DMDA_PELUB
ID DMDA_PELUB Reviewed; 369 AA.
AC Q4FP21;
DT 09-JAN-2013, integrated into UniProtKB/Swiss-Prot.
DT 30-AUG-2005, sequence version 1.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=Dimethylsulfonioproprionate demethylase DmdA;
DE EC=2.1.1.269;
GN Name=dmdA; OrderedLocusNames=SAR11_0246;
OS Pelagibacter ubique (strain HTCC1062).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Pelagibacterales;
OC Pelagibacteraceae; Candidatus Pelagibacter.
OX NCBI_TaxID=335992;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=HTCC1062;
RX PubMed=16109880; DOI=10.1126/science.1114057;
RA Giovannoni S.J., Tripp H.J., Givan S., Podar M., Vergin K.L., Baptista D.,
RA Bibbs L., Eads J., Richardson T.H., Noordewier M., Rappe M.S., Short J.M.,
RA Carrington J.C., Mathur E.J.;
RT "Genome streamlining in a cosmopolitan oceanic bacterium.";
RL Science 309:1242-1245(2005).
RN [2]
RP FUNCTION.
RC STRAIN=HTCC1062;
RX PubMed=17068264; DOI=10.1126/science.1130657;
RA Howard E.C., Henriksen J.R., Buchan A., Reisch C.R., Burgmann H., Welsh R.,
RA Ye W., Gonzalez J.M., Mace K., Joye S.B., Kiene R.P., Whitman W.B.,
RA Moran M.A.;
RT "Bacterial taxa that limit sulfur flux from the ocean.";
RL Science 314:649-652(2006).
RN [3]
RP BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC ACTIVITY, SUBUNIT, AND ACTIVITY
RP REGULATION.
RC STRAIN=HTCC1062;
RX PubMed=18849431; DOI=10.1128/jb.00770-08;
RA Reisch C.R., Moran M.A., Whitman W.B.;
RT "Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter
RT ubique and Silicibacter pomeroyi.";
RL J. Bacteriol. 190:8018-8024(2008).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) WITH AND WITHOUT SUBSTRATE, AND
RP SUBUNIT.
RC STRAIN=HTCC1062;
RX PubMed=22162093; DOI=10.1002/pro.2015;
RA Schuller D.J., Reisch C.R., Moran M.A., Whitman W.B., Lanzilotta W.N.;
RT "Structures of dimethylsulfoniopropionate-dependent demethylase from the
RT marine organism Pelagabacter ubique.";
RL Protein Sci. 21:289-298(2012).
CC -!- FUNCTION: Major contributor to the demethylation of
CC dimethylsulfonioproprionate (DMSP). Demethylates DMSP to methyl-
CC mercaptopropionate (MMPA). {ECO:0000269|PubMed:17068264}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6S)-5,6,7,8-tetrahydrofolate + S,S-dimethyl-beta-propiothetin
CC = (6S)-5-methyl-5,6,7,8-tetrahydrofolate + 3-
CC (methylsulfanyl)propanoate + H(+); Xref=Rhea:RHEA:35467,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16457, ChEBI:CHEBI:18608,
CC ChEBI:CHEBI:49016, ChEBI:CHEBI:57453; EC=2.1.1.269;
CC Evidence={ECO:0000269|PubMed:18849431};
CC -!- ACTIVITY REGULATION: Non-competitively inhibited by MMPA, weakly
CC inhibited by substrate analogs dimethylsulfoniobutanoate and
CC dimethylsulfoniopentanoate. It is used as an intracellular osmolyte.
CC {ECO:0000269|PubMed:18849431}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.29 mM for tetrahydrafolate {ECO:0000269|PubMed:18849431};
CC KM=13.2 mM for dimethylsulfonioproprionate
CC {ECO:0000269|PubMed:18849431};
CC Vmax=11.7 umol/min/mg enzyme {ECO:0000269|PubMed:18849431};
CC Note=Upon expression and purification from E.coli.;
CC pH dependence:
CC Optimum pH is 7.0-8.0. {ECO:0000269|PubMed:18849431};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:18849431,
CC ECO:0000269|PubMed:22162093}.
CC -!- MISCELLANEOUS: DMSP is used as an intracellular osmolyte, predator
CC deterrent and antioxidant. {ECO:0000305|PubMed:17068264}.
CC -!- SIMILARITY: Belongs to the GcvT family. DmdA subfamily. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; CP000084; AAZ21068.1; -; Genomic_DNA.
DR RefSeq; WP_011281570.1; NC_007205.1.
DR PDB; 3TFH; X-ray; 2.10 A; A/B=1-369.
DR PDB; 3TFI; X-ray; 1.60 A; A/B=1-369.
DR PDB; 3TFJ; X-ray; 1.60 A; A/B=1-369.
DR PDBsum; 3TFH; -.
DR PDBsum; 3TFI; -.
DR PDBsum; 3TFJ; -.
DR AlphaFoldDB; Q4FP21; -.
DR SMR; Q4FP21; -.
DR STRING; 335992.SAR11_0246; -.
DR EnsemblBacteria; AAZ21068; AAZ21068; SAR11_0246.
DR GeneID; 66294744; -.
DR KEGG; pub:SAR11_0246; -.
DR eggNOG; COG0404; Bacteria.
DR HOGENOM; CLU_007884_10_2_5; -.
DR OMA; MLNDPVA; -.
DR OrthoDB; 282830at2; -.
DR BRENDA; 2.1.1.269; 10071.
DR Proteomes; UP000002528; Chromosome.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1360.120; -; 1.
DR InterPro; IPR028896; GCST/YgfZ/DmdA.
DR InterPro; IPR013977; GCV_T_C.
DR InterPro; IPR006222; GCV_T_N.
DR InterPro; IPR029043; GcvT/YgfZ_C.
DR InterPro; IPR027266; TrmE/GcvT_dom1.
DR PANTHER; PTHR43757; PTHR43757; 1.
DR Pfam; PF01571; GCV_T; 1.
DR Pfam; PF08669; GCV_T_C; 1.
DR SUPFAM; SSF101790; SSF101790; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Methyltransferase; Reference proteome; Transferase.
FT CHAIN 1..369
FT /note="Dimethylsulfonioproprionate demethylase DmdA"
FT /id="PRO_0000420616"
FT BINDING 122
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:22162093"
FT BINDING 204
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:22162093"
FT BINDING 206
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:22162093"
FT STRAND 10..13
FT /evidence="ECO:0007829|PDB:3TFH"
FT HELIX 18..21
FT /evidence="ECO:0007829|PDB:3TFI"
FT TURN 22..25
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 28..32
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 35..42
FT /evidence="ECO:0007829|PDB:3TFI"
FT HELIX 44..53
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 56..59
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 65..70
FT /evidence="ECO:0007829|PDB:3TFI"
FT HELIX 73..80
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 92..95
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 110..115
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 118..122
FT /evidence="ECO:0007829|PDB:3TFI"
FT HELIX 128..139
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 151..157
FT /evidence="ECO:0007829|PDB:3TFI"
FT HELIX 160..168
FT /evidence="ECO:0007829|PDB:3TFI"
FT HELIX 170..174
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 179..185
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 188..194
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 197..200
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 202..207
FT /evidence="ECO:0007829|PDB:3TFI"
FT HELIX 210..223
FT /evidence="ECO:0007829|PDB:3TFI"
FT HELIX 225..227
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 230..232
FT /evidence="ECO:0007829|PDB:3TFI"
FT HELIX 236..241
FT /evidence="ECO:0007829|PDB:3TFI"
FT TURN 247..249
FT /evidence="ECO:0007829|PDB:3TFI"
FT HELIX 257..259
FT /evidence="ECO:0007829|PDB:3TFI"
FT HELIX 263..265
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 269..271
FT /evidence="ECO:0007829|PDB:3TFI"
FT HELIX 277..286
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 289..300
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 308..311
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 317..327
FT /evidence="ECO:0007829|PDB:3TFI"
FT TURN 328..331
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 332..340
FT /evidence="ECO:0007829|PDB:3TFI"
FT HELIX 341..343
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 349..354
FT /evidence="ECO:0007829|PDB:3TFI"
FT STRAND 357..364
FT /evidence="ECO:0007829|PDB:3TFI"
SQ SEQUENCE 369 AA; 41832 MW; DF1612F05044393B CRC64;
MKNFSIAKSR RLRSTPYTSR IEKQGVTAYT IYNHMLLPAA FGSIEDSYKH LKEHVQIWDV
AAERQVEISG KDSAELVQLM TCRDLSKSKI GRCYYCPIID ENGNLVNDPV VLKLDENKWW
ISIADSDVIF FAKGLASGHK FDVKIVEPVV DIMAIQGPKS FALMEKVFGK KITELKFFGF
DYFDFEGTKH LIARSGWSKQ GGYEVYVENT QSGQKLYDHL FEVGKEFNVG PGCPNLIERI
ESALLSYGND FDNNDNPFEC GFDQYVSLDS DINFLGKEKL KEIKLKGPQK KLRGVKIDIK
EISLTGSKNI YDENNNVIGE LRSACYSPHF QKVIGIAMIK KSHWEASQGF KIQINDNTIN
GNVCDLPFI
