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Protein

Trimethylamine dehydrogenase

Gene

tmd

Organism
Methylophilus methylotrophus (Bacterium W3A1)
Status
Reviewed-Annotation score: 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)DescriptionActionsGraphical viewLength
Binding sitei104FMN1
Active sitei175Proton donorBy similarity1
Binding sitei223FMN1
Binding sitei268FMN1
Binding sitei323FMN1
Metal bindingi346Iron-sulfur (4Fe-4S)1
Metal bindingi349Iron-sulfur (4Fe-4S)1
Metal bindingi352Iron-sulfur (4Fe-4S)1
Metal bindingi365Iron-sulfur (4Fe-4S)1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi392 – 421ADPBy similarityAdd BLAST30

GO - Molecular functioni

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)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved
ChainiPRO_00001944722 – 730Trimethylamine dehydrogenaseAdd BLAST729

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei31S-6-FMN cysteine1

Interactioni

Subunit structurei

Homodimer.1 Publication

Structurei

Secondary structure

1730
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 11Combined sources7
Beta strandi14 – 16Combined sources3
Beta strandi19 – 27Combined sources9
Turni35 – 37Combined sources3
Helixi39 – 51Combined sources13
Beta strandi55 – 65Combined sources11
Helixi81 – 95Combined sources15
Turni96 – 98Combined sources3
Beta strandi100 – 106Combined sources7
Helixi109 – 111Combined sources3
Turni115 – 117Combined sources3
Beta strandi122 – 125Combined sources4
Beta strandi130 – 132Combined sources3
Helixi142 – 161Combined sources20
Beta strandi165 – 171Combined sources7
Helixi176 – 181Combined sources6
Turni183 – 185Combined sources3
Beta strandi193 – 195Combined sources3
Helixi196 – 199Combined sources4
Helixi201 – 214Combined sources14
Turni215 – 217Combined sources3
Beta strandi218 – 227Combined sources10
Turni237 – 239Combined sources3
Helixi240 – 248Combined sources9
Helixi249 – 251Combined sources3
Beta strandi253 – 259Combined sources7
Helixi265 – 267Combined sources3
Turni272 – 274Combined sources3
Turni277 – 280Combined sources4
Helixi281 – 284Combined sources4
Turni285 – 290Combined sources6
Beta strandi295 – 297Combined sources3
Helixi304 – 312Combined sources9
Beta strandi317 – 322Combined sources6
Helixi323 – 327Combined sources5
Helixi331 – 336Combined sources6
Helixi340 – 342Combined sources3
Helixi351 – 358Combined sources8
Beta strandi359 – 361Combined sources3
Turni369 – 373Combined sources5
Helixi374 – 377Combined sources4
Beta strandi392 – 396Combined sources5
Helixi400 – 411Combined sources12
Beta strandi415 – 419Combined sources5
Beta strandi421 – 424Combined sources4
Turni425 – 428Combined sources4
Helixi429 – 432Combined sources4
Helixi439 – 442Combined sources4
Helixi443 – 458Combined sources16
Beta strandi463 – 465Combined sources3
Helixi473 – 477Combined sources5
Beta strandi482 – 486Combined sources5
Beta strandi490 – 492Combined sources3
Turni499 – 501Combined sources3
Helixi518 – 523Combined sources6
Beta strandi530 – 536Combined sources7
Helixi542 – 552Combined sources11
Beta strandi556 – 563Combined sources8
Helixi567 – 571Combined sources5
Helixi575 – 584Combined sources10
Beta strandi588 – 590Combined sources3
Beta strandi592 – 599Combined sources8
Beta strandi602 – 607Combined sources6
Beta strandi632 – 635Combined sources4
Beta strandi637 – 643Combined sources7
Beta strandi645 – 647Combined sources3
Helixi650 – 657Combined sources8
Helixi659 – 661Combined sources3
Helixi663 – 665Combined sources3
Beta strandi669 – 672Combined sources4
Helixi674 – 676Combined sources3
Helixi682 – 694Combined sources13
Turni695 – 697Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP16099.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni170 – 173Substrate-bindingBy similarity4

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.
3.50.50.60. 4 hits.
InterProiIPR013785. Aldolase_TIM.
IPR023753. FAD/NAD-binding_dom.
IPR001155. OxRdtase_FMN_N.
[Graphical view]
PfamiPF00724. Oxidored_FMN. 1 hit.
PF07992. Pyr_redox_2. 1 hit.
[Graphical view]
SUPFAMiSSF51905. SSF51905. 1 hit.

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.
PIRiS24124.

3D structure databases

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

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-13313.

Miscellaneous databases

EvolutionaryTraceiP16099.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.50.50.60. 4 hits.
InterProiIPR013785. Aldolase_TIM.
IPR023753. FAD/NAD-binding_dom.
IPR001155. OxRdtase_FMN_N.
[Graphical view]
PfamiPF00724. Oxidored_FMN. 1 hit.
PF07992. Pyr_redox_2. 1 hit.
[Graphical view]
SUPFAMiSSF51905. SSF51905. 1 hit.
ProtoNetiSearch...

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 30, 2016
This is version 103 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

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.