DDDQ_RUELI
ID DDDQ_RUELI Reviewed; 192 AA.
AC D0CY60;
DT 16-SEP-2015, integrated into UniProtKB/Swiss-Prot.
DT 24-NOV-2009, sequence version 1.
DT 03-AUG-2022, entry version 47.
DE RecName: Full=Dimethylsulfonioproprionate lyase DddQ {ECO:0000305};
DE Short=DMSP lyase;
DE EC=4.4.1.3 {ECO:0000269|PubMed:24395783};
GN Name=dddQ; ORFNames=SL1157_0332 {ECO:0000312|EMBL:EEX08322.1};
OS Ruegeria lacuscaerulensis (strain DSM 11314 / KCTC 2953 / ITI-1157)
OS (Silicibacter lacuscaerulensis).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Roseobacteraceae; Ruegeria.
OX NCBI_TaxID=644107;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 11314 / KCTC 2953 / ITI-1157 {ECO:0000312|EMBL:EEX08322.1};
RA Zinser E., Buchan A., Ferriera S.F., Johnson J.J., Kravitz S.K.,
RA Beeson K.B., Sutton G.S., Rogers Y.-H.R., Friedman R.F., Frazier M.F.,
RA Venter J.C.V.;
RL Submitted (SEP-2008) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP DISCUSSION ON FUNCTION.
RC STRAIN=DSM 11314 / KCTC 2953 / ITI-1157;
RX PubMed=24760823; DOI=10.1073/pnas.1401685111;
RA Alcolombri U., Elias M., Vardi A., Tawfik D.S.;
RT "Ambiguous evidence for assigning DddQ as a dimethylsulfoniopropionate
RT lyase and oceanic dimethylsulfide producer.";
RL Proc. Natl. Acad. Sci. U.S.A. 111:E2078-E2078(2014).
RN [3]
RP DISCUSSION ON FUNCTION.
RC STRAIN=DSM 11314 / KCTC 2953 / ITI-1157;
RX PubMed=24967457; DOI=10.1073/pnas.1403460111;
RA Li C.Y., Chen X.L., Xie B.B., Su H.N., Qin Q.L., Zhang Y.Z.;
RT "Reply to Tawfik et al.: DddQ is a dimethylsulfoniopropionate lyase
RT involved in dimethylsulfoniopropionate catabolism in marine bacterial
RT cells.";
RL Proc. Natl. Acad. Sci. U.S.A. 111:E2080-E2080(2014).
RN [4] {ECO:0007744|PDB:4LA2, ECO:0007744|PDB:4LA3}
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF MUTANT ALA-131 IN COMPLEX WITH
RP ZINC, FUNCTION, SUBUNIT, COFACTOR, AND MUTAGENESIS OF TYR-120; HIS-123;
RP HIS-125; GLU-129; TYR-131 AND HIS-163.
RC STRAIN=DSM 11314 / KCTC 2953 / ITI-1157;
RX PubMed=24395783; DOI=10.1073/pnas.1312354111;
RA Li C.Y., Wei T.D., Zhang S.H., Chen X.L., Gao X., Wang P., Xie B.B.,
RA Su H.N., Qin Q.L., Zhang X.Y., Yu J., Zhang H.H., Zhou B.C., Yang G.P.,
RA Zhang Y.Z.;
RT "Molecular insight into bacterial cleavage of oceanic
RT dimethylsulfoniopropionate into dimethyl sulfide.";
RL Proc. Natl. Acad. Sci. U.S.A. 111:1026-1031(2014).
CC -!- FUNCTION: Able to cleave 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:24395783,
CC PubMed:24967457). 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 very low activity with
CC DMSP as substrate suggests that DMSP is not its native substrate
CC (PubMed:24760823). {ECO:0000269|PubMed:24395783,
CC ECO:0000269|PubMed:24760823, ECO:0000269|PubMed:24967457}.
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:24395783};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000269|PubMed:24395783};
CC Note=Zn(2+) probably constitutes the cofactor in vivo. Excess zinc
CC decreases the activity, possibly due to the binding of a second Zn(2+)
CC in the active site. Mn(2+) and Co(2+) strongly increase activity.
CC {ECO:0000269|PubMed:24395783};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:24395783}.
CC -!- SIMILARITY: Belongs to the non-heme iron-dependent dioxygenase family.
CC {ECO:0000305}.
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DR EMBL; GG704596; EEX08322.1; -; Genomic_DNA.
DR RefSeq; WP_005978225.1; NZ_GG704596.1.
DR PDB; 4LA2; X-ray; 1.60 A; A/B=1-192.
DR PDB; 4LA3; X-ray; 2.70 A; A/B=1-192.
DR PDB; 5JSO; X-ray; 2.00 A; A/B=1-192.
DR PDB; 5JSP; X-ray; 2.20 A; A/B=1-192.
DR PDB; 5JSR; X-ray; 2.50 A; A/B=1-192.
DR PDBsum; 4LA2; -.
DR PDBsum; 4LA3; -.
DR PDBsum; 5JSO; -.
DR PDBsum; 5JSP; -.
DR PDBsum; 5JSR; -.
DR AlphaFoldDB; D0CY60; -.
DR SMR; D0CY60; -.
DR STRING; 644107.SL1157_0332; -.
DR EnsemblBacteria; EEX08322; EEX08322; SL1157_0332.
DR eggNOG; COG1917; Bacteria.
DR HOGENOM; CLU_107154_2_0_5; -.
DR OrthoDB; 1908328at2; -.
DR BRENDA; 4.4.1.3; 13755.
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.
FT CHAIN 1..192
FT /note="Dimethylsulfonioproprionate lyase DddQ"
FT /id="PRO_0000433898"
FT BINDING 125
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:24395783,
FT ECO:0007744|PDB:4LA2, ECO:0007744|PDB:4LA3"
FT BINDING 129
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:24395783,
FT ECO:0007744|PDB:4LA2, ECO:0007744|PDB:4LA3"
FT BINDING 131
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:24395783,
FT ECO:0007744|PDB:4LA2"
FT BINDING 163
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:24395783,
FT ECO:0007744|PDB:4LA2, ECO:0007744|PDB:4LA3"
FT MUTAGEN 120
FT /note="Y->A: Strongly decreased enzyme activity toward DMSP
FT in vitro."
FT /evidence="ECO:0000269|PubMed:24395783"
FT MUTAGEN 123
FT /note="H->A: Strongly decreased enzyme activity toward DMSP
FT in vitro."
FT /evidence="ECO:0000269|PubMed:24395783"
FT MUTAGEN 125
FT /note="H->A: Strongly decreased enzyme activity toward DMSP
FT in vitro."
FT /evidence="ECO:0000269|PubMed:24395783"
FT MUTAGEN 129
FT /note="E->A: Strongly decreased enzyme activity toward DMSP
FT in vitro."
FT /evidence="ECO:0000269|PubMed:24395783"
FT MUTAGEN 131
FT /note="Y->A: Strongly decreased enzyme activity toward DMSP
FT in vitro."
FT /evidence="ECO:0000269|PubMed:24395783"
FT MUTAGEN 163
FT /note="H->A: Strongly decreased enzyme activity toward DMSP
FT in vitro."
FT /evidence="ECO:0000269|PubMed:24395783"
FT HELIX 4..16
FT /evidence="ECO:0007829|PDB:4LA2"
FT HELIX 18..23
FT /evidence="ECO:0007829|PDB:4LA2"
FT HELIX 43..47
FT /evidence="ECO:0007829|PDB:4LA2"
FT TURN 55..57
FT /evidence="ECO:0007829|PDB:4LA2"
FT HELIX 58..67
FT /evidence="ECO:0007829|PDB:4LA2"
FT TURN 68..70
FT /evidence="ECO:0007829|PDB:4LA2"
FT HELIX 79..82
FT /evidence="ECO:0007829|PDB:4LA2"
FT HELIX 84..88
FT /evidence="ECO:0007829|PDB:4LA2"
FT STRAND 89..97
FT /evidence="ECO:0007829|PDB:4LA2"
FT STRAND 100..103
FT /evidence="ECO:0007829|PDB:4LA2"
FT STRAND 108..114
FT /evidence="ECO:0007829|PDB:4LA2"
FT STRAND 119..124
FT /evidence="ECO:0007829|PDB:4LA2"
FT STRAND 126..142
FT /evidence="ECO:0007829|PDB:4LA2"
FT STRAND 145..150
FT /evidence="ECO:0007829|PDB:4LA2"
FT STRAND 154..157
FT /evidence="ECO:0007829|PDB:4LA2"
FT STRAND 163..166
FT /evidence="ECO:0007829|PDB:4LA2"
FT STRAND 172..180
FT /evidence="ECO:0007829|PDB:4LA2"
FT TURN 181..184
FT /evidence="ECO:0007829|PDB:4LA2"
SQ SEQUENCE 192 AA; 21169 MW; 0C97E04923BA00C8 CRC64;
MTLENVLEAA RHLHQTLPAL SEFGNWPTDL TATGLQPRAI PATPLVQALD QPGSPRTTGL
VQAIRSAAHL AHWKRTYTEA EVGADFRNRY GYFELFGPTG HFHSTQLRGY VAYWGAGLDY
DWHSHQAEEL YLTLAGGAVF KVDGERAFVG AEGTRLHASW QSHAMSTGDQ PILTFVLWRG
EGLNALPRMD AA
