DDDP_ROSDO
ID DDDP_ROSDO Reviewed; 447 AA.
AC Q166H0;
DT 16-SEP-2015, integrated into UniProtKB/Swiss-Prot.
DT 25-JUL-2006, sequence version 1.
DT 03-AUG-2022, entry version 94.
DE RecName: Full=Dimethylsulfonioproprionate lyase DddP {ECO:0000305};
DE Short=DMSP lyase;
DE Short=RdDddP {ECO:0000303|PubMed:25054772};
DE EC=4.4.1.3 {ECO:0000250|UniProtKB:A3SK19};
GN Name=dddP {ECO:0000250|UniProtKB:A3SK19};
GN OrderedLocusNames=RD1_2566 {ECO:0000312|EMBL:ABG32123.1};
OS Roseobacter denitrificans (strain ATCC 33942 / OCh 114) (Erythrobacter sp.
OS (strain OCh 114)) (Roseobacter denitrificans).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Roseobacteraceae; Roseobacter.
OX NCBI_TaxID=375451;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33942 / OCh 114;
RX PubMed=17098896; DOI=10.1128/jb.01390-06;
RA Swingley W.D., Sadekar S., Mastrian S.D., Matthies H.J., Hao J., Ramos H.,
RA Acharya C.R., Conrad A.L., Taylor H.L., Dejesa L.C., Shah M.K.,
RA O'Huallachain M.E., Lince M.T., Blankenship R.E., Beatty J.T.,
RA Touchman J.W.;
RT "The complete genome sequence of Roseobacter denitrificans reveals a
RT mixotrophic rather than photosynthetic metabolism.";
RL J. Bacteriol. 189:683-690(2007).
RN [2] {ECO:0007744|PDB:4B28}
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH IRON, SUBUNIT, AND
RP COFACTOR.
RX PubMed=25054772; DOI=10.1371/journal.pone.0103128;
RA Hehemann J.H., Law A., Redecke L., Boraston A.B.;
RT "The structure of RdDddP from Roseobacter denitrificans reveals that DMSP
RT lyases in the DddP-family are metalloenzymes.";
RL PLoS ONE 9:E103128-E103128(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. The real activity of the
CC protein is however subject to debate and it is unclear whether it
CC constitutes a real dimethylsulfonioproprionate lyase in vivo: the low
CC activity with DMSP as substrate suggests that DMSP is not its native
CC substrate. {ECO:0000250|UniProtKB:A3SK19}.
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:A3SK19};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000269|PubMed:25054772};
CC Note=Binds 2 divalent metal cation ions per subunit. Fe(2+), which is
CC the most abundant metal ion found in the X-ray structure, may
CC constitute the physiological cofactor. {ECO:0000269|PubMed:25054772};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:25054772}.
CC -!- SIMILARITY: Belongs to the peptidase M24B family. {ECO:0000305}.
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DR EMBL; CP000362; ABG32123.1; -; Genomic_DNA.
DR RefSeq; WP_011568740.1; NZ_FOOO01000002.1.
DR PDB; 4B28; X-ray; 2.15 A; A=1-447.
DR PDBsum; 4B28; -.
DR AlphaFoldDB; Q166H0; -.
DR SMR; Q166H0; -.
DR STRING; 375451.RD1_2566; -.
DR PRIDE; Q166H0; -.
DR EnsemblBacteria; ABG32123; ABG32123; RD1_2566.
DR KEGG; rde:RD1_2566; -.
DR eggNOG; COG0006; Bacteria.
DR HOGENOM; CLU_052604_0_0_5; -.
DR OMA; CYYRTFS; -.
DR OrthoDB; 415910at2; -.
DR Proteomes; UP000007029; Chromosome.
DR GO; GO:0047869; F:dimethylpropiothetin dethiomethylase activity; IEA:UniProtKB-EC.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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; SSF55920; SSF55920; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Iron; Lyase; Metal-binding; Reference proteome.
FT CHAIN 1..447
FT /note="Dimethylsulfonioproprionate lyase DddP"
FT /id="PRO_0000433897"
FT REGION 1..26
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:0000269|PubMed:25054772,
FT ECO:0007744|PDB:4B28"
FT BINDING 297
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:25054772,
FT ECO:0007744|PDB:4B28"
FT BINDING 307
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:25054772,
FT ECO:0007744|PDB:4B28"
FT BINDING 307
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:25054772,
FT ECO:0007744|PDB:4B28"
FT BINDING 371
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:25054772,
FT ECO:0007744|PDB:4B28"
FT BINDING 406
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:25054772,
FT ECO:0007744|PDB:4B28"
FT BINDING 421
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:25054772,
FT ECO:0007744|PDB:4B28"
FT BINDING 421
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:25054772,
FT ECO:0007744|PDB:4B28"
FT STRAND 13..18
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 22..24
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 36..44
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 52..69
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 73..77
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 80..87
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 93..98
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 103..107
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 112..115
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 121..124
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 141..144
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 145..147
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 148..166
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 172..177
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 180..188
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 192..195
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 196..204
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 209..236
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 244..256
FT /evidence="ECO:0007829|PDB:4B28"
FT TURN 257..259
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 262..264
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 268..270
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 271..274
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 288..295
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 309..317
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 321..339
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 347..352
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 359..362
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 369..382
FT /evidence="ECO:0007829|PDB:4B28"
FT TURN 385..387
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 402..410
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 417..426
FT /evidence="ECO:0007829|PDB:4B28"
FT STRAND 428..433
FT /evidence="ECO:0007829|PDB:4B28"
FT HELIX 441..444
FT /evidence="ECO:0007829|PDB:4B28"
SQ SEQUENCE 447 AA; 50515 MW; CDA52EFC0894C648 CRC64;
MNRHFNATRK IDPSRGATLG DGSPNDMNRV EIGPTQLAFA EWHTARLDLP DLAAMRRFRH
RRLTDHVVAR GYAGLLMFDP LNIRYATDST NMQLWNTHNP FRATLLCADG YMVMWDYKNS
PFLSEFNPLV REQRAGADLF YFDRGDKVDV AADVFANEVR ILLRDHAPGL RRLAVDKVML
HGLRALQAQG FEIMDGEEVT EKARSVKGPD EIRAMRCASH ACEVAVRKME DFARSKVGDG
VTCENDIWAI LHSENVRRGG EWIETRLLAS GPRSNPWFQE CGPRVCQRNE IISFDTDLVG
AYGICTDISR SWWIGDQKPR ADMIYAMQHG VEHIRTNMEM LKPGVMIPEL SANTHVLDAK
FQKQKYGCLM HGVGLCDEWP LVAYPDHAVA GAYDYPLEPG MTLCVEALIS EEGGDFSIKL
EDQVLITEDG YENLTKYPFD PALMGVE
