DDDQ_RUEPO
ID DDDQ_RUEPO Reviewed; 201 AA.
AC Q5LT18;
DT 16-SEP-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 81.
DE RecName: Full=Dimethylsulfonioproprionate lyase DddQ;
DE Short=DMSP lyase;
DE EC=4.4.1.3 {ECO:0000250|UniProtKB:D0CY60};
GN Name=dddQ {ECO:0000312|EMBL:AAV94883.1};
GN OrderedLocusNames=SPO1596 {ECO:0000312|EMBL:AAV94883.1};
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, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 700808 / DSM 15171 / DSS-3;
RX PubMed=20880330; DOI=10.1111/j.1462-2920.2010.02348.x;
RA Todd J.D., Curson A.R., Kirkwood M., Sullivan M.J., Green R.T.,
RA Johnston A.W.;
RT "DddQ, a novel, cupin-containing, dimethylsulfoniopropionate lyase in
RT marine roseobacters and in uncultured marine bacteria.";
RL Environ. Microbiol. 13:427-438(2011).
CC -!- FUNCTION: May act as a dimethylsulfonioproprionate (DMSP) in vitro,
CC releasing dimethyl sulfide (DMS). DMS is the principal form by which
CC sulfur is transported from oceans to the atmosphere (PubMed:20880330).
CC The real activity of the protein is however subject to debate and it is
CC unclear whether it constitutes a real dimethylsulfonioproprionate lyase
CC in vivo (Probable). {ECO:0000269|PubMed:20880330, ECO:0000305}.
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:0000250|UniProtKB:D0CY60};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250|UniProtKB:D0CY60};
CC Note=Zn(2+) probably constitutes the cofactor in vivo.
CC {ECO:0000250|UniProtKB:D0CY60};
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:D0CY60}.
CC -!- DISRUPTION PHENOTYPE: Decreased dimethylsulfonioproprionate (DMSP)
CC catabolism. {ECO:0000269|PubMed:20880330}.
CC -!- SIMILARITY: Belongs to the non-heme iron-dependent dioxygenase family.
CC {ECO:0000305}.
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DR EMBL; CP000031; AAV94883.1; -; Genomic_DNA.
DR RefSeq; WP_011047333.1; NC_003911.12.
DR PDB; 5CU1; X-ray; 2.30 A; A=1-201.
DR PDBsum; 5CU1; -.
DR AlphaFoldDB; Q5LT18; -.
DR SMR; Q5LT18; -.
DR STRING; 246200.SPO1596; -.
DR DNASU; 3193536; -.
DR EnsemblBacteria; AAV94883; AAV94883; SPO1596.
DR KEGG; sil:SPO1596; -.
DR eggNOG; COG1917; Bacteria.
DR HOGENOM; CLU_107154_2_0_5; -.
DR OMA; PHATRTY; -.
DR OrthoDB; 1908328at2; -.
DR BioCyc; MetaCyc:MON-16240; -.
DR BRENDA; 4.4.1.3; 8123.
DR Proteomes; UP000001023; Chromosome.
DR GO; GO:0047869; F:dimethylpropiothetin dethiomethylase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 2.60.120.10; -; 1.
DR InterPro; IPR031723; DMSP_lyase.
DR InterPro; IPR014710; RmlC-like_jellyroll.
DR InterPro; IPR011051; RmlC_Cupin_sf.
DR Pfam; PF16867; DMSP_lyase; 1.
DR SUPFAM; SSF51182; SSF51182; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Metal-binding; Reference proteome.
FT CHAIN 1..201
FT /note="Dimethylsulfonioproprionate lyase DddQ"
FT /id="PRO_0000433899"
FT BINDING 130
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:D0CY60"
FT BINDING 134
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:D0CY60"
FT BINDING 136
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:D0CY60"
FT BINDING 169
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:D0CY60"
FT HELIX 6..21
FT /evidence="ECO:0007829|PDB:5CU1"
FT HELIX 23..28
FT /evidence="ECO:0007829|PDB:5CU1"
FT HELIX 46..53
FT /evidence="ECO:0007829|PDB:5CU1"
FT HELIX 63..72
FT /evidence="ECO:0007829|PDB:5CU1"
FT TURN 73..75
FT /evidence="ECO:0007829|PDB:5CU1"
FT TURN 81..84
FT /evidence="ECO:0007829|PDB:5CU1"
FT HELIX 89..92
FT /evidence="ECO:0007829|PDB:5CU1"
FT STRAND 96..102
FT /evidence="ECO:0007829|PDB:5CU1"
FT STRAND 105..108
FT /evidence="ECO:0007829|PDB:5CU1"
FT STRAND 113..119
FT /evidence="ECO:0007829|PDB:5CU1"
FT STRAND 124..129
FT /evidence="ECO:0007829|PDB:5CU1"
FT STRAND 131..141
FT /evidence="ECO:0007829|PDB:5CU1"
FT STRAND 143..147
FT /evidence="ECO:0007829|PDB:5CU1"
FT STRAND 153..155
FT /evidence="ECO:0007829|PDB:5CU1"
FT STRAND 160..163
FT /evidence="ECO:0007829|PDB:5CU1"
FT STRAND 169..172
FT /evidence="ECO:0007829|PDB:5CU1"
FT STRAND 178..186
FT /evidence="ECO:0007829|PDB:5CU1"
FT STRAND 193..195
FT /evidence="ECO:0007829|PDB:5CU1"
SQ SEQUENCE 201 AA; 22063 MW; 4A25A8CB6A9599D2 CRC64;
MTQTDPAFQN LLAEFQALHA REPALAGFVA LPDSLTPQPV TPVRIPPAAL MESDPDLTTT
AYAAIRDAFI AAGAVAQWRL TYQGSRLGAD FMDRFACYCL IGEGGPFASD SLAAYVVYMP
AGLYYPFHQH PAEEIYFILA GEAEFLMEGH PPRRLGPGDH VFHPSGHPHA TRTYDRPFMA
LVLWRGDLET APVLTYPEGE I
