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Protein

5,6,7,8-tetrahydromethanopterin hydro-lyase

Gene

fae

Organism
Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the condensation of formaldehyde with tetrahydromethanopterin (H4MPT) to 5,10-methylenetetrahydromethanopterin, a reaction which also proceeds spontaneously, but at a lower rate than that of the enzyme-catalyzed reaction. Is an essential enzyme for methylotrophic energy metabolism and formaldehyde detoxification of this bacterium.2 Publications

Catalytic activityi

5,6,7,8-tetrahydromethanopterin + formaldehyde = 5,10-methylenetetrahydromethanopterin + H2O.2 Publications

Enzyme regulationi

Inhibited by the addition of an excess of H4F.1 Publication

Kineticsi

The KM for H4MPT is higher than 60 µM.

  1. KM=0.2 mM for formaldehyde1 Publication

    pH dependencei

    Optimum pH is 7-7.5.1 Publication

    Pathwayi: formaldehyde degradation

    This protein is involved in step 1 of the subpathway that synthesizes formate from formaldehyde (H(4)MPT route).
    Proteins known to be involved in the 5 steps of the subpathway in this organism are:
    1. 5,6,7,8-tetrahydromethanopterin hydro-lyase (fae)
    2. Bifunctional protein MdtA (mtdA), NAD(P)-dependent methylenetetrahydromethanopterin dehydrogenase (mtdB)
    3. Methenyltetrahydromethanopterin cyclohydrolase (mch)
    4. Formyltransferase/hydrolase complex Fhc subunit B (fhcB), Formyltransferase/hydrolase complex Fhc subunit A (fhcA), Formyltransferase/hydrolase complex Fhc subunit C (fhcC), Formyltransferase/hydrolase complex subunit D (fhcD)
    5. no protein annotated in this organism
    This subpathway is part of the pathway formaldehyde degradation, which is itself part of One-carbon metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes formate from formaldehyde (H(4)MPT route), the pathway formaldehyde degradation and in One-carbon metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei22 – 221Proton donor
    Binding sitei24 – 241Substrate
    Binding sitei53 – 531Substrate; via carbonyl oxygen
    Binding sitei71 – 711Substrate
    Binding sitei73 – 731Substrate
    Binding sitei88 – 881Substrate

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Detoxification, One-carbon metabolism

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-4002.
    MEXT272630:GBY6-1689-MONOMER.
    BRENDAi4.2.1.147. 3296.
    SABIO-RKQ9FA38.
    UniPathwayiUPA00562; UER00701.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    5,6,7,8-tetrahydromethanopterin hydro-lyase (EC:4.2.1.147)
    Alternative name(s):
    Formaldehyde-activating enzyme
    Short name:
    Fae
    Gene namesi
    Name:fae
    Ordered Locus Names:MexAM1_META1p1766
    OrganismiMethylobacterium extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)
    Taxonomic identifieri272630 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesMethylobacteriaceaeMethylobacterium
    Proteomesi
    • UP000009081 Componenti: Chromosome

    Subcellular locationi

    • Cytoplasm 1 Publication

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene are unable to grow on methanol but exhibit wild-type growth on succinate. In addition, mutant is shown to be formaldehyde sensitive.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 1701695,6,7,8-tetrahydromethanopterin hydro-lyasePRO_0000087171Add
    BLAST

    Interactioni

    Subunit structurei

    Homopentamer.2 Publications

    Protein-protein interaction databases

    STRINGi272630.MexAM1_META1p1766.

    Structurei

    Secondary structure

    1
    170
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi8 – 147Combined sources
    Helixi17 – 193Combined sources
    Beta strandi21 – 299Combined sources
    Helixi33 – 4311Combined sources
    Beta strandi51 – 533Combined sources
    Beta strandi55 – 573Combined sources
    Beta strandi63 – 7210Combined sources
    Helixi77 – 837Combined sources
    Helixi86 – 10015Combined sources
    Turni106 – 1083Combined sources
    Helixi109 – 1113Combined sources
    Beta strandi112 – 1187Combined sources
    Helixi127 – 14620Combined sources
    Helixi152 – 1587Combined sources
    Helixi159 – 1613Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Y5YX-ray2.00A/B/C/D/E2-170[»]
    1Y60X-ray1.90A/B/C/D/E2-170[»]
    ProteinModelPortaliQ9FA38.
    SMRiQ9FA38. Positions 2-170.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9FA38.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4108P4C. Bacteria.
    COG1795. LUCA.
    HOGENOMiHOG000221499.
    KOiK10713.
    OMAiETAFCNA.

    Family and domain databases

    Gene3Di3.30.230.60. 1 hit.
    InterProiIPR014826. HCHO-activating_enzyme.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    [Graphical view]
    PfamiPF08714. Fae. 1 hit.
    [Graphical view]
    SUPFAMiSSF54211. SSF54211. 1 hit.
    TIGRFAMsiTIGR03126. one_C_fae. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    Q9FA38-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAKITKVQVG EALVGDGNEV AHIDLIIGPR GSPAETAFCN GLVNNKHGFT
    60 70 80 90 100
    SLLAVIAPNL PCKPNTLMFN KVTINDARQA VQMFGPAQHG VAMAVQDAVA
    110 120 130 140 150
    EGIIPADEAD DLYVLVGVFI HWEAADDAKI QKYNYEATKL SIQRAVNGEP
    160 170
    KASVVTEQRK SATHPFAANA
    Length:170
    Mass (Da):18,091
    Last modified:January 23, 2007 - v3
    Checksum:i13BB66B298A44C32
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF032114 Genomic DNA. Translation: AAG32954.1.
    CP001510 Genomic DNA. Translation: ACS39609.1.
    RefSeqiWP_003604760.1. NC_012808.1.

    Genome annotation databases

    EnsemblBacteriaiACS39609; ACS39609; MexAM1_META1p1766.
    KEGGimea:Mex_1p1766.
    PATRICi22509360. VBIMetExt101010_1755.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF032114 Genomic DNA. Translation: AAG32954.1.
    CP001510 Genomic DNA. Translation: ACS39609.1.
    RefSeqiWP_003604760.1. NC_012808.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Y5YX-ray2.00A/B/C/D/E2-170[»]
    1Y60X-ray1.90A/B/C/D/E2-170[»]
    ProteinModelPortaliQ9FA38.
    SMRiQ9FA38. Positions 2-170.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi272630.MexAM1_META1p1766.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiACS39609; ACS39609; MexAM1_META1p1766.
    KEGGimea:Mex_1p1766.
    PATRICi22509360. VBIMetExt101010_1755.

    Phylogenomic databases

    eggNOGiENOG4108P4C. Bacteria.
    COG1795. LUCA.
    HOGENOMiHOG000221499.
    KOiK10713.
    OMAiETAFCNA.

    Enzyme and pathway databases

    UniPathwayiUPA00562; UER00701.
    BioCyciMetaCyc:MONOMER-4002.
    MEXT272630:GBY6-1689-MONOMER.
    BRENDAi4.2.1.147. 3296.
    SABIO-RKQ9FA38.

    Miscellaneous databases

    EvolutionaryTraceiQ9FA38.

    Family and domain databases

    Gene3Di3.30.230.60. 1 hit.
    InterProiIPR014826. HCHO-activating_enzyme.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    [Graphical view]
    PfamiPF08714. Fae. 1 hit.
    [Graphical view]
    SUPFAMiSSF54211. SSF54211. 1 hit.
    TIGRFAMsiTIGR03126. one_C_fae. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiFAE_METEA
    AccessioniPrimary (citable) accession number: Q9FA38
    Secondary accession number(s): C5B145
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 16, 2001
    Last sequence update: January 23, 2007
    Last modified: September 7, 2016
    This is version 82 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, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.