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Q43316

- HEM3_ARATH

UniProt

Q43316 - HEM3_ARATH

Protein

Porphobilinogen deaminase, chloroplastic

Gene

HEMC

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 126 (01 Oct 2014)
      Sequence version 1 (01 Nov 1997)
      Previous versions | rss
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    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

    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 7.7-8.5.1 Publication

    Temperature dependencei

    Heat stable and fully active up to 70 degrees Celsius.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei80 – 801Cofactor
    Binding sitei82 – 821Cofactor
    Active sitei157 – 1571Proton donor/acceptor1 Publication

    GO - Molecular functioni

    1. hydroxymethylbilane synthase activity Source: TAIR

    GO - Biological processi

    1. chlorophyll biosynthetic process Source: TAIR
    2. defense response to bacterium Source: TAIR
    3. peptidyl-pyrromethane cofactor linkage Source: InterPro
    4. protoporphyrinogen IX biosynthetic process Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Transferase

    Keywords - Biological processi

    Chlorophyll biosynthesis, Porphyrin biosynthesis

    Enzyme and pathway databases

    BioCyciARA:AT5G08280-MONOMER.
    MetaCyc:AT5G08280-MONOMER.
    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: Chromosome 5

    Organism-specific databases

    TAIRiAT5G08280.

    Subcellular locationi

    GO - Cellular componenti

    1. apoplast Source: TAIR
    2. chloroplast Source: TAIR
    3. chloroplast envelope Source: TAIR
    4. chloroplast stroma Source: TAIR

    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.

    Expressioni

    Gene expression databases

    GenevestigatoriQ43316.

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Protein-protein interaction databases

    MINTiMINT-8062098.

    Structurei

    Secondary structure

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    OMAiCRSDDET.
    PhylomeDBiQ43316.

    Family and domain databases

    Gene3Di3.30.160.40. 1 hit.
    HAMAPiMF_00260. Porphobil_deam.
    InterProiIPR000860. 4pyrrol_synth_OHMeBilane_synth.
    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]
    PIRSFiPIRSF001438. 4pyrrol_synth_OHMeBilane_synth. 1 hit.
    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

    MDIASSSLSQ AHKVVLTRQP SSRVNTCSLG SVSAIGFSLP QISSPALGKC    50
    RRKQSSSGFV KACVAVEQKT RTAIIRIGTR GSPLALAQAY ETREKLKKKH 100
    PELVEDGAIH IEIIKTTGDK ILSQPLADIG GKGLFTKEID EALINGHIDI 150
    AVHSMKDVPT YLPEKTILPC NLPREDVRDA FICLTAATLA ELPAGSVVGT 200
    ASLRRKSQIL HKYPALHVEE NFRGNVQTRL SKLQGGKVQA TLLALAGLKR 250
    LSMTENVASI LSLDEMLPAV AQGAIGIACR TDDDKMATYL ASLNHEETRL 300
    AISCERAFLE TLDGSCRTPI AGYASKDEEG NCIFRGLVAS PDGTKVLETS 350
    RKGPYVYEDM VKMGKDAGQE LLSRAGPGFF GN 382
    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. 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi S50762.
    RefSeqi NP_196445.1. NM_120911.3.
    UniGenei At.48996.
    At.5343.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4HTG X-ray 1.45 A 63-382 [» ]
    ProteinModelPortali Q43316.
    SMRi Q43316. Positions 72-373.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    MINTi MINT-8062098.

    Proteomic databases

    PaxDbi Q43316.
    PRIDEi Q43316.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT5G08280.1 ; AT5G08280.1 ; AT5G08280 .
    GeneIDi 830724.
    KEGGi ath:AT5G08280.

    Organism-specific databases

    TAIRi AT5G08280.

    Phylogenomic databases

    eggNOGi COG0181.
    HOGENOMi HOG000228588.
    InParanoidi Q43316.
    KOi K01749.
    OMAi CRSDDET.
    PhylomeDBi Q43316.

    Enzyme and pathway databases

    UniPathwayi UPA00251 ; UER00319 .
    UPA00668 .
    BioCyci ARA:AT5G08280-MONOMER.
    MetaCyc:AT5G08280-MONOMER.

    Miscellaneous databases

    PROi Q43316.

    Gene expression databases

    Genevestigatori Q43316.

    Family and domain databases

    Gene3Di 3.30.160.40. 1 hit.
    HAMAPi MF_00260. Porphobil_deam.
    InterProi IPR000860. 4pyrrol_synth_OHMeBilane_synth.
    IPR022419. Porphobilin_deaminase_cofac_BS.
    IPR022417. Porphobilin_deaminase_N.
    IPR022418. Porphobilinogen_deaminase_C.
    [Graphical view ]
    PANTHERi PTHR11557. PTHR11557. 1 hit.
    Pfami PF01379. Porphobil_deam. 1 hit.
    PF03900. Porphobil_deamC. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF001438. 4pyrrol_synth_OHMeBilane_synth. 1 hit.
    PRINTSi PR00151. PORPHBDMNASE.
    SUPFAMi SSF54782. SSF54782. 1 hit.
    TIGRFAMsi TIGR00212. hemC. 1 hit.
    PROSITEi PS00533. PORPHOBILINOGEN_DEAM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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, S-(DIPYRROLYLMETHANEMETHYL)CYSTEINE 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: October 1, 2014
    This is version 126 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