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Q43316

- HEM3_ARATH

UniProt

Q43316 - HEM3_ARATH

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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

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.

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.
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 – 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

        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:
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

« 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: October 29, 2014
This is version 127 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