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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)DescriptionActionsGraphical viewLength
Binding sitei122Tetrahydrofolate1 Publication1
Binding sitei204Tetrahydrofolate1 Publication1
Binding sitei206Tetrahydrofolate1 Publication1

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Enzyme and pathway databases

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)DescriptionActionsGraphical viewLength
ChainiPRO_00004206161 – 369Dimethylsulfonioproprionate demethylase DmdAAdd BLAST369

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

STRINGi335992.SAR11_0246.

Structurei

Secondary structure

1369
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi10 – 13Combined sources4
Helixi18 – 21Combined sources4
Turni22 – 25Combined sources4
Beta strandi28 – 32Combined sources5
Beta strandi35 – 42Combined sources8
Helixi44 – 53Combined sources10
Beta strandi56 – 59Combined sources4
Beta strandi65 – 70Combined sources6
Helixi73 – 80Combined sources8
Beta strandi81 – 83Combined sources3
Beta strandi92 – 95Combined sources4
Beta strandi105 – 107Combined sources3
Beta strandi110 – 115Combined sources6
Beta strandi118 – 122Combined sources5
Helixi128 – 139Combined sources12
Beta strandi144 – 146Combined sources3
Beta strandi151 – 157Combined sources7
Helixi160 – 168Combined sources9
Helixi170 – 174Combined sources5
Beta strandi179 – 185Combined sources7
Beta strandi188 – 194Combined sources7
Beta strandi197 – 200Combined sources4
Beta strandi202 – 207Combined sources6
Helixi210 – 223Combined sources14
Helixi225 – 227Combined sources3
Beta strandi230 – 232Combined sources3
Helixi236 – 241Combined sources6
Turni247 – 249Combined sources3
Helixi257 – 259Combined sources3
Helixi263 – 265Combined sources3
Beta strandi269 – 271Combined sources3
Helixi277 – 286Combined sources10
Beta strandi289 – 300Combined sources12
Beta strandi308 – 311Combined sources4
Beta strandi317 – 327Combined sources11
Turni328 – 331Combined sources4
Beta strandi332 – 340Combined sources9
Helixi341 – 343Combined sources3
Beta strandi349 – 354Combined sources6
Beta strandi357 – 364Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3TFHX-ray2.10A/B1-369[»]
3TFIX-ray1.60A/B1-369[»]
3TFJX-ray1.60A/B1-369[»]
ProteinModelPortaliQ4FP21.
SMRiQ4FP21.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the GcvT family. DmdA subfamily.Curated

Phylogenomic databases

eggNOGiENOG4107TNW. Bacteria.
ENOG410XPN6. LUCA.
HOGENOMiHOG000253737.
KOiK17486.
OMAiWDVACER.
OrthoDBiPOG091H04FV.

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3TFHX-ray2.10A/B1-369[»]
3TFIX-ray1.60A/B1-369[»]
3TFJX-ray1.60A/B1-369[»]
ProteinModelPortaliQ4FP21.
SMRiQ4FP21.
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.
OMAiWDVACER.
OrthoDBiPOG091H04FV.

Enzyme and pathway databases

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...

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: November 2, 2016
This is version 88 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.