DMDB_RUEPO
ID DMDB_RUEPO Reviewed; 539 AA.
AC Q5LRT0;
DT 07-JAN-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 81.
DE RecName: Full=3-methylmercaptopropionyl-CoA ligase {ECO:0000303|PubMed:21562561};
DE Short=MMPA-CoA ligase {ECO:0000303|PubMed:24443527};
DE EC=6.2.1.44 {ECO:0000269|PubMed:24443527};
DE AltName: Full=Acyl-CoA ligase {ECO:0000303|PubMed:24443527};
GN Name=dmdB {ECO:0000303|PubMed:21562561}; OrderedLocusNames=SPO2045;
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, DISRUPTION PHENOTYPE, AND PATHWAY.
RC STRAIN=ATCC 700808 / DSM 15171 / DSS-3;
RX PubMed=21562561; DOI=10.1038/nature10078;
RA Reisch C.R., Stoudemayer M.J., Varaljay V.A., Amster I.J., Moran M.A.,
RA Whitman W.B.;
RT "Novel pathway for assimilation of dimethylsulphoniopropionate widespread
RT in marine bacteria.";
RL Nature 473:208-211(2011).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, SUBUNIT, AND SUBSTRATE SPECIFICITY.
RX PubMed=24443527; DOI=10.1128/jb.00026-14;
RA Bullock H.A., Reisch C.R., Burns A.S., Moran M.A., Whitman W.B.;
RT "Regulatory and functional diversity of methylmercaptopropionate coenzyme A
RT ligases from the dimethylsulfoniopropionate demethylation pathway in
RT Ruegeria pomeroyi DSS-3 and other proteobacteria.";
RL J. Bacteriol. 196:1275-1285(2014).
CC -!- FUNCTION: Involved in the assimilation of dimethylsulphoniopropionate
CC (DMSP), an important compound in the fixation of carbon in marine
CC phytoplankton. Catalyzes the ATP-dependent ligation of
CC methylmercaptopropionate (MMPA) and CoA to yield
CC methylmercaptopropionate-CoA (MMPA-CoA) (PubMed:21562561,
CC PubMed:24443527). It is also active with short-chain-fatty-acid
CC (carboxylic acids up to six carbons in length) (PubMed:21562561,
CC PubMed:24443527). {ECO:0000269|PubMed:21562561,
CC ECO:0000269|PubMed:24443527}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-(methylsulfanyl)propanoate + ATP + CoA = 3-
CC (methylsulfanyl)propanoyl-CoA + AMP + diphosphate;
CC Xref=Rhea:RHEA:43052, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:49016, ChEBI:CHEBI:57287, ChEBI:CHEBI:82815,
CC ChEBI:CHEBI:456215; EC=6.2.1.44;
CC Evidence={ECO:0000269|PubMed:24443527};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q5SKN9};
CC -!- ACTIVITY REGULATION: Activated by LiCl and NH(4)Cl. Inhibited by
CC dimethylsulfoniopropionate (DMSP). MMPA concentrations above 2 mM
CC relieve the DMSP inhibition and 80% of activity is regained at an MMPA
CC concentration of 8 mM. {ECO:0000269|PubMed:24443527}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.02 mM for CoA(with MMPA) {ECO:0000269|PubMed:24443527};
CC KM=0.08 mM for CoA (with butyrate) {ECO:0000269|PubMed:24443527};
CC KM=0.03 mM for ATP(with MMPA) {ECO:0000269|PubMed:24443527};
CC KM=0.07 mM for MMPA {ECO:0000269|PubMed:24443527};
CC KM=0.08 mM for ATP (with butyrate) {ECO:0000269|PubMed:24443527};
CC KM=0.12 mM for butyrate {ECO:0000269|PubMed:24443527};
CC KM=3.11 mM for propionate {ECO:0000269|PubMed:24443527};
CC KM=5.25 mM for acrylate {ECO:0000269|PubMed:24443527};
CC Vmax=15.4 umol/min/mg enzyme with MMPA as substrate
CC {ECO:0000269|PubMed:24443527};
CC Vmax=15.4 umol/min/mg enzyme with CoA as substrate (with MMPA)
CC {ECO:0000269|PubMed:24443527};
CC Vmax=7.6 umol/min/mg enzyme with ATP as substrate (with MMPA)
CC {ECO:0000269|PubMed:24443527};
CC Vmax=7.4 umol/min/mg enzyme with butyrate as substrate
CC {ECO:0000269|PubMed:24443527};
CC Vmax=3.8 umol/min/mg enzyme with propionate as substrate
CC {ECO:0000269|PubMed:24443527};
CC Vmax=3.8 umol/min/mg enzyme with ATP as substrate (with butyrate)
CC {ECO:0000269|PubMed:24443527};
CC Vmax=3.6 umol/min/mg enzyme with CoA as substrate (with butyrate)
CC {ECO:0000269|PubMed:24443527};
CC Vmax=1 umol/min/mg enzyme with acrylate as substrate
CC {ECO:0000269|PubMed:24443527};
CC Note=kcat is 14.9 sec(-1) for ligase activity with MMPA as substrate.
CC kcat is 7.2 sec(-1) for ligase activity with butyrate as substrate.
CC kcat is 3.7 sec(-1) for ligase activity with propionate as substrate.
CC kcat is 1 sec(-1) for ligase activity with acrylate as substrate.
CC {ECO:0000269|PubMed:24443527};
CC pH dependence:
CC Optimum pH is between 7.5. {ECO:0000269|PubMed:24443527};
CC -!- PATHWAY: Lipid metabolism; fatty acid metabolism.
CC {ECO:0000303|PubMed:21562561}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:24443527}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene show a delayed growth on
CC methylmercaptopropionate (MMPA). {ECO:0000269|PubMed:21562561}.
CC -!- SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.
CC {ECO:0000305}.
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DR EMBL; CP000031; AAV95316.1; -; Genomic_DNA.
DR RefSeq; WP_011047771.1; NC_003911.12.
DR AlphaFoldDB; Q5LRT0; -.
DR SMR; Q5LRT0; -.
DR STRING; 246200.SPO2045; -.
DR EnsemblBacteria; AAV95316; AAV95316; SPO2045.
DR KEGG; sil:SPO2045; -.
DR eggNOG; COG0318; Bacteria.
DR HOGENOM; CLU_000022_59_5_5; -.
DR OMA; YNVPIVQ; -.
DR OrthoDB; 377638at2; -.
DR BioCyc; MetaCyc:MON-16783; -.
DR BRENDA; 6.2.1.44; 8123.
DR UniPathway; UPA00199; -.
DR Proteomes; UP000001023; Chromosome.
DR GO; GO:0016878; F:acid-thiol ligase activity; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006631; P:fatty acid metabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.30.300.30; -; 1.
DR Gene3D; 3.40.50.12780; -; 1.
DR InterPro; IPR025110; AMP-bd_C.
DR InterPro; IPR045851; AMP-bd_C_sf.
DR InterPro; IPR020845; AMP-binding_CS.
DR InterPro; IPR000873; AMP-dep_Synth/Lig.
DR InterPro; IPR042099; ANL_N_sf.
DR Pfam; PF00501; AMP-binding; 1.
DR Pfam; PF13193; AMP-binding_C; 1.
DR PROSITE; PS00455; AMP_BINDING; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Fatty acid metabolism; Ligase; Lipid metabolism; Magnesium;
KW Metal-binding; Nucleotide-binding; Reference proteome.
FT CHAIN 1..539
FT /note="3-methylmercaptopropionyl-CoA ligase"
FT /id="PRO_0000431553"
FT BINDING 185
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q5SKN9"
FT BINDING 235
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q5SKN9"
FT BINDING 330
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q5SKN9"
FT BINDING 417
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q5SKN9"
FT BINDING 434
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q5SKN9"
FT BINDING 438
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q5SKN9"
FT BINDING 443
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q5SKN9"
SQ SEQUENCE 539 AA; 59066 MW; CBD81A5B71803D77 CRC64;
MLGQMMYQPL LISSLIDHAA RYHGEAQIWS VSTEGGVEET NWAGIADNAR RLGSVLTDAG
LAPQSRVATL AWNNRRHLEI YYGVSGAGFV LHTINPRLFP EQLVYILNHA EDRILFFDAT
FLPLVEGIRP HLTTVERLVL MGPRDEAAAA RIEGLEFYDE FVATGDAGFD WPDLDERTAS
SLCYTSGTTG NPKGVLYSHR STVLHSFGSN TRDCIGFSAR DVVMPVVPMF HVNAWGTPYA
CAMSGSCMVL PGPDLHGEAL VGLIDRYRVT IALGVPTIWQ GLLATARAKG STLESLTRTV
IGGAACPPSM IAEFRDRYGV DTVHAWGMSE MSPLGTTNQP LAKHGALPIE AQHKLRENQG
RPPYGVELKI VDDDGNTLPN DGQTQGDLMV RGHWVLDSYF QLQDQPILSD GWFATGDVAT
LDRDGYMTIR DRSKDIIKSG GEWISSVELE NIAVAHPKLA TAAVIGVPHP KWDERPLLVA
VKAEGETPDE AELLAFFDGK IAKWQVPDRV VFVEALPLNA TGKVLKRTLR EQFRDVLTG
