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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.

    Pathway:iprotoporphyrin-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 (At2g40490), 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.

    Pathway:ichlorophyll 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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei80 – 801Cofactor
    Binding sitei82 – 821Cofactor
    Active sitei157 – 1571Proton donor/acceptor1 Publication

    GO - Molecular functioni

    • hydroxymethylbilane synthase activity Source: TAIR

    GO - Biological processi

    • chlorophyll biosynthetic process Source: TAIR
    • defense response to bacterium Source: TAIR
    • 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.
    ReactomeiREACT_340934. 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
    ProteomesiUP000006548 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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi246 – 2461A → V in rug1; reduced growth and necrotic leaf lesions. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 6262Chloroplast1 PublicationAdd
    BLAST
    Chaini63 – 382320Porphobilinogen deaminase, chloroplasticPRO_0000013322Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei123 – 1231Phosphoserine1 Publication
    Modified residuei316 – 3161S-(dipyrrolylmethanemethyl)cysteine

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiQ43316.
    PRIDEiQ43316.

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Protein-protein interaction databases

    MINTiMINT-8062098.
    STRINGi3702.AT5G08280.1.

    Structurei

    Secondary structure

    1
    382
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi74 – 796Combined sources
    Helixi83 – 9917Combined sources
    Helixi101 – 1033Combined sources
    Beta strandi108 – 1136Combined sources
    Helixi117 – 1193Combined sources
    Helixi126 – 1283Combined sources
    Turni134 – 1363Combined sources
    Helixi137 – 1448Combined sources
    Beta strandi149 – 1546Combined sources
    Helixi155 – 1573Combined sources
    Beta strandi166 – 1716Combined sources
    Beta strandi179 – 1857Combined sources
    Helixi189 – 1913Combined sources
    Beta strandi197 – 1993Combined sources
    Helixi203 – 21210Combined sources
    Beta strandi216 – 2194Combined sources
    Helixi226 – 2349Combined sources
    Beta strandi237 – 2448Combined sources
    Helixi245 – 2517Combined sources
    Helixi254 – 2563Combined sources
    Beta strandi258 – 2603Combined sources
    Turni263 – 2653Combined sources
    Turni270 – 2734Combined sources
    Beta strandi275 – 2806Combined sources
    Helixi284 – 2918Combined sources
    Helixi296 – 31116Combined sources
    Beta strandi318 – 3269Combined sources
    Beta strandi330 – 33910Combined sources
    Beta strandi346 – 35510Combined sources
    Helixi357 – 37216Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4HTGX-ray1.45A63-382[»]
    ProteinModelPortaliQ43316.
    SMRiQ43316. Positions 72-373.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni156 – 1572Cofactor binding
    Regioni200 – 2056Cofactor binding
    Regioni223 – 2297Cofactor binding

    Sequence similaritiesi

    Belongs to the HMBS family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0181.
    HOGENOMiHOG000228588.
    InParanoidiQ43316.
    KOiK01749.
    OMAiMKDVETW.
    PhylomeDBiQ43316.

    Family and domain databases

    Gene3Di3.30.160.40. 1 hit.
    HAMAPiMF_00260. Porphobil_deam.
    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)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti157 – 1571D → Y in AAM64573 (Ref. 5) Curated

    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_120911.3.
    UniGeneiAt.48996.
    At.5343.

    Genome annotation databases

    EnsemblPlantsiAT5G08280.1; AT5G08280.1; AT5G08280.
    GeneIDi830724.
    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_120911.3.
    UniGeneiAt.48996.
    At.5343.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4HTGX-ray1.45A63-382[»]
    ProteinModelPortaliQ43316.
    SMRiQ43316. Positions 72-373.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    MINTiMINT-8062098.
    STRINGi3702.AT5G08280.1.

    Proteomic databases

    PaxDbiQ43316.
    PRIDEiQ43316.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Organism-specific databases

    TAIRiAT5G08280.

    Phylogenomic databases

    eggNOGiCOG0181.
    HOGENOMiHOG000228588.
    InParanoidiQ43316.
    KOiK01749.
    OMAiMKDVETW.
    PhylomeDBiQ43316.

    Enzyme and pathway databases

    UniPathwayiUPA00251; UER00319.
    UPA00668.
    BioCyciARA:AT5G08280-MONOMER.
    MetaCyc:AT5G08280-MONOMER.
    ReactomeiREACT_340934. Heme biosynthesis.

    Miscellaneous databases

    PROiQ43316.

    Family and domain databases

    Gene3Di3.30.160.40. 1 hit.
    HAMAPiMF_00260. Porphobil_deam.
    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...

    Publicationsi

    « Hide 'large scale' publications
    1. "Porphobilinogen deaminase is encoded by a single gene in Arabidopsis thaliana and is targeted to the chloroplasts."
      Lim S.H., Witty M., Wallace-Cook A.D.M., Ilag L.I., Smith A.G.
      Plant Mol. Biol. 26:863-872(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: cv. Landsberg erecta.
    2. "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
      Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.
      , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
      Nature 408:823-826(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "Full-length cDNA from Arabidopsis thaliana."
      Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
      Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    6. "Purification and properties of porphobilinogen deaminase from Arabidopsis thaliana."
      Jones R.M., Jordan P.M.
      Biochem. J. 299:895-902(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 63-74, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, ENZYME REGULATION.
      Strain: cv. Columbia.
    7. "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks."
      Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S.
      Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-123, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "PORPHOBILINOGEN DEAMINASE deficiency alters vegetative and reproductive development and causes lesions in Arabidopsis."
      Quesada V., Sarmiento-Manus R., Gonzalez-Bayon R., Hricova A., Ponce M.R., Micol J.L.
      PLoS ONE 8:E53378-E53378(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF ALA-246.
      Strain: cv. Landsberg erecta.
    9. "Insights into the mechanism of pyrrole polymerization catalysed by porphobilinogen deaminase: high-resolution X-ray studies of the Arabidopsis thaliana enzyme."
      Roberts A., Gill R., Hussey R.J., Mikolajek H., Erskine P.T., Cooper J.B., Wood S.P., Chrystal E.J., Shoolingin-Jordan P.M.
      Acta Crystallogr. D 69:471-485(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF 63-382 IN COMPLEX WITH DIPYRROMETHENONE, ACTIVE SITE, PROSTHETIC GROUP AT CYS-316.

    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: June 24, 2015
    This is version 132 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 sequentialy 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

    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.