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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

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
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_242385. 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: 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
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.

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 – 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. 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

        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. 1 PublicationCurated

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.

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_242385. Heme biosynthesis.

Miscellaneous databases

PROiQ43316.

Gene expression databases

GenevestigatoriQ43316.

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]
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: January 7, 2015
This is version 129 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.