystal structure complexed with 2 Fe(2+) ions has
CC however been observed for an ortholog, suggesting that it binds 2
CC divalent metal cation ions per subunit (By similarity).
CC {ECO:0000250|UniProtKB:Q166H0, ECO:0000269|PubMed:20378650};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=13.8 mM for dimethylsulfonioproprionate
CC {ECO:0000269|PubMed:20378650};
CC Vmax=0.31 nmol/min/ug enzyme {ECO:0000269|PubMed:20378650};
CC pH dependence:
CC Optimum pH is 6.0. {ECO:0000269|PubMed:20378650};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:20378650}.
CC -!- SIMILARITY: Belongs to the peptidase M24B family. {ECO:0000305}.
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DR EMBL; AALY01000001; EAP77700.1; -; Genomic_DNA.
DR RefSeq; WP_009813101.1; NZ_CH724156.1.
DR AlphaFoldDB; A3SK19; -.
DR SMR; A3SK19; -.
DR STRING; 89187.ISM_05385; -.
DR eggNOG; COG0006; Bacteria.
DR HOGENOM; CLU_052604_0_0_5; -.
DR OrthoDB; 415910at2; -.
DR BioCyc; MetaCyc:MON-15590; -.
DR Proteomes; UP000005954; Unassembled WGS sequence.
DR GO; GO:0047869; F:dimethylpropiothetin dethiomethylase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR Gene3D; 3.40.350.10; -; 1.
DR Gene3D; 3.90.230.10; -; 1.
DR InterPro; IPR029149; Creatin/AminoP/Spt16_NTD.
DR InterPro; IPR036005; Creatinase/aminopeptidase-like.
DR InterPro; IPR000994; Pept_M24.
DR Pfam; PF00557; Peptidase_M24; 1.
DR SUPFAM; SSF53092; SSF53092; 1.
DR SUPFAM; SSF55920; SSF55920; 1.
PE 1: Evidence at protein level;
KW Iron; Lyase; Metal-binding; Reference proteome.
FT CHAIN 1..446
FT /note="Dimethylsulfonioproprionate lyase DddP"
FT /id="PRO_0000433896"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 295
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q166H0"
FT BINDING 297
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q166H0"
FT BINDING 307
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q166H0"
FT BINDING 307
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q166H0"
FT BINDING 371
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q166H0"
FT BINDING 406
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q166H0"
FT BINDING 421
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q166H0"
FT BINDING 421
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q166H0"
FT MUTAGEN 295
FT /note="D->A: Unable to generate dimethyl sulfide (DMS) from
FT dimethylsulfonioproprionate (DMSP)."
FT /evidence="ECO:0000269|PubMed:20378650"
FT MUTAGEN 297
FT /note="D->A: Unable to generate dimethyl sulfide (DMS) from
FT dimethylsulfonioproprionate (DMSP)."
FT /evidence="ECO:0000269|PubMed:20378650"
FT MUTAGEN 307
FT /note="D->A: Unable to generate dimethyl sulfide (DMS) from
FT dimethylsulfonioproprionate (DMSP)."
FT /evidence="ECO:0000269|PubMed:20378650"
FT MUTAGEN 371
FT /note="H->A: Unable to generate dimethyl sulfide (DMS) from
FT dimethylsulfonioproprionate (DMSP)."
FT /evidence="ECO:0000269|PubMed:20378650"
FT MUTAGEN 406
FT /note="E->A: Unable to generate dimethyl sulfide (DMS) from
FT dimethylsulfonioproprionate (DMSP)."
FT /evidence="ECO:0000269|PubMed:20378650"
FT MUTAGEN 421
FT /note="E->A: Unable to generate dimethyl sulfide (DMS) from
FT dimethylsulfonioproprionate (DMSP)."
FT /evidence="ECO:0000269|PubMed:20378650"
SQ SEQUENCE 446 AA; 49971 MW; 97AC0952483B2A24 CRC64;
MNQHYSETRK IDPSRGATLG DNTPNDNNRI EIGPTQLAFG EWATAGLALP DLQRMREFRW
NRLTQAVVDR DYGGVLMFDP LNIRYATDST NMQLWNAHNP FRALLVCADG YMVIWDYKNS
PFLSTFNPLV REQRFGADLF YFDRGDKVDV AADAFSNEVR TLIAEHGGGN MRLAVDKIML
HGLRALEAQG FEIMEGEELT EKTRAIKGPD EILAMRCAVH ACETSVAAME HFAREAVPQG
NTSEDDVWAV LHAENIKRGG EWIETRLLAS GPRTNPWFQE CGPRIIQNNE IISFDTDLIG
SYGICVDISR SWWVGDAAPP ADMVYAMQHA HEHIMTNMEM LKPGVTIPEL SERSHRLDEQ
FQAQKYGCLM HGVGLCDEWP LVAYPDQAVP GSYDYPLEPG MVLCVEAAVG AVGGNFTIKL
EDQVLITETG YENLTSYPFD PALMGR
