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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

Protein has several cofactor binding sites:
  • FMNNote: Binds 1 FMN covalently per subunit.
  • [4Fe-4S] clusterNote: Binds 1 [4Fe-4S] cluster per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei104 – 1041FMN
Active sitei175 – 1751Proton donorBy 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 – 42130ADPBy similarityAdd
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...

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 dehydrogenasePRO_0000194472Add
BLAST

Amino acid modifications

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

Interactioni

Subunit structurei

Homodimer.1 Publication

Structurei

Secondary structure

1
730
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 117Combined sources
Beta strandi14 – 163Combined sources
Beta strandi19 – 279Combined sources
Turni35 – 373Combined sources
Helixi39 – 5113Combined sources
Beta strandi55 – 6511Combined sources
Helixi81 – 9515Combined sources
Turni96 – 983Combined sources
Beta strandi100 – 1067Combined sources
Helixi109 – 1113Combined sources
Turni115 – 1173Combined sources
Beta strandi122 – 1254Combined sources
Beta strandi130 – 1323Combined sources
Helixi142 – 16120Combined sources
Beta strandi165 – 1717Combined sources
Helixi176 – 1816Combined sources
Turni183 – 1853Combined sources
Beta strandi193 – 1953Combined sources
Helixi196 – 1994Combined sources
Helixi201 – 21414Combined sources
Turni215 – 2173Combined sources
Beta strandi218 – 22710Combined sources
Turni237 – 2393Combined sources
Helixi240 – 2489Combined sources
Helixi249 – 2513Combined sources
Beta strandi253 – 2597Combined sources
Helixi265 – 2673Combined sources
Turni272 – 2743Combined sources
Turni277 – 2804Combined sources
Helixi281 – 2844Combined sources
Turni285 – 2906Combined sources
Beta strandi295 – 2973Combined sources
Helixi304 – 3129Combined sources
Beta strandi317 – 3226Combined sources
Helixi323 – 3275Combined sources
Helixi331 – 3366Combined sources
Helixi340 – 3423Combined sources
Helixi351 – 3588Combined sources
Beta strandi359 – 3613Combined sources
Turni369 – 3735Combined sources
Helixi374 – 3774Combined sources
Beta strandi392 – 3965Combined sources
Helixi400 – 41112Combined sources
Beta strandi415 – 4195Combined sources
Beta strandi421 – 4244Combined sources
Turni425 – 4284Combined sources
Helixi429 – 4324Combined sources
Helixi439 – 4424Combined sources
Helixi443 – 45816Combined sources
Beta strandi463 – 4653Combined sources
Helixi473 – 4775Combined sources
Beta strandi482 – 4865Combined sources
Beta strandi490 – 4923Combined sources
Turni499 – 5013Combined sources
Helixi518 – 5236Combined sources
Beta strandi530 – 5367Combined sources
Helixi542 – 55211Combined sources
Beta strandi556 – 5638Combined sources
Helixi567 – 5715Combined sources
Helixi575 – 58410Combined sources
Beta strandi588 – 5903Combined sources
Beta strandi592 – 5998Combined sources
Beta strandi602 – 6076Combined sources
Beta strandi632 – 6354Combined sources
Beta strandi637 – 6437Combined sources
Beta strandi645 – 6473Combined sources
Helixi650 – 6578Combined sources
Helixi659 – 6613Combined sources
Helixi663 – 6653Combined sources
Beta strandi669 – 6724Combined sources
Helixi674 – 6763Combined sources
Helixi682 – 69413Combined sources
Turni695 – 6973Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP16099.

Family & Domainsi

Region

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

Sequence similaritiesi

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

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

        10         20         30         40         50
MARDPKHDIL FEPIQIGPKT LRNRFYQVPH CIGAGSDKPG FQSAHRSVKA
60 70 80 90 100
EGGWAALNTE YCSINPESDD THRLSARIWD EGDVRNLKAM TDEVHKYGAL
110 120 130 140 150
AGVELWYGGA HAPNMESRAT PRGPSQYASE FETLSYCKEM DLSDIAQVQQ
160 170 180 190 200
FYVDAAKRSR DAGFDIVYVY GAHSYLPLQF LNPYYNKRTD KYGGSLENRA
210 220 230 240 250
RFWLETLEKV KHAVGSDCAI ATRFGVDTVY GPGQIEAEVD GQKFVEMADS
260 270 280 290 300
LVDMWDITIG DIAEWGEDAG PSRFYQQGHT IPWVKLVKQV SKKPVLGVGR
310 320 330 340 350
YTDPEKMIEI VTKGYADIIG CARPSIADPF LPQKVEQGRY DDIRVCIGCN
360 370 380 390 400
VCISRWEIGG PPMICTQNAT AGEEYRRGWH PEKFRQTKNK DSVLIVGAGP
410 420 430 440 450
SGSEAARVLM ESGYTVHLTD TAEKIGGHLN QVAALPGLGE WSYHRDYRET
460 470 480 490 500
QITKLLKKNK ESQLALGQKP MTADDVLQYG ADKVIIATGA RWNTDGTNCL
510 520 530 540 550
THDPIPGADA SLPDQLTPEQ VMDGKKKIGK RVVILNADTY FMAPSLAEKL
560 570 580 590 600
ATAGHEVTIV SGVHLANYMH FTLEYPNMMR RLHELHVEEL GDHFCSRIEP
610 620 630 640 650
GRMEIYNIWG DGSKRTYRGP GVSPRDANTS HRWIEFDSLV LVTGRHSECT
660 670 680 690 700
LWNELKARES EWAENDIKGI YLIGDAEAPR LIADATFTGH RVAREIEEAN
710 720 730
PQIAIPYKRE TIAWGTPHMP GGNFKIEYKV
Length:730
Mass (Da):81,629
Last modified:January 23, 2007 - v3
Checksum:iE5D5D1A91E2667EF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X68079 Genomic DNA. Translation: CAA48212.1.
PIRiS24124.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X68079 Genomic DNA. Translation: CAA48212.1 .
PIRi S24124.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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...
MobiDBi 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: November 26, 2014
This is version 95 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