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Protein

Porphobilinogen deaminase, chloroplastic

Gene

HEMC

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps.1 Publication

Catalytic activityi

4 porphobilinogen + H2O = hydroxymethylbilane + 4 NH3.

Cofactori

dipyrromethane1 PublicationNote: Binds 1 dipyrromethane group covalently.1 Publication

Enzyme regulationi

Inhibited by NH3, heavy-metal ions, hydroxylamine and 2-bromoporphobilinogen. Not inhibited by N-ethylmaleimide.1 Publication

Kineticsi

  1. KM=17 µM for porphobilinogen1 Publication

    pH dependencei

    Optimum pH is 7.7-8.5.

    Temperature dependencei

    Heat stable and fully active up to 70 degrees Celsius.

    Pathwayi: protoporphyrin-IX biosynthesis

    This protein is involved in step 2 of the subpathway that synthesizes coproporphyrinogen-III from 5-aminolevulinate.
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. Probable delta-aminolevulinic acid dehydratase 2, chloroplastic (HEMB2), Delta-aminolevulinic acid dehydratase 1, chloroplastic (HEMB1)
    2. Porphobilinogen deaminase, chloroplastic (HEMC)
    3. Uroporphyrinogen-III synthase, chloroplastic (UROS)
    4. Uroporphyrinogen decarboxylase 2, chloroplastic (HEME2), Uroporphyrinogen decarboxylase (AXX17_At3g15570), Uroporphyrinogen decarboxylase (At2g40490), Uroporphyrinogen decarboxylase (AXX17_At2g37600), Uroporphyrinogen decarboxylase 1, chloroplastic (HEME1)
    This subpathway is part of the pathway protoporphyrin-IX 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 coproporphyrinogen-III from 5-aminolevulinate, the pathway protoporphyrin-IX biosynthesis and in Porphyrin-containing compound metabolism.

    Pathwayi: chlorophyll biosynthesis

    This protein is involved in the pathway chlorophyll biosynthesis, which is part of Porphyrin-containing compound metabolism.
    View all proteins of this organism that are known to be involved in the pathway chlorophyll biosynthesis and in Porphyrin-containing compound metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei80Cofactor1
    Binding sitei82Cofactor1
    Active sitei157Proton donor/acceptor1 Publication1

    GO - Molecular functioni

    • hydroxymethylbilane synthase activity Source: TAIR

    GO - Biological processi

    • chlorophyll biosynthetic process Source: TAIR
    • defense response to bacterium Source: TAIR
    • heme biosynthetic process Source: GO_Central
    • peptidyl-pyrromethane cofactor linkage Source: InterPro
    • protoporphyrinogen IX biosynthetic process Source: UniProtKB-UniPathway
    Complete GO annotation...

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Chlorophyll biosynthesis, Porphyrin biosynthesis

    Enzyme and pathway databases

    BioCyciARA:AT5G08280-MONOMER.
    MetaCyc:AT5G08280-MONOMER.
    ReactomeiR-ATH-189451. Heme biosynthesis.
    UniPathwayiUPA00251; UER00319.
    UPA00668.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Porphobilinogen deaminase, chloroplastic (EC:2.5.1.61)
    Short name:
    PBG
    Alternative name(s):
    Hydroxymethylbilane synthase
    Short name:
    HMBS
    Pre-uroporphyrinogen synthase
    Protein RUGOSA1
    Gene namesi
    Name:HEMC
    Synonyms:RUG1
    Ordered Locus Names:At5g08280
    ORF Names:F8L15_10
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 5

    Organism-specific databases

    TAIRiAT5G08280.

    Subcellular locationi

    GO - Cellular componenti

    • apoplast Source: TAIR
    • chloroplast Source: TAIR
    • chloroplast envelope Source: TAIR
    • chloroplast stroma Source: TAIR
    Complete GO annotation...

    Keywords - Cellular componenti

    Chloroplast, Plastid

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi246A → V in rug1; reduced growth and necrotic leaf lesions. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transit peptidei1 – 62Chloroplast1 PublicationAdd BLAST62
    ChainiPRO_000001332263 – 382Porphobilinogen deaminase, chloroplasticAdd BLAST320

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei123PhosphoserineCombined sources1
    Modified residuei316S-(dipyrrolylmethanemethyl)cysteine1

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiQ43316.
    PRIDEiQ43316.

    PTM databases

    iPTMnetiQ43316.

    Expressioni

    Gene expression databases

    GenevisibleiQ43316. AT.

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Protein-protein interaction databases

    BioGridi16002. 3 interactors.
    MINTiMINT-8062098.
    STRINGi3702.AT5G08280.1.

    Structurei

    Secondary structure

    1382
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi74 – 79Combined sources6
    Helixi83 – 99Combined sources17
    Helixi101 – 103Combined sources3
    Beta strandi108 – 113Combined sources6
    Helixi117 – 119Combined sources3
    Helixi126 – 128Combined sources3
    Turni134 – 136Combined sources3
    Helixi137 – 144Combined sources8
    Beta strandi149 – 154Combined sources6
    Helixi155 – 157Combined sources3
    Beta strandi166 – 171Combined sources6
    Beta strandi179 – 185Combined sources7
    Helixi189 – 191Combined sources3
    Beta strandi197 – 199Combined sources3
    Helixi203 – 212Combined sources10
    Beta strandi216 – 219Combined sources4
    Helixi226 – 234Combined sources9
    Beta strandi237 – 244Combined sources8
    Helixi245 – 251Combined sources7
    Helixi254 – 256Combined sources3
    Beta strandi258 – 260Combined sources3
    Turni263 – 265Combined sources3
    Turni270 – 273Combined sources4
    Beta strandi275 – 280Combined sources6
    Helixi284 – 291Combined sources8
    Helixi296 – 311Combined sources16
    Beta strandi318 – 326Combined sources9
    Beta strandi330 – 339Combined sources10
    Beta strandi346 – 355Combined sources10
    Helixi357 – 372Combined sources16

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4HTGX-ray1.45A63-382[»]
    ProteinModelPortaliQ43316.
    SMRiQ43316.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni156 – 157Cofactor binding2
    Regioni200 – 205Cofactor binding6
    Regioni223 – 229Cofactor binding7

    Sequence similaritiesi

    Belongs to the HMBS family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiKOG2892. Eukaryota.
    COG0181. LUCA.
    HOGENOMiHOG000228588.
    InParanoidiQ43316.
    KOiK01749.
    OMAiGAICIES.
    OrthoDBiEOG09360FHV.
    PhylomeDBiQ43316.

    Family and domain databases

    Gene3Di3.30.160.40. 1 hit.
    HAMAPiMF_00260. Porphobil_deam. 1 hit.
    InterProiIPR000860. HemC.
    IPR022419. Porphobilin_deaminase_cofac_BS.
    IPR022417. Porphobilin_deaminase_N.
    IPR022418. Porphobilinogen_deaminase_C.
    [Graphical view]
    PANTHERiPTHR11557. PTHR11557. 1 hit.
    PfamiPF01379. Porphobil_deam. 1 hit.
    PF03900. Porphobil_deamC. 1 hit.
    [Graphical view]
    PRINTSiPR00151. PORPHBDMNASE.
    SUPFAMiSSF54782. SSF54782. 1 hit.
    TIGRFAMsiTIGR00212. hemC. 1 hit.
    PROSITEiPS00533. PORPHOBILINOGEN_DEAM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q43316-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MDIASSSLSQ AHKVVLTRQP SSRVNTCSLG SVSAIGFSLP QISSPALGKC
    60 70 80 90 100
    RRKQSSSGFV KACVAVEQKT RTAIIRIGTR GSPLALAQAY ETREKLKKKH
    110 120 130 140 150
    PELVEDGAIH IEIIKTTGDK ILSQPLADIG GKGLFTKEID EALINGHIDI
    160 170 180 190 200
    AVHSMKDVPT YLPEKTILPC NLPREDVRDA FICLTAATLA ELPAGSVVGT
    210 220 230 240 250
    ASLRRKSQIL HKYPALHVEE NFRGNVQTRL SKLQGGKVQA TLLALAGLKR
    260 270 280 290 300
    LSMTENVASI LSLDEMLPAV AQGAIGIACR TDDDKMATYL ASLNHEETRL
    310 320 330 340 350
    AISCERAFLE TLDGSCRTPI AGYASKDEEG NCIFRGLVAS PDGTKVLETS
    360 370 380
    RKGPYVYEDM VKMGKDAGQE LLSRAGPGFF GN
    Length:382
    Mass (Da):41,043
    Last modified:November 1, 1997 - v1
    Checksum:i3DB771BD4E6C9D37
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti157D → Y in AAM64573 (Ref. 5) Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X73839 Genomic DNA. Translation: CAA52061.1.
    X73535 Genomic DNA. Translation: CAA51941.1.
    AL392174 Genomic DNA. Translation: CAC08328.1.
    CP002688 Genomic DNA. Translation: AED91277.1.
    AF419614 mRNA. Translation: AAL31946.1.
    AY070431 mRNA. Translation: AAL49926.1.
    AY123037 mRNA. Translation: AAM67570.1.
    AY087012 mRNA. Translation: AAM64573.1.
    PIRiS50762.
    RefSeqiNP_196445.1. NM_120911.4.
    UniGeneiAt.48996.
    At.5343.

    Genome annotation databases

    EnsemblPlantsiAT5G08280.1; AT5G08280.1; AT5G08280.
    GeneIDi830724.
    GrameneiAT5G08280.1; AT5G08280.1; AT5G08280.
    KEGGiath:AT5G08280.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X73839 Genomic DNA. Translation: CAA52061.1.
    X73535 Genomic DNA. Translation: CAA51941.1.
    AL392174 Genomic DNA. Translation: CAC08328.1.
    CP002688 Genomic DNA. Translation: AED91277.1.
    AF419614 mRNA. Translation: AAL31946.1.
    AY070431 mRNA. Translation: AAL49926.1.
    AY123037 mRNA. Translation: AAM67570.1.
    AY087012 mRNA. Translation: AAM64573.1.
    PIRiS50762.
    RefSeqiNP_196445.1. NM_120911.4.
    UniGeneiAt.48996.
    At.5343.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4HTGX-ray1.45A63-382[»]
    ProteinModelPortaliQ43316.
    SMRiQ43316.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi16002. 3 interactors.
    MINTiMINT-8062098.
    STRINGi3702.AT5G08280.1.

    PTM databases

    iPTMnetiQ43316.

    Proteomic databases

    PaxDbiQ43316.
    PRIDEiQ43316.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT5G08280.1; AT5G08280.1; AT5G08280.
    GeneIDi830724.
    GrameneiAT5G08280.1; AT5G08280.1; AT5G08280.
    KEGGiath:AT5G08280.

    Organism-specific databases

    TAIRiAT5G08280.

    Phylogenomic databases

    eggNOGiKOG2892. Eukaryota.
    COG0181. LUCA.
    HOGENOMiHOG000228588.
    InParanoidiQ43316.
    KOiK01749.
    OMAiGAICIES.
    OrthoDBiEOG09360FHV.
    PhylomeDBiQ43316.

    Enzyme and pathway databases

    UniPathwayiUPA00251; UER00319.
    UPA00668.
    BioCyciARA:AT5G08280-MONOMER.
    MetaCyc:AT5G08280-MONOMER.
    ReactomeiR-ATH-189451. Heme biosynthesis.

    Miscellaneous databases

    PROiQ43316.

    Gene expression databases

    GenevisibleiQ43316. AT.

    Family and domain databases

    Gene3Di3.30.160.40. 1 hit.
    HAMAPiMF_00260. Porphobil_deam. 1 hit.
    InterProiIPR000860. HemC.
    IPR022419. Porphobilin_deaminase_cofac_BS.
    IPR022417. Porphobilin_deaminase_N.
    IPR022418. Porphobilinogen_deaminase_C.
    [Graphical view]
    PANTHERiPTHR11557. PTHR11557. 1 hit.
    PfamiPF01379. Porphobil_deam. 1 hit.
    PF03900. Porphobil_deamC. 1 hit.
    [Graphical view]
    PRINTSiPR00151. PORPHBDMNASE.
    SUPFAMiSSF54782. SSF54782. 1 hit.
    TIGRFAMsiTIGR00212. hemC. 1 hit.
    PROSITEiPS00533. PORPHOBILINOGEN_DEAM. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiHEM3_ARATH
    AccessioniPrimary (citable) accession number: Q43316
    Secondary accession number(s): Q8LBT0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1997
    Last modified: November 30, 2016
    This is version 140 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The porphobilinogen subunits are added sequentially to the dipyrromethane cofactor that is covalently attached to the enzyme. The last step of the reaction involves the hydrolysis of the bound polypyrrole chain and the release of hydroxymethylbilane.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.