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Protein

Uroporphyrinogen-III C-methyltransferase

Gene

cobA

Organism
Pseudomonas denitrificans
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the methylation of both C-2 and C-7 of uroporphyrinogen III leading to precorrin-1 and precorrin-2; their oxidative esterification gives respectively factor I octamethyl ester and sirohydrochlorin.

Catalytic activityi

S-adenosyl-L-methionine + uroporphyrinogen III = S-adenosyl-L-homocysteine + precorrin-1.
S-adenosyl-L-methionine + precorrin-1 = S-adenosyl-L-homocysteine + precorrin-2.

Kineticsi

  1. KM=6.3 µM for S-adenosyl-L-methionine1 Publication
  2. KM=1.0 µM for uroporphyrinogen III1 Publication

    Pathway: adenosylcobalamin biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes precorrin-2 from uroporphyrinogen III.
    Proteins known to be involved in this subpathway in this organism are:
    1. Uroporphyrinogen-III C-methyltransferase (cobA)
    This subpathway is part of the pathway adenosylcobalamin biosynthesis, which is itself part of Cofactor biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes precorrin-2 from uroporphyrinogen III, the pathway adenosylcobalamin biosynthesis and in Cofactor biosynthesis.

    Pathway: siroheme biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes precorrin-2 from uroporphyrinogen III.
    Proteins known to be involved in this subpathway in this organism are:
    1. Uroporphyrinogen-III C-methyltransferase (cobA)
    This subpathway is part of the pathway siroheme biosynthesis, which is itself part of Porphyrin-containing compound metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes precorrin-2 from uroporphyrinogen III, the pathway siroheme biosynthesis and in Porphyrin-containing compound metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei24 – 241S-adenosyl-L-methionine; via carbonyl oxygen1 Publication
    Binding sitei130 – 1301S-adenosyl-L-methionine1 Publication
    Binding sitei184 – 1841S-adenosyl-L-methionine; via amide nitrogen1 Publication

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    Cobalamin biosynthesis, Porphyrin biosynthesis

    Keywords - Ligandi

    S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-82.
    RETL1328306-WGS:GSTH-2506-MONOMER.
    UniPathwayiUPA00148; UER00211.
    UPA00262; UER00211.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Uroporphyrinogen-III C-methyltransferase (EC:2.1.1.107)
    Short name:
    Urogen III methylase
    Alternative name(s):
    SUMT
    Uroporphyrinogen III methylase
    Short name:
    UROM
    Gene namesi
    Name:cobA
    OrganismiPseudomonas denitrificans
    Taxonomic identifieri43306 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi47 – 471D → N: Reduces S-adenosyl-L-methionine binding by about 75%. Causes accumulation of precorrin-1. 1 Publication
    Mutagenesisi49 – 491L → A: Reduces S-adenosyl-L-methionine binding by about 50%. Causes slow synthesis of precorrin-2 and accumulation of precorrin-1. 1 Publication
    Mutagenesisi106 – 1061F → A: Strongly reduces S-adenosyl-L-methionine binding. Loss of activity. 1 Publication
    Mutagenesisi130 – 1301T → A: Strongly reduces S-adenosyl-L-methionine binding. Causes slow synthesis of precorrin-2. 1 Publication
    Mutagenesisi183 – 1831Y → A: Strongly reduces S-adenosyl-L-methionine binding. Loss of activity. 1 Publication
    Mutagenesisi184 – 1841M → A: Strongly reduces S-adenosyl-L-methionine binding. Causes drastic effects on enzyme activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 280280Uroporphyrinogen-III C-methyltransferasePRO_0000150372Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Structurei

    Secondary structure

    1
    280
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi17 – 215Combined sources
    Beta strandi23 – 253Combined sources
    Beta strandi29 – 313Combined sources
    Helixi32 – 409Combined sources
    Beta strandi42 – 465Combined sources
    Helixi54 – 574Combined sources
    Beta strandi64 – 663Combined sources
    Helixi78 – 9013Combined sources
    Beta strandi95 – 1017Combined sources
    Beta strandi105 – 1084Combined sources
    Helixi109 – 1179Combined sources
    Turni118 – 1203Combined sources
    Beta strandi123 – 1264Combined sources
    Turni131 – 1333Combined sources
    Helixi134 – 1385Combined sources
    Turni146 – 1483Combined sources
    Beta strandi150 – 1567Combined sources
    Helixi170 – 1745Combined sources
    Beta strandi178 – 1847Combined sources
    Helixi189 – 19810Combined sources
    Beta strandi206 – 2127Combined sources
    Beta strandi219 – 2246Combined sources
    Turni225 – 2273Combined sources
    Helixi228 – 2358Combined sources
    Beta strandi239 – 2468Combined sources
    Helixi247 – 2515Combined sources
    Helixi252 – 2554Combined sources
    Helixi257 – 2615Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1S4DX-ray2.70A/B/D/E/F/G/H/I/J/K/L/M1-280[»]
    ProteinModelPortaliP21631.
    SMRiP21631. Positions 4-270.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP21631.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 248248Uroporphyrinogen-III C-methyltransferaseAdd
    BLAST
    Regioni100 – 1023S-adenosyl-L-methionine binding

    Sequence similaritiesi

    Belongs to the precorrin methyltransferase family.Curated

    Family and domain databases

    Gene3Di3.30.950.10. 1 hit.
    3.40.1010.10. 1 hit.
    InterProiIPR000878. 4pyrrol_Mease.
    IPR014777. 4pyrrole_Mease_sub1.
    IPR014776. 4pyrrole_Mease_sub2.
    IPR006366. CobA/CysG_C.
    IPR003043. Uropor_MeTrfase_CS.
    [Graphical view]
    PfamiPF00590. TP_methylase. 1 hit.
    [Graphical view]
    SUPFAMiSSF53790. SSF53790. 1 hit.
    TIGRFAMsiTIGR01469. cobA_cysG_Cterm. 1 hit.
    PROSITEiPS00839. SUMT_1. 1 hit.
    PS00840. SUMT_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P21631-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MIDDLFAGLP ALEKGSVWLV GAGPGDPGLL TLHAANALRQ ADVIVHDALV
    60 70 80 90 100
    NEDCLKLARP GAVLEFAGKR GGKPSPKQRD ISLRLVELAR AGNRVLRLKG
    110 120 130 140 150
    GDPFVFGRGG EEALTLVEHQ VPFRIVPGIT AGIGGLAYAG IPVTHREVNH
    160 170 180 190 200
    AVTFLTGHDS SGLVPDRINW QGIASGSPVI VMYMAMKHIG AITANLIAGG
    210 220 230 240 250
    RSPDEPVAFV CNAATPQQAV LETTLARAEA DVAAAGLEPP AIVVVGEVVR
    260 270 280
    LRAALDWIGA LDGRKLAADP FANRILRNPA
    Length:280
    Mass (Da):29,253
    Last modified:May 1, 1991 - v1
    Checksum:i3D593C535CF0610E
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M59236 Genomic DNA. Translation: AAA25773.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M59236 Genomic DNA. Translation: AAA25773.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1S4DX-ray2.70A/B/D/E/F/G/H/I/J/K/L/M1-280[»]
    ProteinModelPortaliP21631.
    SMRiP21631. Positions 4-270.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    UniPathwayiUPA00148; UER00211.
    UPA00262; UER00211.
    BioCyciMetaCyc:MONOMER-82.
    RETL1328306-WGS:GSTH-2506-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP21631.

    Family and domain databases

    Gene3Di3.30.950.10. 1 hit.
    3.40.1010.10. 1 hit.
    InterProiIPR000878. 4pyrrol_Mease.
    IPR014777. 4pyrrole_Mease_sub1.
    IPR014776. 4pyrrole_Mease_sub2.
    IPR006366. CobA/CysG_C.
    IPR003043. Uropor_MeTrfase_CS.
    [Graphical view]
    PfamiPF00590. TP_methylase. 1 hit.
    [Graphical view]
    SUPFAMiSSF53790. SSF53790. 1 hit.
    TIGRFAMsiTIGR01469. cobA_cysG_Cterm. 1 hit.
    PROSITEiPS00839. SUMT_1. 1 hit.
    PS00840. SUMT_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    1. "Nucleotide sequence of a Pseudomonas denitrificans 5.4-kilobase DNA fragment containing five cob genes and identification of structural genes encoding S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase and cobyrinic acid a,c-diamide synthase."
      Crouzet J., Cauchois L., Blanche F., Debussche L., Thibaut D., Rouyez M.-C., Rigault S., Mayaux J.-F., Cameron B.
      J. Bacteriol. 172:5968-5979(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10.
      Strain: SC510.
    2. "Purification and characterization of S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase from Pseudomonas denitrificans."
      Blanche F., Debussche L., Thibaut D., Crouzet J., Cameron B.
      J. Bacteriol. 171:4222-4231(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    3. "Structure/function studies on a S-adenosyl-L-methionine-dependent uroporphyrinogen III C methyltransferase (SUMT), a key regulatory enzyme of tetrapyrrole biosynthesis."
      Vevodova J., Graham R.M., Raux E., Schubert H.L., Roper D.I., Brindley A.A., Ian Scott A., Roessner C.A., Stamford N.P.J., Stroupe M.E., Getzoff E.D., Warren M.J., Wilson K.S.
      J. Mol. Biol. 344:419-433(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF APOPROTEIN IN COMPLEX WITH S-ADENOSYL-L-METHIONINE, SUBUNIT, KINETIC PARAMETERS, MUTAGENESIS OF ASP-47; LEU-49; PHE-106; THR-130; TYR-183 AND MET-184.

    Entry informationi

    Entry nameiSUMT_PSEDE
    AccessioniPrimary (citable) accession number: P21631
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1991
    Last sequence update: May 1, 1991
    Last modified: November 26, 2014
    This is version 80 of the entry and version 1 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. 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

    External Data

    Dasty 3

    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 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.