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Protein

Dimethylsulfonioproprionate demethylase DmdA

Gene

dmdA

Organism
Pelagibacter ubique (strain HTCC1062)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Major contributor to the demethylation of dimethlysulfonioproprionate (DMSP). Demethylates DMSP to methyl-mercaptopropionate (MMPA).1 Publication

Catalytic activityi

S,S-dimethyl-beta-propiothetin + tetrahydrofolate = 3-(methylthio)propanoate + 5-methyltetrahydrofolate.1 Publication

Enzyme regulationi

Non-competitively inhibited by MMPA, weakly inhibited by substrate analogs dimethylsulfoniobutanoate and dimethylsulfoniopentanoate. It is used as an intracellular osmolyte.1 Publication

Kineticsi

Upon expression and purification from E.coli.

  1. KM=0.29 mM for tetrahydrafolate1 Publication
  2. KM=13.2 mM for dimethlysulfonioproprionate1 Publication
  1. Vmax=11.7 µmol/min/mg enzyme1 Publication

pH dependencei

Optimum pH is 7.0-8.0.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei122 – 1221Tetrahydrofolate1 Publication
Binding sitei204 – 2041Tetrahydrofolate1 Publication
Binding sitei206 – 2061Tetrahydrofolate1 Publication

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Enzyme and pathway databases

BioCyciCPEL335992:GH3Z-246-MONOMER.
BRENDAi2.1.1.269. 10071.

Names & Taxonomyi

Protein namesi
Recommended name:
Dimethylsulfonioproprionate demethylase DmdA (EC:2.1.1.269)
Gene namesi
Name:dmdA
Ordered Locus Names:SAR11_0246
OrganismiPelagibacter ubique (strain HTCC1062)
Taxonomic identifieri335992 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaPelagibacteralesPelagibacteraceaeCandidatus Pelagibacter
Proteomesi
  • UP000002528 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 369369Dimethylsulfonioproprionate demethylase DmdAPRO_0000420616Add
BLAST

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

STRINGi335992.SAR11_0246.

Structurei

Secondary structure

1
369
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi10 – 134Combined sources
Helixi18 – 214Combined sources
Turni22 – 254Combined sources
Beta strandi28 – 325Combined sources
Beta strandi35 – 428Combined sources
Helixi44 – 5310Combined sources
Beta strandi56 – 594Combined sources
Beta strandi65 – 706Combined sources
Helixi73 – 808Combined sources
Beta strandi81 – 833Combined sources
Beta strandi92 – 954Combined sources
Beta strandi105 – 1073Combined sources
Beta strandi110 – 1156Combined sources
Beta strandi118 – 1225Combined sources
Helixi128 – 13912Combined sources
Beta strandi144 – 1463Combined sources
Beta strandi151 – 1577Combined sources
Helixi160 – 1689Combined sources
Helixi170 – 1745Combined sources
Beta strandi179 – 1857Combined sources
Beta strandi188 – 1947Combined sources
Beta strandi197 – 2004Combined sources
Beta strandi202 – 2076Combined sources
Helixi210 – 22314Combined sources
Helixi225 – 2273Combined sources
Beta strandi230 – 2323Combined sources
Helixi236 – 2416Combined sources
Turni247 – 2493Combined sources
Helixi257 – 2593Combined sources
Helixi263 – 2653Combined sources
Beta strandi269 – 2713Combined sources
Helixi277 – 28610Combined sources
Beta strandi289 – 30012Combined sources
Beta strandi308 – 3114Combined sources
Beta strandi317 – 32711Combined sources
Turni328 – 3314Combined sources
Beta strandi332 – 3409Combined sources
Helixi341 – 3433Combined sources
Beta strandi349 – 3546Combined sources
Beta strandi357 – 3648Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3TFHX-ray2.10A/B1-369[»]
3TFIX-ray1.60A/B1-369[»]
3TFJX-ray1.60A/B1-369[»]
ProteinModelPortaliQ4FP21.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the GcvT family. DmdA subfamily.Curated

Phylogenomic databases

eggNOGiENOG4107TNW. Bacteria.
ENOG410XPN6. LUCA.
HOGENOMiHOG000253737.
KOiK17486.
OMAiGGMLNDP.
OrthoDBiEOG66XBB1.

Family and domain databases

Gene3Di2.40.30.110. 1 hit.
3.30.1360.120. 2 hits.
InterProiIPR028896. GCST/DmdA.
IPR013977. GCV_T_C.
IPR006222. GCV_T_N.
IPR029043. GcvT/YgfZ_C.
IPR027266. TrmE/GcvT_dom1.
[Graphical view]
PfamiPF01571. GCV_T. 1 hit.
PF08669. GCV_T_C. 1 hit.
[Graphical view]
PIRSFiPIRSF006487. GcvT. 1 hit.
SUPFAMiSSF101790. SSF101790. 1 hit.

Sequencei

Sequence statusi: Complete.

Q4FP21-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKNFSIAKSR RLRSTPYTSR IEKQGVTAYT IYNHMLLPAA FGSIEDSYKH
60 70 80 90 100
LKEHVQIWDV AAERQVEISG KDSAELVQLM TCRDLSKSKI GRCYYCPIID
110 120 130 140 150
ENGNLVNDPV VLKLDENKWW ISIADSDVIF FAKGLASGHK FDVKIVEPVV
160 170 180 190 200
DIMAIQGPKS FALMEKVFGK KITELKFFGF DYFDFEGTKH LIARSGWSKQ
210 220 230 240 250
GGYEVYVENT QSGQKLYDHL FEVGKEFNVG PGCPNLIERI ESALLSYGND
260 270 280 290 300
FDNNDNPFEC GFDQYVSLDS DINFLGKEKL KEIKLKGPQK KLRGVKIDIK
310 320 330 340 350
EISLTGSKNI YDENNNVIGE LRSACYSPHF QKVIGIAMIK KSHWEASQGF
360
KIQINDNTIN GNVCDLPFI
Length:369
Mass (Da):41,832
Last modified:August 30, 2005 - v1
Checksum:iDF1612F05044393B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000084 Genomic DNA. Translation: AAZ21068.1.
RefSeqiWP_011281570.1. NC_007205.1.

Genome annotation databases

EnsemblBacteriaiAAZ21068; AAZ21068; SAR11_0246.
KEGGipub:SAR11_0246.
PATRICi31989949. VBICanPel5618_0245.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000084 Genomic DNA. Translation: AAZ21068.1.
RefSeqiWP_011281570.1. NC_007205.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3TFHX-ray2.10A/B1-369[»]
3TFIX-ray1.60A/B1-369[»]
3TFJX-ray1.60A/B1-369[»]
ProteinModelPortaliQ4FP21.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi335992.SAR11_0246.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAZ21068; AAZ21068; SAR11_0246.
KEGGipub:SAR11_0246.
PATRICi31989949. VBICanPel5618_0245.

Phylogenomic databases

eggNOGiENOG4107TNW. Bacteria.
ENOG410XPN6. LUCA.
HOGENOMiHOG000253737.
KOiK17486.
OMAiGGMLNDP.
OrthoDBiEOG66XBB1.

Enzyme and pathway databases

BioCyciCPEL335992:GH3Z-246-MONOMER.
BRENDAi2.1.1.269. 10071.

Family and domain databases

Gene3Di2.40.30.110. 1 hit.
3.30.1360.120. 2 hits.
InterProiIPR028896. GCST/DmdA.
IPR013977. GCV_T_C.
IPR006222. GCV_T_N.
IPR029043. GcvT/YgfZ_C.
IPR027266. TrmE/GcvT_dom1.
[Graphical view]
PfamiPF01571. GCV_T. 1 hit.
PF08669. GCV_T_C. 1 hit.
[Graphical view]
PIRSFiPIRSF006487. GcvT. 1 hit.
SUPFAMiSSF101790. SSF101790. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HTCC1062.
  2. Cited for: FUNCTION.
    Strain: HTCC1062.
  3. "Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi."
    Reisch C.R., Moran M.A., Whitman W.B.
    J. Bacteriol. 190:8018-8024(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC ACTIVITY, SUBUNIT, ENZYME REGULATION.
    Strain: HTCC1062.
  4. "Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique."
    Schuller D.J., Reisch C.R., Moran M.A., Whitman W.B., Lanzilotta W.N.
    Protein Sci. 21:289-298(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) WITH AND WITHOUT SUBSTRATE, SUBUNIT.
    Strain: HTCC1062.

Entry informationi

Entry nameiDMDA_PELUB
AccessioniPrimary (citable) accession number: Q4FP21
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 9, 2013
Last sequence update: August 30, 2005
Last modified: December 9, 2015
This is version 86 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

DMSP is used as an intracellular osmolyte, predator deterrent and antioxidant.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.