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107  structures 679  species 1  interaction 2951  sequences 45  architectures

Family: FMO-like (PF00743)

Summary: Flavin-binding monooxygenase-like

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Flavin-containing monooxygenase". More...

Flavin-containing monooxygenase Edit Wikipedia article

flavin-containing monooxygenase
Identifiers
EC number 1.14.13.8
CAS number 37256-73-8
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Flavin-containing monooxygenase FMO
Identifiers
Symbol Flavin_mOase
Pfam PF00743
InterPro IPR000960

The flavin-containing monooxygenase (FMO) protein family consists of a group of enzymes that catalyze chemical reactions via the bound cofactor flavin. These reactions involve oxidation of heteroatoms, particularly nucleophilic atoms such as the nitrogen of amines.[1]

These enzymes metabolise xenobiotics.[2] Using an NADPH cofactor and FAD prosthetic group, these microsomal proteins catalyse the oxygenation of nucleophilic nitrogen, sulphur, phosphorus and selenium atoms in a range of structurally diverse compounds. FMOs have been implicated in the metabolism of a number of pharmaceuticals, pesticides and toxicants. In humans, lack of hepatic FMO-catalysed trimethylamine metabolism results in trimethylaminuria (fish odour syndrome). Five mammalian forms of FMO are now known and have been designated FMO1-FMO5.[3][4][5][6][7]

The best-known such protein is called FMO3 and is mutated in the vast majority of cases of trimethylaminuria, a genetic disease that causes deficiencies in breakdown of trimethylamine and gives the patient a fishy body odor.[8] In yeast, FMO proteins are associated with redox cycling of glutathione to glutathione disulfide, a system that maintains the redox state of the cell and heavily influences the protein folding rates of disulfide bond-containing proteins.[9]

Genes

References

  1. ^ Cashman JR (1995). "Structural and catalytic properties of the mammalian flavin-containing monooxygenase". Chem Res Toxicol 8 (2): 166–81. doi:10.1021/tx00044a001. PMID 7766799. 
  2. ^ Lawton MP, Cashman JR, Cresteil T, Dolphin CT, Elfarra AA, Hines RN, Hodgson E, Kimura T, Ozols J, Phillips IR (1994). "A nomenclature for the mammalian flavin-containing monooxygenase gene family based on amino acid sequence identities". Arch. Biochem. Biophys. 308 (1): 254–257. doi:10.1006/abbi.1994.1035. PMID 8311461. 
  3. ^ Phillips IR, Shephard EA, Ziegler DM, Povey S, Smith RL, Ayesh R, Dolphin C, Palmer CN (1991). "Cloning, primary sequence, and chromosomal mapping of a human flavin-containing monooxygenase (FMO1)". J. Biol. Chem. 266 (19): 12379–12385. PMID 1712018. 
  4. ^ Lawton MP, Hodgson E, Philpot RM, Gasser R, Tynes RE (1990). "The flavin-containing monooxygenase enzymes expressed in rabbit liver and lung are products of related but distinctly different genes". J. Biol. Chem. 265 (10): 5855–5861. PMID 2318837. 
  5. ^ Cashman JR, Gu Q, Lomri N (1992). "Molecular cloning of the flavin-containing monooxygenase (form II) cDNA from adult human liver". Proc. Natl. Acad. Sci. U.S.A. 89 (5): 1685–1689. doi:10.1073/pnas.89.5.1685. PMC 48517. PMID 1542660. 
  6. ^ Dolphin CT, Phillips IR, Shephard EA, Povey S, Smith RL (1992). "Cloning, primary sequence and chromosomal localization of human FMO2, a new member of the flavin-containing mono-oxygenase family". Biochem. J. 287: 261–267. PMC 1133153. PMID 1417778. 
  7. ^ Lawton MP, Philpot RM, Atta-Asafo-Adjei E (1993). "Cloning, sequencing, distribution, and expression in Escherichia coli of flavin-containing monooxygenase 1C1. Evidence for a third gene subfamily in rabbits". J. Biol. Chem. 268 (13): 9681–9689. PMID 8486656. 
  8. ^ Hernandez D, Addou S, Lee D, Orengo C, Shephard EA, Phillips IR (September 2003). "Trimethylaminuria and a humanFMO3 mutation database". Human Mutation 22 (3): 209–13. doi:10.1002/humu.10252. PMID 12938085. 
  9. ^ Suh JK, Poulsen LL, Ziegler DM, Robertus JD (1999). "Yeast flavin-containing monooxygenase generates oxidizing equivalents that control protein folding in the endoplasmic reticulum". Proc. Natl. Acad. Sci. USA 96 (6): 2687–91. doi:10.1073/pnas.96.6.2687. PMC 15830. PMID 10077572. 

External links


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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Flavin-binding monooxygenase-like Provide feedback

This family includes FMO proteins, cyclohexanone mono-oxygenase and a number of different mono-oxygenases.

Literature references

  1. Stehr M, Diekmann H, Smau L, Seth O, Ghisla S, Singh M, Macheroux P; , Trends Biochem Sci 1998;23:56-57.: A hydrophobic sequence motif common to N-hydroxylating enzymes. PUBMED:9538688 EPMC:9538688


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020946

Flavin-containing monooxygenases (FMOs) constitute a family of xenobiotic-metabolising enzymes [PUBMED:8311461]. Using an NADPH cofactor and FAD prosthetic group, these microsomal proteins catalyse the oxygenation of nucleophilic nitrogen, sulphur, phosphorous and selenium atoms in a range of structurally diverse compounds. FMOs have been implicated in the metabolism of a number of pharmaceuticals, pesticides and toxicants. In man, lack of hepatic FMO-catalysed trimethylamine metabolism results in trimethylaminuria (fish odour syndrome). Five mammalian forms of FMO are now known and have been designated FMO1-FMO5 [PUBMED:1712018, PUBMED:2318837, PUBMED:1542660, PUBMED:1417778, PUBMED:8486656]. This is a recent nomenclature based on comparison of amino acid sequences, and has been introduced in an attempt to eliminate confusion inherent in multiple, laboratory-specific designations and tissue-based classifications [PUBMED:8311461]. Following the determination of the complete nucleotide sequence of Saccharomyces cerevisiae (Baker's yeast) [PUBMED:8091229], a novel gene was found to encode a protein with similarity to mammalian monooygenases.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan NADP_Rossmann (CL0063), which has the following description:

A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme. The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction. Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site [1]. In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.

The clan contains the following 180 members:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa Bac_GDH Bin3 CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 DAO DapB_N DFP DNA_circ_N DNA_methylase DOT1 DREV dTMP_synthase DUF1442 DUF1776 DUF2431 DUF268 DUF3321 DUF43 DUF633 DUF938 DXP_redisom_C DXP_reductoisom Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ G-7-MTase G6PD_N GCD14 GDI GFO_IDH_MocA GIDA GidB GLF Glyco_hydro_4 GMC_oxred_N Gp_dh_N GRAS GRDA HI0933_like HIM1 IlvN K_oxygenase KR LCM Ldh_1_N Lycopene_cycl Malic_M Mannitol_dh Met_10 Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_26 Methyltransf_27 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C Mqo MT-A70 MTS Mur_ligase N2227 N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_11 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS Nol1_Nop2_Fmu Nol1_Nop2_Fmu_2 NSP13 OCD_Mu_crystall PARP_regulatory PCMT PDH Polysacc_synt_2 Pox_MCEL Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Saccharop_dh SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth Strep_67kDa_ant TehB THF_DHG_CYH_C Thi4 ThiF TPMT TrkA_N TRM TRM13 tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 V_cholerae_RfbT XdhC_C YjeF_N

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(5)
Full
(2951)
Representative proteomes NCBI
(7810)
Meta
(2768)
RP15
(525)
RP35
(1056)
RP55
(1588)
RP75
(1914)
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Format an alignment

  Seed
(5)
Full
(2951)
Representative proteomes NCBI
(7810)
Meta
(2768)
RP15
(525)
RP35
(1056)
RP55
(1588)
RP75
(1914)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(5)
Full
(2951)
Representative proteomes NCBI
(7810)
Meta
(2768)
RP15
(525)
RP35
(1056)
RP55
(1588)
RP75
(1914)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_437 (release 2.1)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 5
Number in full: 2951
Average length of the domain: 277.00 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 77.52 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.6 19.6
Trusted cut-off 19.6 19.6
Noise cut-off 19.5 19.5
Model length: 532
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

FMO-like

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the FMO-like domain has been found. There are 107 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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