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P16099

- DHTM_METME

UniProt

P16099 - DHTM_METME

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Protein
Trimethylamine dehydrogenase
Gene
tmd
Organism
Methylophilus methylotrophus (Bacterium W3A1)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

Trimethylamine + H2O + electron-transferring flavoprotein = dimethylamine + formaldehyde + reduced electron-transferring flavoprotein.

Cofactori

Binds 1 FMN covalently per subunit.
Binds 1 4Fe-4S cluster per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei104 – 1041FMN
Active sitei175 – 1751Proton donor By similarity
Binding sitei223 – 2231FMN
Binding sitei268 – 2681FMN
Binding sitei323 – 3231FMN
Metal bindingi346 – 3461Iron-sulfur (4Fe-4S)
Metal bindingi349 – 3491Iron-sulfur (4Fe-4S)
Metal bindingi352 – 3521Iron-sulfur (4Fe-4S)
Metal bindingi365 – 3651Iron-sulfur (4Fe-4S)

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi392 – 42130ADP By similarity
Add
BLAST

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  2. FMN binding Source: InterPro
  3. metal ion binding Source: UniProtKB-KW
  4. trimethylamine dehydrogenase activity Source: UniProtKB-EC
Complete GO annotation...

GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    4Fe-4S, Flavoprotein, FMN, Iron, Iron-sulfur, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13313.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Trimethylamine dehydrogenase (EC:1.5.8.2)
    Short name:
    TMADh
    Gene namesi
    Name:tmd
    OrganismiMethylophilus methylotrophus (Bacterium W3A1)
    Taxonomic identifieri17 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaMethylophilalesMethylophilaceaeMethylophilus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed
    Chaini2 – 730729Trimethylamine dehydrogenase
    PRO_0000194472Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei31 – 311S-6-FMN cysteine

    Interactioni

    Subunit structurei

    Homodimer.

    Structurei

    Secondary structure

    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi5 – 117
    Beta strandi14 – 163
    Beta strandi19 – 279
    Turni35 – 373
    Helixi39 – 5113
    Beta strandi55 – 6511
    Helixi81 – 9515
    Turni96 – 983
    Beta strandi100 – 1067
    Helixi109 – 1113
    Turni115 – 1173
    Beta strandi122 – 1254
    Beta strandi130 – 1323
    Helixi142 – 16120
    Beta strandi165 – 1717
    Helixi176 – 1816
    Turni183 – 1853
    Beta strandi193 – 1953
    Helixi196 – 1994
    Helixi201 – 21414
    Turni215 – 2173
    Beta strandi218 – 22710
    Turni237 – 2393
    Helixi240 – 2489
    Helixi249 – 2513
    Beta strandi253 – 2597
    Helixi265 – 2673
    Turni272 – 2743
    Turni277 – 2804
    Helixi281 – 2844
    Turni285 – 2906
    Beta strandi295 – 2973
    Helixi304 – 3129
    Beta strandi317 – 3226
    Helixi323 – 3275
    Helixi331 – 3366
    Helixi340 – 3423
    Helixi351 – 3588
    Beta strandi359 – 3613
    Turni369 – 3735
    Helixi374 – 3774
    Beta strandi392 – 3965
    Helixi400 – 41112
    Beta strandi415 – 4195
    Beta strandi421 – 4244
    Turni425 – 4284
    Helixi429 – 4324
    Helixi439 – 4424
    Helixi443 – 45816
    Beta strandi463 – 4653
    Helixi473 – 4775
    Beta strandi482 – 4865
    Beta strandi490 – 4923
    Turni499 – 5013
    Helixi518 – 5236
    Beta strandi530 – 5367
    Helixi542 – 55211
    Beta strandi556 – 5638
    Helixi567 – 5715
    Helixi575 – 58410
    Beta strandi588 – 5903
    Beta strandi592 – 5998
    Beta strandi602 – 6076
    Beta strandi632 – 6354
    Beta strandi637 – 6437
    Beta strandi645 – 6473
    Helixi650 – 6578
    Helixi659 – 6613
    Helixi663 – 6653
    Beta strandi669 – 6724
    Helixi674 – 6763
    Helixi682 – 69413
    Turni695 – 6973

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DJNX-ray2.20A/B2-730[»]
    1DJQX-ray2.20A/B2-730[»]
    1O94X-ray2.00A/B2-730[»]
    1O95X-ray3.70A/B2-730[»]
    2TMDX-ray2.40A/B2-730[»]
    ProteinModelPortaliP16099.
    SMRiP16099. Positions 2-730.

    Miscellaneous databases

    EvolutionaryTraceiP16099.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni170 – 1734Substrate-binding By similarity

    Sequence similaritiesi

    In the N-terminal section; belongs to the NADH:flavin oxidoreductase/NADH oxidase family.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    3.40.50.720. 2 hits.
    InterProiIPR013785. Aldolase_TIM.
    IPR013027. FAD_pyr_nucl-diS_OxRdtase.
    IPR016040. NAD(P)-bd_dom.
    IPR001155. OxRdtase_FMN_N.
    IPR023753. Pyr_nucl-diS_OxRdtase_FAD/NAD.
    [Graphical view]
    PfamiPF00724. Oxidored_FMN. 1 hit.
    PF07992. Pyr_redox_2. 1 hit.
    [Graphical view]
    PRINTSiPR00368. FADPNR.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P16099-1 [UniParc]FASTAAdd to Basket

    « Hide

    MARDPKHDIL FEPIQIGPKT LRNRFYQVPH CIGAGSDKPG FQSAHRSVKA    50
    EGGWAALNTE YCSINPESDD THRLSARIWD EGDVRNLKAM TDEVHKYGAL 100
    AGVELWYGGA HAPNMESRAT PRGPSQYASE FETLSYCKEM DLSDIAQVQQ 150
    FYVDAAKRSR DAGFDIVYVY GAHSYLPLQF LNPYYNKRTD KYGGSLENRA 200
    RFWLETLEKV KHAVGSDCAI ATRFGVDTVY GPGQIEAEVD GQKFVEMADS 250
    LVDMWDITIG DIAEWGEDAG PSRFYQQGHT IPWVKLVKQV SKKPVLGVGR 300
    YTDPEKMIEI VTKGYADIIG CARPSIADPF LPQKVEQGRY DDIRVCIGCN 350
    VCISRWEIGG PPMICTQNAT AGEEYRRGWH PEKFRQTKNK DSVLIVGAGP 400
    SGSEAARVLM ESGYTVHLTD TAEKIGGHLN QVAALPGLGE WSYHRDYRET 450
    QITKLLKKNK ESQLALGQKP MTADDVLQYG ADKVIIATGA RWNTDGTNCL 500
    THDPIPGADA SLPDQLTPEQ VMDGKKKIGK RVVILNADTY FMAPSLAEKL 550
    ATAGHEVTIV SGVHLANYMH FTLEYPNMMR RLHELHVEEL GDHFCSRIEP 600
    GRMEIYNIWG DGSKRTYRGP GVSPRDANTS HRWIEFDSLV LVTGRHSECT 650
    LWNELKARES EWAENDIKGI YLIGDAEAPR LIADATFTGH RVAREIEEAN 700
    PQIAIPYKRE TIAWGTPHMP GGNFKIEYKV 730
    Length:730
    Mass (Da):81,629
    Last modified:January 23, 2007 - v3
    Checksum:iE5D5D1A91E2667EF
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X68079 Genomic DNA. Translation: CAA48212.1.
    PIRiS24124.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X68079 Genomic DNA. Translation: CAA48212.1 .
    PIRi S24124.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1DJN X-ray 2.20 A/B 2-730 [» ]
    1DJQ X-ray 2.20 A/B 2-730 [» ]
    1O94 X-ray 2.00 A/B 2-730 [» ]
    1O95 X-ray 3.70 A/B 2-730 [» ]
    2TMD X-ray 2.40 A/B 2-730 [» ]
    ProteinModelPortali P16099.
    SMRi P16099. Positions 2-730.
    ModBasei Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    BioCyci MetaCyc:MONOMER-13313.

    Miscellaneous databases

    EvolutionaryTracei P16099.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    3.40.50.720. 2 hits.
    InterProi IPR013785. Aldolase_TIM.
    IPR013027. FAD_pyr_nucl-diS_OxRdtase.
    IPR016040. NAD(P)-bd_dom.
    IPR001155. OxRdtase_FMN_N.
    IPR023753. Pyr_nucl-diS_OxRdtase_FAD/NAD.
    [Graphical view ]
    Pfami PF00724. Oxidored_FMN. 1 hit.
    PF07992. Pyr_redox_2. 1 hit.
    [Graphical view ]
    PRINTSi PR00368. FADPNR.
    ProtoNeti Search...

    Publicationsi

    1. "Trimethylamine dehydrogenase of bacterium W3A1. Molecular cloning, sequence determination and over-expression of the gene."
      Boyd G., Mathews F.S., Packman L.C., Scrutton N.S.
      FEBS Lett. 308:271-276(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Amino acid sequence of a cofactor peptide from trimethylamine dehydrogenase."
      Kenney W.C., McIntire W., Steenkamp D.J., Benisek W.F.
      FEBS Lett. 85:137-140(1978) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 32-43.
    3. "Correlation of X-ray deduced and experimental amino acid sequences of trimethylamine dehydrogenase."
      Barber M.J., Neame P.J., Lim L.W., White S., Mathews F.S.
      J. Biol. Chem. 267:6611-6619(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), PARTIAL PROTEIN SEQUENCE.
    4. "Extensive conformational sampling in a ternary electron transfer complex."
      Leys D., Basran J., Talfournier F., Sutcliffe M.J., Scrutton N.S.
      Nat. Struct. Biol. 10:219-225(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH ETF.

    Entry informationi

    Entry nameiDHTM_METME
    AccessioniPrimary (citable) accession number: P16099
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1990
    Last sequence update: January 23, 2007
    Last modified: July 9, 2014
    This is version 93 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

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

    External Data

    Dasty 3

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